Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes

LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryote...

Full description

Saved in:
Bibliographic Details
Published inMolecular biology and evolution Vol. 38; no. 8; pp. 3267 - 3278
Main Authors Wang, Jianhua, Han, Guan-Zhu
Format Journal Article
LanguageEnglish
Published United States Oxford University Press 01.08.2021
Subjects
Analysis
Angiosperms
Animals
Discoveries
Eukaryotes
Evolution
Evolutionary genetics
Gag protein
Gene expression
Genes
Genetic research
Genomes
Genomics
Phylogeny
Plants
Positive selection
Taxonomy
Transposons
phylogenetics
co-option
LTR retrotransposon
Online AccessGet full text
ISSN1537-1719
0737-4038
1537-1719
DOI10.1093/molbev/msab101

Cover

Abstract LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
AbstractList LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely co-option occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and Bel-Pao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes.
LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse functions, a process formally referred to as co-option. However, a comprehensive picture of LTR retrotransposon gag gene co-option in eukaryotes is still lacking, with several documented cases exclusively involving Ty3/Gypsy retrotransposons in animals. Here, we use a phylogenomic approach to systemically unearth co-option of retrotransposon gag genes above the family level of taxonomy in 2,011 eukaryotes, namely cooption occurring during the deep evolution of eukaryotes. We identify a total of 14 independent gag gene co-option events across more than 740 eukaryote families, eight of which have not been reported previously. Among these retrotransposon gag gene co-option events, nine, four, and one involve gag genes of Ty3/Gypsy, Ty1/Copia, and BelPao retrotransposons, respectively. Seven, four, and three co-option events occurred in animals, plants, and fungi, respectively. Interestingly, two co-option events took place in the early evolution of angiosperms. Both selective pressure and gene expression analyses further support that these co-opted gag genes might perform diverse cellular functions in their hosts, and several co-opted gag genes might be subject to positive selection. Taken together, our results provide a comprehensive picture of LTR retrotransposon gag gene co-option events that occurred during the deep evolution of eukaryotes and suggest paucity of LTR retrotransposon gag gene co-option during the deep evolution of eukaryotes. Key words: LTR retrotransposon, co-option, phylogenetics.
Audience Academic
Author Wang, Jianhua
Han, Guan-Zhu
AuthorAffiliation Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University , Nanjing, Jiangsu, China
AuthorAffiliation_xml – name: Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University , Nanjing, Jiangsu, China
Author_xml – sequence: 1
  givenname: Jianhua
  surname: Wang
  fullname: Wang, Jianhua
  organization: Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
– sequence: 2
  givenname: Guan-Zhu
  surname: Han
  fullname: Han, Guan-Zhu
  email: guanzhu@njnu.edu.cn
  organization: Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33871607$$D View this record in MEDLINE/PubMed
BookMark eNqFkd1r2zAUxcVoWT-21z0OwV7aByeSJVv2y6BkWTcIFErzLBT5ylFnS55lZ_S_r4KztSuUIoGE9DuHe889Q0fOO0DoEyUzSko2b32zgd28DWpDCX2HTmnGREIFLY-e3U_QWQj3hFDO8_w9OmGsEDQn4hSt1w5UP2ytq_Hq7hbfwtD7oVcudD54h2tV42twEPDCJ74boMLW4WEL-BtAh5c734yDjaA3eDn-Uv2DHyB8QMdGNQE-Hs5ztP6-vFv8SFY31z8XV6tEc5LTRJeEmazIBdE5LSkjqREMTKo45QWrDDBCNyw3RhPFK5ICp7kWpKpIXsZXxc7RfPIdXace_qimkV1v21iFpETuA5JTQPIQUFR8nRTduGmh0uBis08qr6z8_8fZraz9ThYspVmaRoOLg0Hvf48QBtnaoKFplAM_BplmNCOCZ2kR0S8v0Hs_9i4GIlmcSloWTLBIzSaqVg1I68w-fh1XBa3VcdrGxvcrITiPO9sLPj9v4V_tf4caAT4Buvch9GCktoPaTyk62-b1aGYvZG9meTkJ_Ni9xT4CukzXQA
CitedBy_id crossref_primary_10_1186_s13100_024_00312_1
crossref_primary_10_3390_genes13081337
crossref_primary_10_1371_journal_pone_0310946
crossref_primary_10_3390_cells10123590
crossref_primary_10_1093_gbe_evab254
crossref_primary_10_1093_molbev_msae025
crossref_primary_10_1016_j_virs_2022_01_019
crossref_primary_10_3390_plants11243579
crossref_primary_10_1093_molbev_msae010
crossref_primary_10_1093_molbev_msae154
crossref_primary_10_1093_gbe_evae193
Cites_doi 10.3852/11-077
10.1038/nature03481
10.1093/molbev/mst014
10.3390/genes11040396
10.1371/journal.pcbi.1002195
10.1016/j.tree.2019.08.008
10.1016/j.cmi.2016.02.001
10.1093/gbe/evt028
10.1016/j.cell.2017.12.024
10.1038/nrg2165
10.1038/s41467-017-02644-4
10.1111/nph.15596
10.1016/S0092-8674(00)80185-3
10.1371/journal.pgen.1002931
10.1016/j.tig.2006.09.006
10.1038/ng1699
10.1093/molbev/msw067
10.1093/nar/gkf436
10.1016/j.gep.2010.12.005
10.1016/j.cell.2017.12.022
10.1128/MCB.21.11.3609-3615.2001
10.1186/1471-2148-8-276
10.1126/science.1178534
10.1093/nar/gkaa937
10.1093/nar/gkm286
10.1101/2020.08.23.262857
10.1128/JVI.00542-19
10.1093/molbev/msm088
10.1038/nrg.2016.139
10.1186/1471-2229-12-192
10.1016/j.tplants.2015.04.003
10.1038/nrg2337
10.1186/s13100-020-00229-5
10.1007/s00438-002-0679-0
10.1007/s00251-017-0979-5
10.3852/09-230
10.1038/nri3295
10.1016/j.cellsig.2018.01.022
10.1186/s13059-019-1910-1
10.1038/s41467-017-01374-x
10.1093/cercor/bhp062
10.1016/j.gene.2005.06.022
10.1073/pnas.1012675108
10.1093/nar/29.12.2581
10.1016/j.virol.2013.12.024
10.3389/fpls.2018.00692
10.1093/molbev/msx116
10.1128/JVI.00867-11
10.1038/nmeth.4285
10.1371/journal.pone.0009490
10.1093/molbev/msv042
10.1016/j.cell.2016.05.032
10.1146/annurev-genet-110711-155522
10.1007/s13225-015-0350-9
10.1093/bioinformatics/btu170
10.1093/bioinformatics/bts635
10.1186/1745-6150-4-41
10.1038/ng.2007.51
10.1111/j.1364-3703.2008.00517.x
10.1093/molbev/msaa180
10.1093/molbev/msv035
10.1093/molbev/msu300
10.1126/science.1146281
10.1126/science.aad5497
10.1038/s41579-019-0189-2
10.1371/journal.ppat.1003968
10.1093/molbev/msx281
10.1093/bioinformatics/btp352
10.1016/j.tig.2017.07.011
10.1093/nar/gkz991
10.1016/S0169-5347(00)01994-7
10.1186/1471-2105-9-18
10.1038/382826a0
10.1016/j.virusres.2019.197645
10.1016/S0378-1119(03)00509-2
10.1038/nrmicro2783
10.1093/molbev/mst030
10.1159/000084963
10.1038/nrg3905
10.1093/molbev/msj011
10.1128/JVI.00850-18
10.1038/nature03667
10.1093/gbe/evt141
10.1038/nature06499
10.3897/BDJ.8.e39677
10.1093/molbev/msw054
ContentType Journal Article
Copyright The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2021
The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
COPYRIGHT 2021 Oxford University Press
The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Copyright_xml – notice: The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 2021
– notice: The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
– notice: COPYRIGHT 2021 Oxford University Press
– notice: The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This work is published under http://creativecommons.org/licenses/by-nc/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.
– notice: The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
DBID TOX
AAYXX
CITATION
NPM
3V.
7QG
7QP
7QR
7SN
7SS
7TK
7TM
7TO
7U9
7X7
7XB
88A
88E
8AO
8FD
8FE
8FH
8FI
8FJ
8FK
8G5
ABUWG
AEUYN
AFKRA
AZQEC
BBNVY
BENPR
BHPHI
C1K
CCPQU
DWQXO
FR3
FYUFA
GHDGH
GNUQQ
GUQSH
H94
HCIFZ
K9.
LK8
M0S
M1P
M2O
M7N
M7P
MBDVC
P64
PHGZM
PHGZT
PJZUB
PKEHL
PPXIY
PQEST
PQGLB
PQQKQ
PQUKI
PRINS
Q9U
RC3
7X8
5PM
ADTOC
UNPAY
DOI 10.1093/molbev/msab101
DatabaseName Oxford University Press Open Access Journals (LUT & LAB)
CrossRef
PubMed
ProQuest Central (Corporate)
Animal Behavior Abstracts
Calcium & Calcified Tissue Abstracts
Chemoreception Abstracts
Ecology Abstracts
Entomology Abstracts (Full archive)
Neurosciences Abstracts
Nucleic Acids Abstracts
Oncogenes and Growth Factors Abstracts
Virology and AIDS Abstracts
ProQuest Central Health & Medical Collection (via ProQuest)
ProQuest Central (purchase pre-March 2016)
Biology Database (Alumni Edition)
Medical Database (Alumni Edition)
ProQuest Pharma Collection
Technology Research Database
ProQuest SciTech Collection
ProQuest Natural Science Journals
Hospital Premium Collection
Hospital Premium Collection (Alumni Edition)
ProQuest Central (Alumni) (purchase pre-March 2016)
Research Library
ProQuest Central (Alumni)
ProQuest One Sustainability
ProQuest Central UK/Ireland
ProQuest Central Essentials
Biological Science Collection
ProQuest Central
ProQuest Natural Science Collection
Environmental Sciences and Pollution Management
ProQuest One
ProQuest Central
Engineering Research Database
Health Research Premium Collection
Health Research Premium Collection (Alumni)
ProQuest Central Student
ProQuest Research Library
AIDS and Cancer Research Abstracts
SciTech Premium Collection
ProQuest Health & Medical Complete (Alumni)
Biological Sciences
Health & Medical Collection (Alumni)
Medical Database
ProQuest Central Research Library (via ProQuest)
Algology Mycology and Protozoology Abstracts (Microbiology C)
Biological science database
Research Library (Corporate)
Biotechnology and BioEngineering Abstracts
ProQuest Central Premium
ProQuest One Academic
ProQuest Health & Medical Research Collection
ProQuest One Academic Middle East (New)
ProQuest One Health & Nursing
ProQuest One Academic Eastern Edition (DO NOT USE)
ProQuest One Applied & Life Sciences
ProQuest One Academic
ProQuest One Academic UKI Edition
ProQuest Central China
ProQuest Central Basic
Genetics Abstracts
MEDLINE - Academic
PubMed Central (Full Participant titles)
Unpaywall for CDI: Periodical Content
Unpaywall
DatabaseTitle CrossRef
PubMed
Research Library Prep
ProQuest Central Student
Oncogenes and Growth Factors Abstracts
ProQuest Central Essentials
Nucleic Acids Abstracts
SciTech Premium Collection
ProQuest Central China
Environmental Sciences and Pollution Management
ProQuest One Applied & Life Sciences
ProQuest One Sustainability
Health Research Premium Collection
Natural Science Collection
Health & Medical Research Collection
Biological Science Collection
Chemoreception Abstracts
ProQuest Central (New)
ProQuest Medical Library (Alumni)
Virology and AIDS Abstracts
ProQuest Biological Science Collection
ProQuest One Academic Eastern Edition
ProQuest Hospital Collection
Health Research Premium Collection (Alumni)
Biological Science Database
Ecology Abstracts
Neurosciences Abstracts
ProQuest Hospital Collection (Alumni)
Biotechnology and BioEngineering Abstracts
Entomology Abstracts
ProQuest Health & Medical Complete
ProQuest One Academic UKI Edition
Engineering Research Database
ProQuest One Academic
Calcium & Calcified Tissue Abstracts
ProQuest One Academic (New)
Technology Research Database
ProQuest One Academic Middle East (New)
ProQuest Health & Medical Complete (Alumni)
ProQuest Central (Alumni Edition)
ProQuest One Community College
ProQuest One Health & Nursing
Research Library (Alumni Edition)
ProQuest Natural Science Collection
ProQuest Pharma Collection
ProQuest Biology Journals (Alumni Edition)
ProQuest Central
ProQuest Health & Medical Research Collection
Genetics Abstracts
Health and Medicine Complete (Alumni Edition)
ProQuest Central Korea
Algology Mycology and Protozoology Abstracts (Microbiology C)
AIDS and Cancer Research Abstracts
ProQuest Research Library
ProQuest Central Basic
ProQuest SciTech Collection
ProQuest Medical Library
Animal Behavior Abstracts
ProQuest Central (Alumni)
MEDLINE - Academic
DatabaseTitleList Research Library Prep

MEDLINE - Academic

CrossRef
PubMed
Database_xml – sequence: 1
  dbid: NPM
  name: PubMed
  url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed
  sourceTypes: Index Database
– sequence: 2
  dbid: TOX
  name: Oxford Academic Open Access Journals
  url: https://academic.oup.com/journals/
  sourceTypes: Publisher
– sequence: 3
  dbid: UNPAY
  name: Unpaywall
  url: https://proxy.k.utb.cz/login?url=https://unpaywall.org/
  sourceTypes: Open Access Repository
– sequence: 4
  dbid: BENPR
  name: ProQuest Central
  url: http://www.proquest.com/pqcentral?accountid=15518
  sourceTypes: Aggregation Database
DeliveryMethod fulltext_linktorsrc
Discipline Biology
EISSN 1537-1719
EndPage 3278
ExternalDocumentID 10.1093/molbev/msab101
PMC8321522
A774474453
33871607
10_1093_molbev_msab101
Genre Journal Article
GrantInformation_xml – fundername: ;
  grantid: 31922001
GroupedDBID ---
-E4
-~X
.2P
.GJ
.I3
.ZR
0R~
18M
1TH
29M
2WC
4.4
48X
53G
5VS
5WA
70D
7X7
AAFWJ
AAIJN
AAIMJ
AAJKP
AAJQQ
AAMDB
AAMVS
AAOGV
AAPNW
AAPQZ
AAPXW
AAUQX
AAVAP
AAVLN
ABEJV
ABEUO
ABGNP
ABIXL
ABKDP
ABLJU
ABNKS
ABPTD
ABQLI
ABQTQ
ABSMQ
ABTAH
ABXVV
ABZBJ
ACGFO
ACGFS
ACIPB
ACIWK
ACMRT
ACNCT
ACPRK
ACUFI
ACUTO
ACYTK
ADBBV
ADEYI
ADEZT
ADFTL
ADGZP
ADHKW
ADHZD
ADJQC
ADOCK
ADRIX
ADRTK
ADYVW
ADZTZ
ADZXQ
AECKG
AEGPL
AEJOX
AEKKA
AEKSI
AELWJ
AEMDU
AENEX
AENZO
AEPUE
AETBJ
AEWNT
AFFNX
AFIYH
AFOFC
AFPKN
AFRAH
AFULF
AFXEN
AGINJ
AGKEF
AGSYK
AHMBA
AHXPO
AIAGR
AIJHB
AJEUX
AKHUL
AKWXX
ALMA_UNASSIGNED_HOLDINGS
ALTZX
ALUQC
AMNDL
APIBT
APWMN
ARIXL
ASAOO
ATDFG
AXUDD
AYOIW
AZVOD
BAWUL
BAYMD
BCRHZ
BEYMZ
BHONS
BQDIO
BQUQU
BSWAC
BTQHN
BTRTY
BVRKM
C1A
CAG
CDBKE
COF
CS3
CXTWN
CZ4
DAKXR
DFGAJ
DIK
DILTD
DU5
D~K
E3Z
EBS
EE~
EJD
EMOBN
F5P
F9B
FHSFR
FLIZI
FOTVD
GAUVT
GJXCC
GROUPED_DOAJ
GX1
H13
H5~
HAR
HH5
HW0
HZ~
IAO
IGS
IHR
IOX
ITC
J21
KOP
KQ8
KSI
KSN
M-Z
M49
MBTAY
ML0
MVM
N9A
NGC
NLBLG
NMDNZ
NOYVH
NTWIH
NU-
O0~
O9-
OAWHX
ODMLO
OJQWA
OK1
OVD
O~Y
P2P
PAFKI
PEELM
PQQKQ
Q1.
Q5Y
RD5
RHF
RNI
ROL
ROX
ROZ
RPM
RUSNO
RW1
RXO
RZO
TEORI
TJP
TJX
TLC
TN5
TOX
TR2
VQA
W8F
WOQ
X7H
XJT
XSW
YAYTL
YHZ
YKOAZ
YXANX
ZCA
ZCG
ZKX
ZXP
ZY4
~02
~91
88E
8AO
8FI
8FJ
8G5
AAYXX
ABUWG
AEUYN
AFKRA
AZQEC
BBNVY
BENPR
BHPHI
CCPQU
CITATION
DWQXO
FYUFA
GNUQQ
GUQSH
HCIFZ
HMCUK
M1P
M2O
M7P
PHGZM
PHGZT
PJZUB
PPXIY
PQGLB
PSQYO
PUEGO
UKHRP
NPM
ABUFD
3V.
7QG
7QP
7QR
7SN
7SS
7TK
7TM
7TO
7U9
7XB
88A
8FD
8FE
8FH
8FK
C1K
FR3
H94
K9.
LK8
M7N
MBDVC
P64
PKEHL
PQEST
PQUKI
PRINS
Q9U
RC3
7X8
5PM
ADTOC
ADXHL
UNPAY
ID FETCH-LOGICAL-c4061-c903f58670c6191302f73ef2a41483dfe301b36ffc0a4d02e416c70dd0696ffa3
IEDL.DBID UNPAY
ISSN 1537-1719
0737-4038
IngestDate Sun Oct 26 03:28:00 EDT 2025
Tue Sep 30 16:50:11 EDT 2025
Fri Sep 05 09:27:44 EDT 2025
Mon Oct 06 18:13:53 EDT 2025
Mon Oct 20 17:14:02 EDT 2025
Wed Feb 19 02:28:58 EST 2025
Wed Oct 01 04:24:00 EDT 2025
Thu Apr 24 23:06:01 EDT 2025
Fri Feb 07 10:35:33 EST 2025
IsDoiOpenAccess true
IsOpenAccess true
IsPeerReviewed true
IsScholarly true
Issue 8
Keywords phylogenetics
co-option
LTR retrotransposon
Language English
License This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
http://creativecommons.org/licenses/by-nc/4.0
The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
LinkModel DirectLink
MergedId FETCHMERGED-LOGICAL-c4061-c903f58670c6191302f73ef2a41483dfe301b36ffc0a4d02e416c70dd0696ffa3
Notes ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
OpenAccessLink https://proxy.k.utb.cz/login?url=https://academic.oup.com/mbe/article-pdf/38/8/3267/39457199/msab101.pdf
PMID 33871607
PQID 3171298373
PQPubID 36253
PageCount 12
ParticipantIDs unpaywall_primary_10_1093_molbev_msab101
pubmedcentral_primary_oai_pubmedcentral_nih_gov_8321522
proquest_miscellaneous_2515074528
proquest_journals_3171298373
gale_infotracacademiconefile_A774474453
pubmed_primary_33871607
crossref_citationtrail_10_1093_molbev_msab101
crossref_primary_10_1093_molbev_msab101
oup_primary_10_1093_molbev_msab101
ProviderPackageCode CITATION
AAYXX
PublicationCentury 2000
PublicationDate 2021-08-01
PublicationDateYYYYMMDD 2021-08-01
PublicationDate_xml – month: 08
  year: 2021
  text: 2021-08-01
  day: 01
PublicationDecade 2020
PublicationPlace United States
PublicationPlace_xml – name: United States
– name: Oxford
PublicationTitle Molecular biology and evolution
PublicationTitleAlternate Mol Biol Evol
PublicationYear 2021
Publisher Oxford University Press
Publisher_xml – name: Oxford University Press
References Han (2021072920000229700_msab101-B28) 2019; 222
Chuong (2021072920000229700_msab101-B12) 2016; 351
Wicker (2021072920000229700_msab101-B83) 2007; 8
Cam (2021072920000229700_msab101-B9) 2008; 451
Kumar (2021072920000229700_msab101-B43) 2017; 34
Lu (2021072920000229700_msab101-B52) 2020; 48
Lander (2021072920000229700_msab101-B45) 2012; 409
Makhnovskii (2021072920000229700_msab101-B54) 2020; 11
Price (2021072920000229700_msab101-B66) 2010; 5
Jangam (2021072920000229700_msab101-B33) 2017; 33
Wang (2021072920000229700_msab101-B82) 2020; 37
Duggal (2021072920000229700_msab101-B17) 2012; 12
Chuong (2021072920000229700_msab101-B13) 2017; 18
Graur (2021072920000229700_msab101-B27) 2013; 5
Wang (2021072920000229700_msab101-B81) 2019; 93
Ma (2021072920000229700_msab101-B53) 2018; 9
Dobin (2021072920000229700_msab101-B16) 2013; 29
Yap (2021072920000229700_msab101-B88) 2014; 10
Kalyaanamoorthy (2021072920000229700_msab101-B38) 2017; 14
Raja (2021072920000229700_msab101-B67) 2011; 103
Joly-Lopez (2021072920000229700_msab101-B37) 2016; 33
Lin (2021072920000229700_msab101-B49) 2007; 318
Murrell (2021072920000229700_msab101-B58) 2015; 32
Best (2021072920000229700_msab101-B3) 1996; 382
Skirmuntt (2021072920000229700_msab101-B74) 2019; 270
Yang (2021072920000229700_msab101-B86) 2007; 24
Edelstein (2021072920000229700_msab101-B19) 2005; 359
Thanaraj (2021072920000229700_msab101-B78) 2001; 29
Hirayama (2021072920000229700_msab101-B29) 2010; 102
Wang (2021072920000229700_msab101-B80) 2015; 20
Pastuzyn (2021072920000229700_msab101-B65) 2018; 172
Sasaki (2021072920000229700_msab101-B70) 2009; 10
Brandt (2021072920000229700_msab101-B6) 2005; 110
Etchegaray (2021072920000229700_msab101-B23) 2021; 12
Joly-Lopez (2021072920000229700_msab101-B36) 2012; 8
Oliver (2021072920000229700_msab101-B62) 2013; 5
Morales Poole (2021072920000229700_msab101-B56) 2017; 69
Nguyen (2021072920000229700_msab101-B61) 2015; 32
Li (2021072920000229700_msab101-B48)
Sanchez (2021072920000229700_msab101-B68) 2017; 8
Cho (2021072920000229700_msab101-B11) 2011; 11
Schnable (2021072920000229700_msab101-B71) 2009; 326
Li (2021072920000229700_msab101-B47) 2009; 25
Sekita (2021072920000229700_msab101-B72) 2008; 40
Yang (2021072920000229700_msab101-B87) 2000; 15
Hoen (2021072920000229700_msab101-B31) 2015; 32
Eichinger (2021072920000229700_msab101-B20) 2005; 435
Tian (2021072920000229700_msab101-B79) 2015; 74
Kovaka (2021072920000229700_msab101-B42) 2019; 20
Feschotte (2021072920000229700_msab101-B25) 2008; 9
Eddy (2021072920000229700_msab101-B18) 2011; 7
Burki (2021072920000229700_msab101-B8) 2020; 35
Emerson (2021072920000229700_msab101-B22) 2011; 85
Bolger (2021072920000229700_msab101-B4) 2014; 30
Llorens (2021072920000229700_msab101-B51) 2009; 4
Daugherty (2021072920000229700_msab101-B15) 2012; 46
Johnson (2021072920000229700_msab101-B35) 2019; 17
Llorens (2021072920000229700_msab101-B50) 2008; 8
Martin (2021072920000229700_msab101-B55) 2019; 3
Campillos (2021072920000229700_msab101-B10) 2006; 22
Katoh (2021072920000229700_msab101-B39) 2002; 30
Takaji (2021072920000229700_msab101-B77) 2009; 19
Janssens (2021072920000229700_msab101-B34) 2020; 8
Murrell (2021072920000229700_msab101-B57) 2013; 30
Huang (2021072920000229700_msab101-B32) 2016; 166
Kumar (2021072920000229700_msab101-B44) 2016; 33
Letunic (2021072920000229700_msab101-B46) 2021; 49
Nefedova (2021072920000229700_msab101-B60) 2014; 450–451
Albertini (2021072920000229700_msab101-B1) 1997; 89
Wiegmann (2021072920000229700_msab101-B84) 2011; 108
Bundock (2021072920000229700_msab101-B7) 2005; 436
Ellinghaus (2021072920000229700_msab101-B21) 2008; 9
Hoang (2021072920000229700_msab101-B30) 2018; 35
Ono (2021072920000229700_msab101-B63) 2006; 38
Xu (2021072920000229700_msab101-B85) 2007; 35
Pang (2021072920000229700_msab101-B64) 2018; 45
Ashley (2021072920000229700_msab101-B2) 2018; 172
Goodwin (2021072920000229700_msab101-B26) 2002; 267
Sironi (2021072920000229700_msab101-B73) 2015; 16
Zhang (2021072920000229700_msab101-B89) 2018; 9
Sander (2021072920000229700_msab101-B69) 2003; 310
Collins (2021072920000229700_msab101-B14) 2001; 21
Boso (2021072920000229700_msab101-B5) 2018; 92
Knip (2021072920000229700_msab101-B40) 2012; 12
Kokošar (2021072920000229700_msab101-B41) 2013; 30
Stoye (2021072920000229700_msab101-B76) 2012; 10
Naville (2021072920000229700_msab101-B59) 2016; 22
Steenkamp (2021072920000229700_msab101-B75) 2006; 23
References_xml – volume: 103
  start-page: 1421
  issue: 6
  year: 2011
  ident: 2021072920000229700_msab101-B67
  article-title: Freshwater ascomycetes: two new species of Lindgomyces (Lindgomycetaceae, Pleosporales, Dothideomycetes) from Japan and USA
  publication-title: Mycologia
  doi: 10.3852/11-077
– volume: 435
  start-page: 43
  issue: 7038
  year: 2005
  ident: 2021072920000229700_msab101-B20
  article-title: The genome of the social amoeba Dictyostelium discoideum
  publication-title: Nature
  doi: 10.1038/nature03481
– volume: 30
  start-page: 1015
  issue: 5
  year: 2013
  ident: 2021072920000229700_msab101-B41
  article-title: Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/mst014
– volume: 11
  start-page: 396
  issue: 4
  year: 2020
  ident: 2021072920000229700_msab101-B54
  article-title: Domesticated gag gene of Drosophila LTR retrotransposons is involved in response to oxidative stress
  publication-title: Genes (Basel)
  doi: 10.3390/genes11040396
– volume: 7
  start-page: e1002195
  issue: 10
  year: 2011
  ident: 2021072920000229700_msab101-B18
  article-title: Accelerated profile HMM searches
  publication-title: PLoS Comp Biol
  doi: 10.1371/journal.pcbi.1002195
– volume: 35
  start-page: 43
  issue: 1
  year: 2020
  ident: 2021072920000229700_msab101-B8
  article-title: The new tree of eukaryotes
  publication-title: Trends Ecol Evol
  doi: 10.1016/j.tree.2019.08.008
– volume: 22
  start-page: 312
  issue: 4
  year: 2016
  ident: 2021072920000229700_msab101-B59
  article-title: Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates
  publication-title: Clin Microbiol Infect
  doi: 10.1016/j.cmi.2016.02.001
– volume: 5
  start-page: 578
  issue: 3
  year: 2013
  ident: 2021072920000229700_msab101-B27
  article-title: On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE
  publication-title: Genome Biol Evol
  doi: 10.1093/gbe/evt028
– volume: 172
  start-page: 275
  issue: 1–2
  year: 2018
  ident: 2021072920000229700_msab101-B65
  article-title: The neuronal gene arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer
  publication-title: Cell
  doi: 10.1016/j.cell.2017.12.024
– volume: 8
  start-page: 973
  issue: 12
  year: 2007
  ident: 2021072920000229700_msab101-B83
  article-title: A unified classification system for eukaryotic transposable elements
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg2165
– volume: 9
  start-page: 205
  year: 2018
  ident: 2021072920000229700_msab101-B89
  article-title: Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
  publication-title: Nat Commun
  doi: 10.1038/s41467-017-02644-4
– volume: 3
  start-page: 1
  issue: 6
  year: 2019
  ident: 2021072920000229700_msab101-B55
  article-title: Higher-level phylogeny and reclassification of Lampyridae (Coleoptera: Elateroidea)
  publication-title: Insect Syst Divers
– volume: 222
  start-page: 70
  issue: 1
  year: 2019
  ident: 2021072920000229700_msab101-B28
  article-title: Origin and evolution of the plant immune system
  publication-title: New Phytol
  doi: 10.1111/nph.15596
– volume: 89
  start-page: 83
  issue: 1
  year: 1997
  ident: 2021072920000229700_msab101-B1
  article-title: Pex14p, a peroxisomal membrane protein binding both receptors of the two PTS-dependent import pathways
  publication-title: Cell
  doi: 10.1016/S0092-8674(00)80185-3
– volume: 8
  start-page: e1002931
  issue: 9
  year: 2012
  ident: 2021072920000229700_msab101-B36
  article-title: A gene family derived from transposable elements during early angiosperm evolution has reproductive fitness benefits in Arabidopsis thaliana
  publication-title: PLoS Genet
  doi: 10.1371/journal.pgen.1002931
– volume: 22
  start-page: 585
  issue: 11
  year: 2006
  ident: 2021072920000229700_msab101-B10
  article-title: Computational characterization of multiple Gag-like human proteins
  publication-title: Trends Genet
  doi: 10.1016/j.tig.2006.09.006
– volume: 38
  start-page: 101
  issue: 1
  year: 2006
  ident: 2021072920000229700_msab101-B63
  article-title: Deletion of Peg10, an imprinted gene acquired from a retrotransposon, causes early embryonic lethality
  publication-title: Nat Genet
  doi: 10.1038/ng1699
– volume: 33
  start-page: 1937
  issue: 8
  year: 2016
  ident: 2021072920000229700_msab101-B37
  article-title: Phylogenetic and genomic analyses resolve the origin of important plant genes derived from transposable elements
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msw067
– volume: 30
  start-page: 3059
  issue: 14
  year: 2002
  ident: 2021072920000229700_msab101-B39
  article-title: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkf436
– volume: 11
  start-page: 216
  issue: 3–4
  year: 2011
  ident: 2021072920000229700_msab101-B11
  article-title: XLMR candidate mouse gene, Zcchc12 (Sizn1) is a novel marker of Cajal–Retzius cells
  publication-title: Gene Expr Patterns
  doi: 10.1016/j.gep.2010.12.005
– volume: 172
  start-page: 262
  issue: 1–2
  year: 2018
  ident: 2021072920000229700_msab101-B2
  article-title: Retrovirus-like gag protein Arc1 binds RNA and traffics across synaptic boutons
  publication-title: Cell
  doi: 10.1016/j.cell.2017.12.022
– volume: 21
  start-page: 3609
  issue: 11
  year: 2001
  ident: 2021072920000229700_msab101-B14
  article-title: All in the family: the BTB/POZ, KRAB, and SCAN domains
  publication-title: Mol Cell Biol
  doi: 10.1128/MCB.21.11.3609-3615.2001
– volume: 8
  start-page: 276
  issue: 1
  year: 2008
  ident: 2021072920000229700_msab101-B50
  article-title: Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis
  publication-title: BMC Evol Biol
  doi: 10.1186/1471-2148-8-276
– volume: 326
  start-page: 1112
  issue: 5956
  year: 2009
  ident: 2021072920000229700_msab101-B71
  article-title: The B73 maize genome: complexity, diversity, and dynamics
  publication-title: Science
  doi: 10.1126/science.1178534
– volume: 49
  start-page: D458
  issue: D1
  year: 2021
  ident: 2021072920000229700_msab101-B46
  article-title: SMART: recent updates, new developments and status in 2020
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkaa937
– volume: 35
  start-page: W265
  issue: Web Server issue
  year: 2007
  ident: 2021072920000229700_msab101-B85
  article-title: LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkm286
– start-page: 1
  ident: 2021072920000229700_msab101-B48
  doi: 10.1101/2020.08.23.262857
– volume: 93
  start-page: e00542–19
  issue: 14
  year: 2019
  ident: 2021072920000229700_msab101-B81
  article-title: Convergent co-option of the retroviral gag gene during the early evolution of mammals
  publication-title: J Virol
  doi: 10.1128/JVI.00542-19
– volume: 24
  start-page: 1586
  issue: 8
  year: 2007
  ident: 2021072920000229700_msab101-B86
  article-title: PAML 4: phylogenetic analysis by maximum likelihood
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msm088
– volume: 18
  start-page: 71
  issue: 2
  year: 2017
  ident: 2021072920000229700_msab101-B13
  article-title: Regulatory activities of transposable elements: from conflicts to benefits
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg.2016.139
– volume: 12
  start-page: 192
  year: 2012
  ident: 2021072920000229700_msab101-B40
  article-title: The SLEEPER genes: a transposase-derived angiosperm-specific gene family
  publication-title: BMC Plant Biol
  doi: 10.1186/1471-2229-12-192
– volume: 20
  start-page: 453
  issue: 7
  year: 2015
  ident: 2021072920000229700_msab101-B80
  article-title: Multifaceted roles of FHY3 and FAR1 in light signaling and beyond
  publication-title: Trends Plant Sci
  doi: 10.1016/j.tplants.2015.04.003
– volume: 9
  start-page: 397
  issue: 5
  year: 2008
  ident: 2021072920000229700_msab101-B25
  article-title: Transposable elements and the evolution of regulatory networks
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg2337
– volume: 12
  start-page: 1
  year: 2021
  ident: 2021072920000229700_msab101-B23
  article-title: Transposable element-derived sequences in vertebrate development
  publication-title: Mob DNA
  doi: 10.1186/s13100-020-00229-5
– volume: 267
  start-page: 481
  issue: 4
  year: 2002
  ident: 2021072920000229700_msab101-B26
  article-title: A group of deuterostome Ty3/gypsy-like retrotransposons with Ty1/copia-like pol-domain orders
  publication-title: Mol Genet Genomics
  doi: 10.1007/s00438-002-0679-0
– volume: 69
  start-page: 391
  issue: 6
  year: 2017
  ident: 2021072920000229700_msab101-B56
  article-title: The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates
  publication-title: Immunogenetics
  doi: 10.1007/s00251-017-0979-5
– volume: 102
  start-page: 729
  issue: 3
  year: 2010
  ident: 2021072920000229700_msab101-B29
  article-title: A molecular phylogenetic assessment of Massarina ingoldiana sensu lato
  publication-title: Mycologia
  doi: 10.3852/09-230
– volume: 12
  start-page: 687
  issue: 10
  year: 2012
  ident: 2021072920000229700_msab101-B17
  article-title: Evolutionary conflicts between viruses and restriction factors shape immunity
  publication-title: Nat Rev Immunol
  doi: 10.1038/nri3295
– volume: 45
  start-page: 54
  year: 2018
  ident: 2021072920000229700_msab101-B64
  article-title: PNMA family: protein interaction network and cell signalling pathways implicated in cancer and apoptosis
  publication-title: Cell Signal.
  doi: 10.1016/j.cellsig.2018.01.022
– volume: 20
  start-page: 278
  issue: 1
  year: 2019
  ident: 2021072920000229700_msab101-B42
  article-title: Transcriptome assembly from long-read RNA-seq alignments with StringTie2
  publication-title: Genome Biol
  doi: 10.1186/s13059-019-1910-1
– volume: 8
  start-page: 1283
  issue: 1
  year: 2017
  ident: 2021072920000229700_msab101-B68
  article-title: High-frequency recombination between members of an LTR retrotransposon family during transposition bursts
  publication-title: Nat Commun
  doi: 10.1038/s41467-017-01374-x
– volume: 19
  start-page: 2865
  issue: 12
  year: 2009
  ident: 2021072920000229700_msab101-B77
  article-title: Paraneoplastic antigen-like 5 gene (PNMA5) is preferentially expressed in the association areas in a primate specific manner
  publication-title: Cereb Cortex
  doi: 10.1093/cercor/bhp062
– volume: 359
  start-page: 1
  year: 2005
  ident: 2021072920000229700_msab101-B19
  article-title: The SCAN domain family of zinc finger transcription factors
  publication-title: Gene
  doi: 10.1016/j.gene.2005.06.022
– volume: 108
  start-page: 5690
  issue: 14
  year: 2011
  ident: 2021072920000229700_msab101-B84
  article-title: Episodic radiations in the fly tree of life
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.1012675108
– volume: 29
  start-page: 2581
  issue: 12
  year: 2001
  ident: 2021072920000229700_msab101-B78
  article-title: Human GC-AG alternative intron isoforms with weak donor sites show enhanced consensus at acceptor exon positions
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/29.12.2581
– volume: 450–451
  start-page: 196
  year: 2014
  ident: 2021072920000229700_msab101-B60
  article-title: Domesticated retroviral GAG gene in Drosophila: new functions for an old gene
  publication-title: Virology
  doi: 10.1016/j.virol.2013.12.024
– volume: 9
  start-page: 692
  year: 2018
  ident: 2021072920000229700_msab101-B53
  article-title: FAR1-related sequence (FRS) and FRS-related factor (FRF) family proteins in Arabidopsis growth and development
  publication-title: Front Plant Sci.
  doi: 10.3389/fpls.2018.00692
– volume: 34
  start-page: 1812
  issue: 7
  year: 2017
  ident: 2021072920000229700_msab101-B43
  article-title: TimeTree: a resource for timelines, timetrees, and divergence times
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msx116
– volume: 85
  start-page: 12043
  issue: 22
  year: 2011
  ident: 2021072920000229700_msab101-B22
  article-title: Gypsy and the birth of the SCAN domain
  publication-title: J Virol
  doi: 10.1128/JVI.00867-11
– volume: 14
  start-page: 587
  issue: 6
  year: 2017
  ident: 2021072920000229700_msab101-B38
  article-title: ModelFinder: fast model selection for accurate phylogenetic estimates
  publication-title: Nat Methods
  doi: 10.1038/nmeth.4285
– volume: 5
  start-page: e9490
  issue: 3
  year: 2010
  ident: 2021072920000229700_msab101-B66
  article-title: FastTree 2—approximately maximum-likelihood trees for large alignments
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0009490
– volume: 32
  start-page: 1487
  issue: 6
  year: 2015
  ident: 2021072920000229700_msab101-B31
  article-title: Discovery of novel genes derived from transposable elements using integrative genomic analysis
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msv042
– volume: 166
  start-page: 102
  issue: 1
  year: 2016
  ident: 2021072920000229700_msab101-B32
  article-title: Discovery of an active RAG transposon illuminates the origins of V(D)
  publication-title: J Recombin Cell
  doi: 10.1016/j.cell.2016.05.032
– volume: 46
  start-page: 677
  year: 2012
  ident: 2021072920000229700_msab101-B15
  article-title: Rules of engagement: molecular insights from host–virus arms races
  publication-title: Annu Rev Genet
  doi: 10.1146/annurev-genet-110711-155522
– volume: 74
  start-page: 267
  issue: 1
  year: 2015
  ident: 2021072920000229700_msab101-B79
  article-title: Phylogenetic relationships and morphological reappraisal of Melanommataceae (Pleosporales)
  publication-title: Fungal Divers
  doi: 10.1007/s13225-015-0350-9
– volume: 30
  start-page: 2114
  issue: 15
  year: 2014
  ident: 2021072920000229700_msab101-B4
  article-title: Trimmomatic: a flexible trimmer for Illumina sequence data
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu170
– volume: 29
  start-page: 15
  issue: 1
  year: 2013
  ident: 2021072920000229700_msab101-B16
  article-title: STAR: ultrafast universal RNA-seq aligner
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts635
– volume: 4
  start-page: 41
  year: 2009
  ident: 2021072920000229700_msab101-B51
  article-title: Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees
  publication-title: Biol Direct.
  doi: 10.1186/1745-6150-4-41
– volume: 40
  start-page: 243
  issue: 2
  year: 2008
  ident: 2021072920000229700_msab101-B72
  article-title: Role of retrotransposon-derived imprinted gene, Rtl1, in the feto-maternal interface of mouse placenta
  publication-title: Nat Genet
  doi: 10.1038/ng.2007.51
– volume: 10
  start-page: 161
  issue: 2
  year: 2009
  ident: 2021072920000229700_msab101-B70
  article-title: Over-expression of putative transcriptional coactivator KELP interferes with Tomato mosaic virus cell-to-cell movement
  publication-title: Mol Plant Pathol
  doi: 10.1111/j.1364-3703.2008.00517.x
– volume: 37
  start-page: 3232
  issue: 11
  year: 2020
  ident: 2021072920000229700_msab101-B82
  article-title: Frequent retroviral gene co-option during the evolution of vertebrates
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msaa180
– volume: 32
  start-page: 1365
  issue: 5
  year: 2015
  ident: 2021072920000229700_msab101-B58
  article-title: Gene-wide identification of episodic selection
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msv035
– volume: 32
  start-page: 268
  issue: 1
  year: 2015
  ident: 2021072920000229700_msab101-B61
  article-title: IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msu300
– volume: 318
  start-page: 1302
  issue: 5854
  year: 2007
  ident: 2021072920000229700_msab101-B49
  article-title: Transposase-derived transcription factors regulate light signaling in Arabidopsis
  publication-title: Science
  doi: 10.1126/science.1146281
– volume: 351
  start-page: 1083
  issue: 6277
  year: 2016
  ident: 2021072920000229700_msab101-B12
  article-title: Regulatory evolution of innate immunity through co-option of endogenous retroviruses
  publication-title: Science
  doi: 10.1126/science.aad5497
– volume: 17
  start-page: 355
  issue: 6
  year: 2019
  ident: 2021072920000229700_msab101-B35
  article-title: Origins and evolutionary consequences of ancient endogenous retroviruses
  publication-title: Nat Rev Microbiol
  doi: 10.1038/s41579-019-0189-2
– volume: 10
  start-page: e1003968
  issue: 3
  year: 2014
  ident: 2021072920000229700_msab101-B88
  article-title: Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses
  publication-title: PLoS Pathog
  doi: 10.1371/journal.ppat.1003968
– volume: 35
  start-page: 518
  issue: 2
  year: 2018
  ident: 2021072920000229700_msab101-B30
  article-title: UFBoot2: improving the ultrafast bootstrap approximation
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msx281
– volume: 25
  start-page: 2078
  issue: 16
  year: 2009
  ident: 2021072920000229700_msab101-B47
  article-title: The Sequence Alignment/Map format and SAMtools
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btp352
– volume: 33
  start-page: 817
  issue: 11
  year: 2017
  ident: 2021072920000229700_msab101-B33
  article-title: Transposable element domestication as an adaptation to evolutionary conflicts
  publication-title: Trends Genet
  doi: 10.1016/j.tig.2017.07.011
– volume: 48
  start-page: D265
  issue: D1
  year: 2020
  ident: 2021072920000229700_msab101-B52
  article-title: CDD/SPARCLE: the conserved domain database in 2020
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkz991
– volume: 15
  start-page: 496
  issue: 12
  year: 2000
  ident: 2021072920000229700_msab101-B87
  article-title: Statistical methods for detecting molecular adaptation
  publication-title: Trends Ecol Evol
  doi: 10.1016/S0169-5347(00)01994-7
– volume: 9
  start-page: 18
  issue: 1
  year: 2008
  ident: 2021072920000229700_msab101-B21
  article-title: LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons
  publication-title: BMC Bioinformatics
  doi: 10.1186/1471-2105-9-18
– volume: 409
  start-page: 860
  year: 2012
  ident: 2021072920000229700_msab101-B45
  article-title: Initial sequencing and analysis of the human genome
  publication-title: Nature
– volume: 382
  start-page: 826
  issue: 6594
  year: 1996
  ident: 2021072920000229700_msab101-B3
  article-title: Positional cloning of the mouse retrovirus restriction gene Fv1
  publication-title: Nature
  doi: 10.1038/382826a0
– volume: 270
  start-page: 197645
  year: 2019
  ident: 2021072920000229700_msab101-B74
  article-title: The evolution of endogenous retroviral envelope genes in bats and their potential contribution to host biology
  publication-title: Virus Res
  doi: 10.1016/j.virusres.2019.197645
– volume: 310
  start-page: 29
  year: 2003
  ident: 2021072920000229700_msab101-B69
  article-title: The SCAN domain defines a large family of zinc finger transcription factors
  publication-title: Gene
  doi: 10.1016/S0378-1119(03)00509-2
– volume: 10
  start-page: 395
  issue: 6
  year: 2012
  ident: 2021072920000229700_msab101-B76
  article-title: Studies of endogenous retroviruses reveal a continuing evolutionary saga
  publication-title: Nat Rev Microbiol
  doi: 10.1038/nrmicro2783
– volume: 30
  start-page: 1196
  issue: 5
  year: 2013
  ident: 2021072920000229700_msab101-B57
  article-title: FUBAR: a fast, unconstrained Bayesian approximation for inferring selection
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/mst030
– volume: 110
  start-page: 307
  issue: 1–4
  year: 2005
  ident: 2021072920000229700_msab101-B6
  article-title: A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes
  publication-title: Cytogenet Genome Res
  doi: 10.1159/000084963
– volume: 16
  start-page: 224
  issue: 4
  year: 2015
  ident: 2021072920000229700_msab101-B73
  article-title: Evolutionary insights into host-pathogen interactions from mammalian sequence data
  publication-title: Nat Rev Genet
  doi: 10.1038/nrg3905
– volume: 23
  start-page: 93
  issue: 1
  year: 2006
  ident: 2021072920000229700_msab101-B75
  article-title: The protistan origins of animals and fungi
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msj011
– volume: 92
  start-page: e00850–18
  issue: 18
  year: 2018
  ident: 2021072920000229700_msab101-B5
  article-title: Ancient evolutionary origin and positive selection of the retroviral restriction factor Fv1 in muroid rodents
  publication-title: J Virol
  doi: 10.1128/JVI.00850-18
– volume: 436
  start-page: 282
  issue: 7048
  year: 2005
  ident: 2021072920000229700_msab101-B7
  article-title: An Arabidopsis hAT-like transposase is essential for plant development
  publication-title: Nature
  doi: 10.1038/nature03667
– volume: 5
  start-page: 1886
  issue: 10
  year: 2013
  ident: 2021072920000229700_msab101-B62
  article-title: Transposable elements: powerful contributors to angiosperm evolution and diversity
  publication-title: Genome Biol Evol
  doi: 10.1093/gbe/evt141
– volume: 451
  start-page: 431
  issue: 7177
  year: 2008
  ident: 2021072920000229700_msab101-B9
  article-title: Host genome surveillance for retrotransposons by transposon-derived proteins
  publication-title: Nature
  doi: 10.1038/nature06499
– volume: 8
  start-page: e39677
  year: 2020
  ident: 2021072920000229700_msab101-B34
  article-title: A large-scale species level dated angiosperm phylogeny for evolutionary and ecological analyses
  publication-title: Biodivers Data J
  doi: 10.3897/BDJ.8.e39677
– volume: 33
  start-page: 1870
  issue: 7
  year: 2016
  ident: 2021072920000229700_msab101-B44
  article-title: MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msw054
SSID ssj0014466
Score 2.4559038
Snippet LTR retrotransposons comprise a major component of the genomes of eukaryotes. On occasion, retrotransposon genes can be recruited by their hosts for diverse...
SourceID unpaywall
pubmedcentral
proquest
gale
pubmed
crossref
oup
SourceType Open Access Repository
Aggregation Database
Index Database
Enrichment Source
Publisher
StartPage 3267
SubjectTerms Analysis
Angiosperms
Animals
Discoveries
Eukaryotes
Evolution
Evolutionary genetics
Gag protein
Gene expression
Genes
Genetic research
Genomes
Genomics
Phylogeny
Plants
Positive selection
Taxonomy
Transposons
SummonAdditionalLinks – databaseName: ProQuest Central
  dbid: BENPR
  link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwhV3db9MwED-NTgheEJ8jMJBBSPASNY2duHtAaIxOE4IKVau0t8ifY6JLSpsO9b_nrnHCKgST8pRYjj_ufD_7zr8DeDPIjBIq13GeOhcLQUEAnsvYei905rzPOF1O_jrOT6bi81l2tgPj9i4MhVW2a-JmobaVoTPyPto5NE24neIf5j9jyhpF3tU2hYYKqRXs-w3F2C3YTYkZqwe7H0fjb5POr9B6LyU2RyR82NE48v5lNdPuqn-5VHoQUsS0Zios1ls34K4B0b_jKe-syrla_1Kz2TVjdXwf7gWUyQ4bsXgAO658CLebvJPrRzCdlijgNR0-sS-nEzZx9aKqG5pzxN_sXJ0z4qNesqMqruYIStlFyRAqsk_OzdnoKsgrqzwbrX6oxbpCxPoYpsej06OTOORXiA2Z8dgcJNxnw1wmBrdR5MH0kjufKoF7JG69Q-XXPPfeJErYJHUI3oxMrE3yA3yr-BPolVXpngLLnVYDa7XURgrncu1kqjOfCZuL3BseQdwOZ2EC-TjlwJgVjROcF83wF2H4I3jblZ83tBv_LkmzU5A-Yo1GhWsF2C5itioOEd8KfDJsw2ucwBur22_ntwjavCz-yF4Er7rPqIfkXFGlq1bLAnEiQmuRpcMI9hpx6H7FOW1LExmB3BKUrgBxfG9_KS--b7i-KZEUQuQI3nUidUMPnv2_B8_hbkphOZsYxn3o1YuVe4G4qtYvg7L8BulxJnQ
  priority: 102
  providerName: ProQuest
Title Unearthing LTR Retrotransposon gag Genes Co-opted in the Deep Evolution of Eukaryotes
URI https://www.ncbi.nlm.nih.gov/pubmed/33871607
https://www.proquest.com/docview/3171298373
https://www.proquest.com/docview/2515074528
https://pubmed.ncbi.nlm.nih.gov/PMC8321522
https://academic.oup.com/mbe/article-pdf/38/8/3267/39457199/msab101.pdf
UnpaywallVersion publishedVersion
Volume 38
hasFullText 1
inHoldings 1
isFullTextHit
isPrint
journalDatabaseRights – providerCode: PRVFSB
  databaseName: Free Full-Text Journals in Chemistry
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: HH5
  dateStart: 19830101
  isFulltext: true
  titleUrlDefault: http://abc-chemistry.org/
  providerName: ABC ChemistRy
– providerCode: PRVAFT
  databaseName: Open Access Digital Library
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: KQ8
  dateStart: 19831201
  isFulltext: true
  titleUrlDefault: http://grweb.coalliance.org/oadl/oadl.html
  providerName: Colorado Alliance of Research Libraries
– providerCode: PRVAON
  databaseName: Directory of Open Access Journals
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: DOA
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: https://www.doaj.org/
  providerName: Directory of Open Access Journals
– providerCode: PRVBFR
  databaseName: Free Medical Journals
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 20241105
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: DIK
  dateStart: 19830101
  isFulltext: true
  titleUrlDefault: http://www.freemedicaljournals.com
  providerName: Flying Publisher
– providerCode: PRVFQY
  databaseName: GFMER Free Medical Journals
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 20241105
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: GX1
  dateStart: 19830101
  isFulltext: true
  titleUrlDefault: http://www.gfmer.ch/Medical_journals/Free_medical.php
  providerName: Geneva Foundation for Medical Education and Research
– providerCode: PRVAQN
  databaseName: PubMed Central
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: RPM
  dateStart: 20080101
  isFulltext: true
  titleUrlDefault: https://www.ncbi.nlm.nih.gov/pmc/
  providerName: National Library of Medicine
– providerCode: PRVASL
  databaseName: Oxford Academic Open Access Journals
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: TOX
  dateStart: 19831201
  isFulltext: true
  titleUrlDefault: https://academic.oup.com/journals/
  providerName: Oxford University Press
– providerCode: PRVASL
  databaseName: Oxford Academic Open Access Journals
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: TOX
  dateStart: 20020101
  isFulltext: true
  titleUrlDefault: https://academic.oup.com/journals/
  providerName: Oxford University Press
– providerCode: PRVPQU
  databaseName: Health & Medical Collection
  customDbUrl:
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: 7X7
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: https://search.proquest.com/healthcomplete
  providerName: ProQuest
– providerCode: PRVPQU
  databaseName: ProQuest Central
  customDbUrl: http://www.proquest.com/pqcentral?accountid=15518
  eissn: 1537-1719
  dateEnd: 99991231
  omitProxy: true
  ssIdentifier: ssj0014466
  issn: 0737-4038
  databaseCode: BENPR
  dateStart: 20210101
  isFulltext: true
  titleUrlDefault: https://www.proquest.com/central
  providerName: ProQuest
link http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1bb9MwFLa2VgheuA86RmUQErykSeNb81hGx4SgTFUrlafIduxtWptUbbqp_HqOm4tWEBoPSFEeYsfXc-zP9vF3EHrXZVpSyZXHQ2M8Sp0RgCXCS6ylihlrGXGXk78N-emEfpmy6R76XN2FkaVVeKe60jBXxi8b0Vsk1ic9v-cD5hA-iSgT3Sjy5yupQLI6ELyPmpwBKG-g5mR41v-xJeGErGmw9WkN6u0oEbtRTd9I_Hk2U-a6SmRneioH6Z2bb7cA6J92lPfX6UJubuRsdmuSOnmELqrqFbYpV511rjr652_Mj_-h_o_RwxLI4n7x0xO0Z9Kn6F7h2nLzDE0mKehQ7va38NfxCI9MvszygkkdID4-l-fYUV6v8HHmZQvAvfgyxYBG8SdjFnhwXaoEziwerK_kcpMBKH6OJieD8fGpV7pw8LRDCp6OAmJZj4tAw0rNHZJaQYwNJYVlGEmsgfFFEW6tDiRNgtAAPtQiSJKAR_BVkgPUSLPUvESYGyW7SaKE0oIaw5URoWKW0YRTbjVpIa_quViX_ObOzcYsLs7ZSVz0dFw2Vwu9r-MvCmaPv8d0ghA7lYcUddVHUC5HnhX3AUJTeBiU4S30253JHVWiFJcDxioGGAfIq0cEpPGmDgZVd-c3MjXZehUDFAX0TlnYa6EXheTVWRHiVr6BaCGxI5N1BEcjvhuSXl5s6cSdrypA4S30oZbeO2pw-O9RX6EHobMC2ppMHqFGvlyb1wDjctVG-2Iq2qj5cTA8G7W3myHwHn-ftkvl_QVLZk2C
linkProvider Unpaywall
linkToHtml http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3db9MwED-NTWi8IL7JGGAQCF6iprGTtA8TGlunjnUVqlppb5nt2GNal4Qm3dR_jr-Nc-OEVQj2NClPieXE5zvf73JfAB_ageSMh8INfaVcxkwQgKaRm2jNRKC0DqhJTj4ehv0J-3YSnKzBrzoXxoRV1mfi8qBOMmn-kbdQz6FqQnOKfsl_uqZrlPGu1i00uG2tkOwsS4zZxI4jtbhGE67YOdzH_f7o-we98V7ftV0GXGmUmSu7HtVBJ4w8icaE8ePpiCrtc4aWAk20QhEQNNRaepwlnq8QwsjISxIv7OJdTnHee7DBKOui8bfxtTf8Pmr8GLW3NMLlM492mrKRtHWZTYW6al0WXLRtS5paLVrlsJJxdwP4_h2_uTlPc7645tPpDeV48AgeWlRLdis2fAxrKn0C96s-l4unMJmkSKnS_Owig_GIjFQ5y8qqrDrifXLGz4ipf12QvczNcgTB5DwlCE3JvlI56V1Z-SCZJr35BZ8tMkTIz2ByJ5R-DutplqqXQEIleDtJRCRkxJQKhYp8EeiAJSELtaQOuDU5Y2mLnZueG9O4crrTuCJ_bMnvwKdmfF6V-fj3SLM7sZF_nFFym8aA32UqacW7iKcZXgF-w3vcwFun2673N7anRxH_4XUH3jWPUe6NM4enKpsXMeJShPIs8DsOvKjYoXkVpcYM9iIHohVGaQaYmuKrT9LzH8va4qZxFUJyBz43LHXLCrb-v4K3sNkfHw_iweHw6BU88E1I0DJ-chvWy9lcvUZMV4o3VnAInN61rP4GjLliKg
linkToUnpaywall http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrZ3bb9MwFIet0QnBC_dLYCCDkOAlTRrfksdqdEwIJjQt0niKbMfeprVJ1CZD5a_nuLloBaHxgNSn2nXi-Bznc338Owi9mzAtqeTK55ExPqUuCMAS4efWUsWMtYy4w8lfj_hhSj-fstMd9Kk_CyO7qPBxf6RhoUzQPUS_ym1A4iAOgDlEQBLKxCRJgsVKKrCsMRTfQrucAZSP0G569G36fSPCCZem4SanNbi3k0ScJIN8IwkW5VyZq76RrddTN0lvnXy7BqB_xlHeaYpKrn_I-fzaS-rgPjrvu9fGplyOm1qN9c_flB__Q_8foHsdyOJp-6OHaMcUj9DtNrXl-jFK0wJ8qHb_b-EvJ8f42NTLsm6V1AHx8Zk8w07yeoX3S7-sgHvxRYGBRvFHYyo8u-pcApcWz5pLuVyXAMVPUHowO9k_9LsUDr52pODrJCSWxVyEGlZqbpPUCmJsJCksw0huDcwvinBrdShpHkYG-FCLMM9DnsC3kjxFo6IszHOEuVFykudKKC2oMVwZESlmGc055VYTD_n9yGW60zd3aTbmWbvPTrJ2pLPucXno_VC_apU9_l7TGULmXB5a1P0YwX058axsCghN4cPgHt7CuN3Y3F5vSlk3YawywDggr5gIaOPNUAyu7vZvZGHKZpUBigK9UxbFHnrWWt5wKULcyjcUHhJbNjlUcDLi2yXFxflGTtzlqgIK99CHwXpv6MGLf6_6Et2NXBTQJmRyD43qZWNeAcbV6nXnor8AsitI8A
openUrl ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Unearthing+LTR+retrotransposon+gag+genes+co-opted+in+the+deep+evolution+of+eukaryotes&rft.jtitle=Molecular+biology+and+evolution&rft.au=Wang%2C+Jianhua&rft.au=Han%2C+Guan-Zhu&rft.date=2021-08-01&rft.eissn=1537-1719&rft_id=info:doi/10.1093%2Fmolbev%2Fmsab101&rft_id=info%3Apmid%2F33871607&rft.externalDocID=33871607
thumbnail_l http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1537-1719&client=summon
thumbnail_m http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1537-1719&client=summon
thumbnail_s http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1537-1719&client=summon