Distinguish Dianthus species or varieties based on chloroplast genomes
Most plants belonging to the widely distributed genus are used for gardening. Interspecific hybridization of different species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among species, the chloroplast genomes of 12 species, in...
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| Published in | Open life sciences Vol. 18; no. 1; pp. 20220772 - 31 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
De Gruyter
28.11.2023
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| Subjects | |
| Online Access | Get full text |
| ISSN | 2391-5412 2391-5412 |
| DOI | 10.1515/biol-2022-0772 |
Cover
| Abstract | Most plants belonging to the widely distributed genus
are used for gardening. Interspecific hybridization of different
species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among
species, the chloroplast genomes of 12
species, including nine
varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with
having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of
, we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably,
had 83 protein-coding genes but lacked
. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of
indicated that
and
were most closely related, suggesting that the degree of variation within nine
varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within
species. |
|---|---|
| AbstractList | Most plants belonging to the widely distributed genus
are used for gardening. Interspecific hybridization of different
species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among
species, the chloroplast genomes of 12
species, including nine
varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with
having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of
, we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably,
had 83 protein-coding genes but lacked
. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of
indicated that
and
were most closely related, suggesting that the degree of variation within nine
varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within
species. Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus, we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species. Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474–149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus , we identified 124–126 annotated genes, including 83–84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2 . The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species. Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474-149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus, we identified 124-126 annotated genes, including 83-84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species.Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to blurred genetic backgrounds. To obtain more genomic resources and understand the phylogenetic relationships among Dianthus species, the chloroplast genomes of 12 Dianthus species, including nine Dianthus gratianopolitanus varieties, were analyzed. The chloroplast genomes of these 12 species exhibited similar sizes (149,474-149,735 bp), with Dianthus caryophyllus having a chloroplast genome size of 149,604 bp marked by a significant contraction in inverted repeats. In the chloroplast genome of Dianthus, we identified 124-126 annotated genes, including 83-84 protein-coding genes. Notably, D. caryophyllus had 83 protein-coding genes but lacked rpl2. The repeat sequences of the chloroplast genome were consistent among species, and variations in the sequence were limited and not prominent. However, notable gene replacements were observed in the boundary region. Phylogenetic analysis of Dianthus indicated that D. caryophyllus and D. gratianopolitanus were most closely related, suggesting that the degree of variation within nine Dianthus varieties was no less than the variation observed between species. These differences provide a theoretical foundation for a more comprehensive understanding of the diversity within Dianthus species. |
| Author | Guiyan, Yang Zhenggang, Xu Meng, Dong Yang, Liu Yunlin, Zhao Shuwen, Chen |
| Author_xml | – sequence: 1 givenname: Dong surname: Meng fullname: Meng, Dong organization: Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan, China – sequence: 2 givenname: Liu surname: Yang fullname: Yang, Liu organization: Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan, China – sequence: 3 givenname: Zhao surname: Yunlin fullname: Yunlin, Zhao organization: Hunan Research Center of Engineering Technology for Utilization of Environmental and Resources Plant, College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, Hunan, China – sequence: 4 givenname: Yang surname: Guiyan fullname: Guiyan, Yang organization: College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China – sequence: 5 givenname: Chen surname: Shuwen fullname: Shuwen, Chen organization: College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China – sequence: 6 givenname: Xu surname: Zhenggang fullname: Zhenggang, Xu email: xuzhenggang@nwafu.edu.cn organization: College of Forestry, Northwest A & F University, Yangling 712100, Shaanxi, China |
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| Cites_doi | 10.1186/1471-2164-13-292 10.3389/fpls.2020.00375 10.1073/pnas.1430924100 10.1186/s12864-022-08706-2 10.3389/fpls.2017.00530 10.1186/1471-2164-12-402 10.7717/peerj.7210 10.1093/nar/29.22.4633 10.3389/fpls.2017.01986 10.3389/fgene.2020.00073 10.1016/j.mib.2014.09.008 10.1038/30234 10.1093/nar/gkh458 10.1186/s12870-015-0432-6 10.1016/j.indcrop.2022.115408 10.1093/bioinformatics/btp187 10.1186/s12862-021-01800-1 10.1093/molbev/msw054 10.1016/j.phytol.2016.04.020 10.1016/j.indcrop.2021.114210 10.1016/j.imr.2015.06.004 10.1016/j.indcrop.2023.116974 10.1016/j.scienta.2008.04.001 10.1007/s11105-016-1010-2 10.1016/j.indcrop.2023.116674 10.1371/journal.pone.0111988 10.1016/j.plantsci.2004.04.029 10.1002/ece3.1611 10.1093/bioinformatics/btx198 10.1007/s11738-020-03089-x 10.1080/23802359.2018.1521313 10.1073/pnas.92.17.7759 10.1016/j.indcrop.2021.113248 10.3390/ijms22116143 10.1007/s11104-015-2396-6 10.1093/nar/gkz238 10.1016/j.plaphy.2023.107698 10.1007/s00606-007-0608-0 10.1093/jhered/92.4.371 |
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| Snippet | Most plants belonging to the widely distributed genus
are used for gardening. Interspecific hybridization of different
species leads to blurred genetic... Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to... Most plants belonging to the widely distributed genus Dianthus are used for gardening. Interspecific hybridization of different Dianthus species leads to... |
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| Title | Distinguish Dianthus species or varieties based on chloroplast genomes |
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