Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments
is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of in subseafloor sediments remain limited. Here, we performed sequencing and assembly of the 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-ye...
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| Published in | Frontiers in microbiology Vol. 14; p. 1216714 |
|---|---|
| Main Authors | , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Switzerland
Frontiers Media S.A
29.06.2023
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| Online Access | Get full text |
| ISSN | 1664-302X 1664-302X |
| DOI | 10.3389/fmicb.2023.1216714 |
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| Abstract | is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of
in subseafloor sediments remain limited.
Here, we performed
sequencing and assembly of the
29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.
The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N
of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that
possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years. |
|---|---|
| AbstractList | is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of
in subseafloor sediments remain limited.
Here, we performed
sequencing and assembly of the
29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.
The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N
of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that
possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years. Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.IntroductionAspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.Here, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.MethodsHere, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.The generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years.Results and DiscussionThe generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years. IntroductionAspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in subseafloor sediments remain limited.MethodsHere, we performed de novo sequencing and assembly of the A. sydowii 29R-4-F02 genome, an isolate obtained from approximately 2.4 km deep, 20-million-year-old coal-bearing sediments beneath the seafloor by employing the Nanopore sequencing platform.Results and DiscussionThe generated genome was 37.19 Mb with GC content of 50.05%. The final assembly consisted of 11 contigs with N50 of 4.6 Mb, encoding 12,488 putative genes. Notably, the subseafloor strain 29R-4-F02 showed a higher number of carbohydrate-active enzymes (CAZymes) and distinct genes related to vesicular fusion and autophagy compared to the terrestrial strain CBS593.65. Furthermore, 257 positively selected genes, including those involved in DNA repair and CAZymes were identified in subseafloor strain 29R-4-F02. These findings suggest that A. sydowii possesses a unique genetic repertoire enabling its survival in the extreme subseafloor environments over tens of millions of years. |
| Author | Liu, Xuan Jiang, Jun-Peng Shan, Jun Liu, Chang-Hong Liao, Yi-Fan Zhu, Yu-Ping |
| AuthorAffiliation | 1 State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing , China 2 State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China |
| AuthorAffiliation_xml | – name: 2 State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences , Nanjing , China – name: 1 State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing , China |
| Author_xml | – sequence: 1 givenname: Jun-Peng surname: Jiang fullname: Jiang, Jun-Peng – sequence: 2 givenname: Xuan surname: Liu fullname: Liu, Xuan – sequence: 3 givenname: Yi-Fan surname: Liao fullname: Liao, Yi-Fan – sequence: 4 givenname: Jun surname: Shan fullname: Shan, Jun – sequence: 5 givenname: Yu-Ping surname: Zhu fullname: Zhu, Yu-Ping – sequence: 6 givenname: Chang-Hong surname: Liu fullname: Liu, Chang-Hong |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/37455735$$D View this record in MEDLINE/PubMed |
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| Copyright | Copyright © 2023 Jiang, Liu, Liao, Shan, Zhu and Liu. Copyright © 2023 Jiang, Liu, Liao, Shan, Zhu and Liu. 2023 Jiang, Liu, Liao, Shan, Zhu and Liu |
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| Keywords | subseafloor sediments Aspergillus sydowii adaptive evolution fungi CAZymes |
| Language | English |
| License | Copyright © 2023 Jiang, Liu, Liao, Shan, Zhu and Liu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
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in subseafloor sediments remain... Aspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A. sydowii in... IntroductionAspergillussydowii is an important filamentous fungus that inhabits diverse environments. However, investigations on the biology and genetics of A.... |
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| Title | Genomic insights into Aspergillus sydowii 29R-4-F02: unraveling adaptive mechanisms in subseafloor coal-bearing sediment environments |
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