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Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus

Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicau...

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Autores principales: Yi, Shaokui, Zhou, Xiaoyun, Li, Jie, Zhang, Manman, Luo, Shuangshuang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076316/
https://www.ncbi.nlm.nih.gov/pubmed/30076392
http://dx.doi.org/10.1038/s41598-018-29991-6
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author Yi, Shaokui
Zhou, Xiaoyun
Li, Jie
Zhang, Manman
Luo, Shuangshuang
author_facet Yi, Shaokui
Zhou, Xiaoyun
Li, Jie
Zhang, Manman
Luo, Shuangshuang
author_sort Yi, Shaokui
collection PubMed
description Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs. Phylogenetic tree of the Misgurnus species was inferred based on the 1,905 single copy orthologous genes. The tetraploid and diploid M. anguillicaudatus grouped into a clade, and M. bipartitus showed a closer relationship with the M. anguillicaudatus. The overall evolutionary rates of tetraploid M. anguillicaudatus were significantly higher than those of other Misgurnus species. Meanwhile, 28 positively selected genes were identified in M. anguillicaudatus clade. These positively selected genes may play critical roles in the adaptation to various habitat environments for M. anguillicaudatus. This study could facilitate further exploration of the genomic signatures of M. anguillicaudatus and provide potential insights into unveiling the evolutionary history of tetraploid loach.
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spelling pubmed-60763162018-08-08 Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus Yi, Shaokui Zhou, Xiaoyun Li, Jie Zhang, Manman Luo, Shuangshuang Sci Rep Article Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs. Phylogenetic tree of the Misgurnus species was inferred based on the 1,905 single copy orthologous genes. The tetraploid and diploid M. anguillicaudatus grouped into a clade, and M. bipartitus showed a closer relationship with the M. anguillicaudatus. The overall evolutionary rates of tetraploid M. anguillicaudatus were significantly higher than those of other Misgurnus species. Meanwhile, 28 positively selected genes were identified in M. anguillicaudatus clade. These positively selected genes may play critical roles in the adaptation to various habitat environments for M. anguillicaudatus. This study could facilitate further exploration of the genomic signatures of M. anguillicaudatus and provide potential insights into unveiling the evolutionary history of tetraploid loach. Nature Publishing Group UK 2018-08-03 /pmc/articles/PMC6076316/ /pubmed/30076392 http://dx.doi.org/10.1038/s41598-018-29991-6 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Yi, Shaokui
Zhou, Xiaoyun
Li, Jie
Zhang, Manman
Luo, Shuangshuang
Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title_full Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title_fullStr Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title_full_unstemmed Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title_short Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus
title_sort full-length transcriptome of misgurnus anguillicaudatus provides insights into evolution of genus misgurnus
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6076316/
https://www.ncbi.nlm.nih.gov/pubmed/30076392
http://dx.doi.org/10.1038/s41598-018-29991-6
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