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Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation

BACKGROUND: Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is n...

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Autores principales: Xu, Jian, Ji, Peifeng, Wang, Baosen, Zhao, Lan, Wang, Jian, Zhao, Zixia, Zhang, Yan, Li, Jiongtang, Xu, Peng, Sun, Xiaowen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613414/
https://www.ncbi.nlm.nih.gov/pubmed/23573207
http://dx.doi.org/10.1371/journal.pone.0059703
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author Xu, Jian
Ji, Peifeng
Wang, Baosen
Zhao, Lan
Wang, Jian
Zhao, Zixia
Zhang, Yan
Li, Jiongtang
Xu, Peng
Sun, Xiaowen
author_facet Xu, Jian
Ji, Peifeng
Wang, Baosen
Zhao, Lan
Wang, Jian
Zhao, Zixia
Zhang, Yan
Li, Jiongtang
Xu, Peng
Sun, Xiaowen
author_sort Xu, Jian
collection PubMed
description BACKGROUND: Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is needed for conservation and aquaculture purposes, as well as to gain further understanding into the genetics of stress tolerance. The objective of the study is to sequence the transcriptome and obtain a well-assembled transcriptome of Amur ide. RESULTS: The transcriptome of Amur ide was sequenced using the Illumina platform and assembled into 53,632 cDNA contigs, with an average length of 647 bp and a N50 length of 1,094 bp. A total of 19,338 unique proteins were identified, and gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses classified all contigs into functional categories. Open Reading Frames (ORFs) were detected from 34,888 (65.1%) of contigs with an average length of 577 bp, while 9,638 full-length cDNAs were identified. Comparative analyses revealed that 31,790 (59.3%) contigs have a significant similarity to zebrafish proteins, and 27,096 (50.5%), 27,524 (51.3%) and 27,996 (52.2%) to teraodon, medaka and three-spined stickleback proteins, respectively. A total of 10,395 microsatellites and 34,299 SNPs were identified and classified. A dN/dS analysis on unigenes was performed, which identified that 61 of the genes were under strong positive selection. Most of the genes are associated with stress adaptation and immunity, suggesting that the extreme alkaline-saline environment resulted in fast evolution of certain genes. CONCLUSIONS: The transcriptome of Amur ide had been deeply sequenced, assembled and characterized, providing a valuable resource for a better understanding of the Amur ide genome. The transcriptome data will facilitate future functional studies on the Amur ide genome, as well as provide insight into potential mechanisms for adaptation to an extreme alkaline-saline environment.
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spelling pubmed-36134142013-04-09 Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation Xu, Jian Ji, Peifeng Wang, Baosen Zhao, Lan Wang, Jian Zhao, Zixia Zhang, Yan Li, Jiongtang Xu, Peng Sun, Xiaowen PLoS One Research Article BACKGROUND: Amur ide (Leuciscus waleckii) is an economically and ecologically important species in Northern Asia. The Dali Nor population inhabiting Dali Nor Lake, a typical saline-alkaline lake in Inner Mongolia, is well-known for its adaptation to extremely high alkalinity. Genome information is needed for conservation and aquaculture purposes, as well as to gain further understanding into the genetics of stress tolerance. The objective of the study is to sequence the transcriptome and obtain a well-assembled transcriptome of Amur ide. RESULTS: The transcriptome of Amur ide was sequenced using the Illumina platform and assembled into 53,632 cDNA contigs, with an average length of 647 bp and a N50 length of 1,094 bp. A total of 19,338 unique proteins were identified, and gene ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses classified all contigs into functional categories. Open Reading Frames (ORFs) were detected from 34,888 (65.1%) of contigs with an average length of 577 bp, while 9,638 full-length cDNAs were identified. Comparative analyses revealed that 31,790 (59.3%) contigs have a significant similarity to zebrafish proteins, and 27,096 (50.5%), 27,524 (51.3%) and 27,996 (52.2%) to teraodon, medaka and three-spined stickleback proteins, respectively. A total of 10,395 microsatellites and 34,299 SNPs were identified and classified. A dN/dS analysis on unigenes was performed, which identified that 61 of the genes were under strong positive selection. Most of the genes are associated with stress adaptation and immunity, suggesting that the extreme alkaline-saline environment resulted in fast evolution of certain genes. CONCLUSIONS: The transcriptome of Amur ide had been deeply sequenced, assembled and characterized, providing a valuable resource for a better understanding of the Amur ide genome. The transcriptome data will facilitate future functional studies on the Amur ide genome, as well as provide insight into potential mechanisms for adaptation to an extreme alkaline-saline environment. Public Library of Science 2013-04-01 /pmc/articles/PMC3613414/ /pubmed/23573207 http://dx.doi.org/10.1371/journal.pone.0059703 Text en © 2013 Xu et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Xu, Jian
Ji, Peifeng
Wang, Baosen
Zhao, Lan
Wang, Jian
Zhao, Zixia
Zhang, Yan
Li, Jiongtang
Xu, Peng
Sun, Xiaowen
Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title_full Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title_fullStr Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title_full_unstemmed Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title_short Transcriptome Sequencing and Analysis of Wild Amur Ide (Leuciscus waleckii) Inhabiting an Extreme Alkaline-Saline Lake Reveals Insights into Stress Adaptation
title_sort transcriptome sequencing and analysis of wild amur ide (leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3613414/
https://www.ncbi.nlm.nih.gov/pubmed/23573207
http://dx.doi.org/10.1371/journal.pone.0059703
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