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Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species

The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed de novo transcriptome sequencing of four cDNA libraries r...

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Autores principales: Liao, Xiaolin, Cheng, Lei, Xu, Peng, Lu, Guoqing, Wachholtz, Michael, Sun, Xiaowen, Chen, Songlin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632525/
https://www.ncbi.nlm.nih.gov/pubmed/23630630
http://dx.doi.org/10.1371/journal.pone.0062308
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author Liao, Xiaolin
Cheng, Lei
Xu, Peng
Lu, Guoqing
Wachholtz, Michael
Sun, Xiaowen
Chen, Songlin
author_facet Liao, Xiaolin
Cheng, Lei
Xu, Peng
Lu, Guoqing
Wachholtz, Michael
Sun, Xiaowen
Chen, Songlin
author_sort Liao, Xiaolin
collection PubMed
description The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed de novo transcriptome sequencing of four cDNA libraries representing brain, muscle, liver and kidney tissues respectively, each with six specimens. The removal of low quality reads resulted in 2.62 million raw reads, which were assembled as 127,711 unigenes, including 84,867 isotigs and 42,844 singletons. A total of 22,273 unigenes were found with significant matches to 14,449 unique proteins. Around14,398 unigenes were assigned with at least one Gene Ontology (GO) category in 84,876 total assignments, and 6,382 unigenes were found in 237 predicted KEGG pathways. The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues. In addition, 23 enzymes in the glycolysis/gluconeogenesis pathway were recovered. Importantly, we identified 5,784 high-quality putative SNP and 11,295 microsatellite markers which include 5,364 microsatellites with flanking sequences ≥50 bp. This study produced the most comprehensive genomic resources that have been derived from crucian carp, including thousands of genetic markers, which will not only lay a foundation for further studies on polyploidy origin and anoxic survival but will also facilitate selective breeding of this important aquaculture species.
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spelling pubmed-36325252013-04-29 Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species Liao, Xiaolin Cheng, Lei Xu, Peng Lu, Guoqing Wachholtz, Michael Sun, Xiaowen Chen, Songlin PLoS One Research Article The crucian carp is an important aquaculture species and a potential model to study genome evolution and physiological adaptation. However, so far the genomics and transcriptomics data available for this species are still scarce. We performed de novo transcriptome sequencing of four cDNA libraries representing brain, muscle, liver and kidney tissues respectively, each with six specimens. The removal of low quality reads resulted in 2.62 million raw reads, which were assembled as 127,711 unigenes, including 84,867 isotigs and 42,844 singletons. A total of 22,273 unigenes were found with significant matches to 14,449 unique proteins. Around14,398 unigenes were assigned with at least one Gene Ontology (GO) category in 84,876 total assignments, and 6,382 unigenes were found in 237 predicted KEGG pathways. The gene expression analysis revealed more genes expressed in brain, more up-regulated genes in muscle and more down-regulated genes in liver as compared with gene expression profiles of other tissues. In addition, 23 enzymes in the glycolysis/gluconeogenesis pathway were recovered. Importantly, we identified 5,784 high-quality putative SNP and 11,295 microsatellite markers which include 5,364 microsatellites with flanking sequences ≥50 bp. This study produced the most comprehensive genomic resources that have been derived from crucian carp, including thousands of genetic markers, which will not only lay a foundation for further studies on polyploidy origin and anoxic survival but will also facilitate selective breeding of this important aquaculture species. Public Library of Science 2013-04-22 /pmc/articles/PMC3632525/ /pubmed/23630630 http://dx.doi.org/10.1371/journal.pone.0062308 Text en © 2013 Liao 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
Liao, Xiaolin
Cheng, Lei
Xu, Peng
Lu, Guoqing
Wachholtz, Michael
Sun, Xiaowen
Chen, Songlin
Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title_full Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title_fullStr Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title_full_unstemmed Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title_short Transcriptome Analysis of Crucian Carp (Carassius auratus), an Important Aquaculture and Hypoxia-Tolerant Species
title_sort transcriptome analysis of crucian carp (carassius auratus), an important aquaculture and hypoxia-tolerant species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632525/
https://www.ncbi.nlm.nih.gov/pubmed/23630630
http://dx.doi.org/10.1371/journal.pone.0062308
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