Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).

<h4>Background</h4>Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquacu...

Descripción completa

Guardado en:
Detalles Bibliográficos
Autores principales: Huixia Du, Zhenmin Bao, Rui Hou, Shan Wang, Hailin Su, Jingjing Yan, Meilin Tian, Yan Li, Wen Wei, Wei Lu, Xiaoli Hu, Shi Wang, Jingjie Hu
Formato: article
Lenguaje:EN
Publicado: Public Library of Science (PLoS) 2012
Materias:
R
Q
Acceso en línea:https://doaj.org/article/1cc75f30c7b34dc99904944ddcb1e03f
Etiquetas: Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
id oai:doaj.org-article:1cc75f30c7b34dc99904944ddcb1e03f
record_format dspace
spelling oai:doaj.org-article:1cc75f30c7b34dc99904944ddcb1e03f2021-11-18T07:25:24ZTranscriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).1932-620310.1371/journal.pone.0033311https://doaj.org/article/1cc75f30c7b34dc99904944ddcb1e03f2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22428017/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus.<h4>Results</h4>In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome.<h4>Conclusion</h4>Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.Huixia DuZhenmin BaoRui HouShan WangHailin SuJingjing YanMeilin TianYan LiWen WeiWei LuXiaoli HuShi WangJingjie HuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 3, p e33311 (2012)
institution DOAJ
collection DOAJ
language EN
topic Medicine
R
Science
Q
spellingShingle Medicine
R
Science
Q
Huixia Du
Zhenmin Bao
Rui Hou
Shan Wang
Hailin Su
Jingjing Yan
Meilin Tian
Yan Li
Wen Wei
Wei Lu
Xiaoli Hu
Shi Wang
Jingjie Hu
Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
description <h4>Background</h4>Sea cucumbers are a special group of marine invertebrates. They occupy a taxonomic position that is believed to be important for understanding the origin and evolution of deuterostomes. Some of them such as Apostichopus japonicus represent commercially important aquaculture species in Asian countries. Many efforts have been devoted to increasing the number of expressed sequence tags (ESTs) for A. japonicus, but a comprehensive characterization of its transcriptome remains lacking. Here, we performed the large-scale transcriptome profiling and characterization by pyrosequencing diverse cDNA libraries from A. japonicus.<h4>Results</h4>In total, 1,061,078 reads were obtained by 454 sequencing of eight cDNA libraries representing different developmental stages and adult tissues in A. japonicus. These reads were assembled into 29,666 isotigs, which were further clustered into 21,071 isogroups. Nearly 40% of the isogroups showed significant matches to known proteins based on sequence similarity. Gene ontology (GO) and KEGG pathway analyses recovered diverse biological functions and processes. Candidate genes that were potentially involved in aestivation were identified. Transcriptome comparison with the sea urchin Strongylocentrotus purpuratus revealed similar patterns of GO term representation. In addition, 4,882 putative orthologous genes were identified, of which 202 were not present in the non-echinoderm organisms. More than 700 simple sequence repeats (SSRs) and 54,000 single nucleotide polymorphisms (SNPs) were detected in the A. japonicus transcriptome.<h4>Conclusion</h4>Pyrosequencing was proven to be efficient in rapidly identifying a large set of genes for the sea cucumber A. japonicus. Through the large-scale transcriptome sequencing as well as public EST data integration, we performed a comprehensive characterization of the A. japonicus transcriptome and identified candidate aestivation-related genes. A large number of potential genetic markers were also identified from the A. japonicus transcriptome. This transcriptome resource would lay an important foundation for future genetic or genomic studies on this species.
format article
author Huixia Du
Zhenmin Bao
Rui Hou
Shan Wang
Hailin Su
Jingjing Yan
Meilin Tian
Yan Li
Wen Wei
Wei Lu
Xiaoli Hu
Shi Wang
Jingjie Hu
author_facet Huixia Du
Zhenmin Bao
Rui Hou
Shan Wang
Hailin Su
Jingjing Yan
Meilin Tian
Yan Li
Wen Wei
Wei Lu
Xiaoli Hu
Shi Wang
Jingjie Hu
author_sort Huixia Du
title Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
title_short Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
title_full Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
title_fullStr Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
title_full_unstemmed Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867).
title_sort transcriptome sequencing and characterization for the sea cucumber apostichopus japonicus (selenka, 1867).
publisher Public Library of Science (PLoS)
publishDate 2012
url https://doaj.org/article/1cc75f30c7b34dc99904944ddcb1e03f
work_keys_str_mv AT huixiadu transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT zhenminbao transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT ruihou transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT shanwang transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT hailinsu transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT jingjingyan transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT meilintian transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT yanli transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT wenwei transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT weilu transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT xiaolihu transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT shiwang transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
AT jingjiehu transcriptomesequencingandcharacterizationfortheseacucumberapostichopusjaponicusselenka1867
_version_ 1718423460473995264