Cargando…
Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources
A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (E...
Autores principales: | , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793998/ https://www.ncbi.nlm.nih.gov/pubmed/24130698 http://dx.doi.org/10.1371/journal.pone.0075265 |
_version_ | 1782287160372625408 |
---|---|
author | Mochida, Keiichi Uehara-Yamaguchi, Yukiko Takahashi, Fuminori Yoshida, Takuhiro Sakurai, Tetsuya Shinozaki, Kazuo |
author_facet | Mochida, Keiichi Uehara-Yamaguchi, Yukiko Takahashi, Fuminori Yoshida, Takuhiro Sakurai, Tetsuya Shinozaki, Kazuo |
author_sort | Mochida, Keiichi |
collection | PubMed |
description | A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. |
format | Online Article Text |
id | pubmed-3793998 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37939982013-10-15 Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources Mochida, Keiichi Uehara-Yamaguchi, Yukiko Takahashi, Fuminori Yoshida, Takuhiro Sakurai, Tetsuya Shinozaki, Kazuo PLoS One Research Article A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of Brachypodium distachyon Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of Brachypodium genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant cis-motifs in the −3 kb promoter regions and determined a genome-wide Brachypodium promoter architecture. Furthermore, we integrated the Brachypodium full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN Brachypodium FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops. Public Library of Science 2013-10-09 /pmc/articles/PMC3793998/ /pubmed/24130698 http://dx.doi.org/10.1371/journal.pone.0075265 Text en © 2013 Mochida 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 Mochida, Keiichi Uehara-Yamaguchi, Yukiko Takahashi, Fuminori Yoshida, Takuhiro Sakurai, Tetsuya Shinozaki, Kazuo Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title | Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title_full | Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title_fullStr | Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title_full_unstemmed | Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title_short | Large-Scale Collection and Analysis of Full-Length cDNAs from Brachypodium distachyon and Integration with Pooideae Sequence Resources |
title_sort | large-scale collection and analysis of full-length cdnas from brachypodium distachyon and integration with pooideae sequence resources |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3793998/ https://www.ncbi.nlm.nih.gov/pubmed/24130698 http://dx.doi.org/10.1371/journal.pone.0075265 |
work_keys_str_mv | AT mochidakeiichi largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources AT ueharayamaguchiyukiko largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources AT takahashifuminori largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources AT yoshidatakuhiro largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources AT sakuraitetsuya largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources AT shinozakikazuo largescalecollectionandanalysisoffulllengthcdnasfrombrachypodiumdistachyonandintegrationwithpooideaesequenceresources |