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...

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Autores principales:	Keiichi Mochida, Yukiko Uehara-Yamaguchi, Fuminori Takahashi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d3fb7476035944deb3d6882df8c7e796
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spelling	oai:doaj.org-article:d3fb7476035944deb3d6882df8c7e7962021-11-18T08:51:52ZLarge-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.1932-620310.1371/journal.pone.0075265https://doaj.org/article/d3fb7476035944deb3d6882df8c7e7962013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24130698/?tool=EBIhttps://doaj.org/toc/1932-6203A 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.Keiichi MochidaYukiko Uehara-YamaguchiFuminori TakahashiTakuhiro YoshidaTetsuya SakuraiKazuo ShinozakiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 10, p e75265 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Keiichi Mochida Yukiko Uehara-Yamaguchi Fuminori Takahashi Takuhiro Yoshida Tetsuya Sakurai Kazuo Shinozaki Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.
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	article
author	Keiichi Mochida Yukiko Uehara-Yamaguchi Fuminori Takahashi Takuhiro Yoshida Tetsuya Sakurai Kazuo Shinozaki
author_facet	Keiichi Mochida Yukiko Uehara-Yamaguchi Fuminori Takahashi Takuhiro Yoshida Tetsuya Sakurai Kazuo Shinozaki
author_sort	Keiichi Mochida
title	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_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_sort	large-scale collection and analysis of full-length cdnas from brachypodium distachyon and integration with pooideae sequence resources.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/d3fb7476035944deb3d6882df8c7e796
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Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources.

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