Development of 5006 full-length CDNAs in barley: A tool for accessing cereal genomics resources

Kazuhiro Sato; Tadasu Shin-I; Motoaki Seki; Kazuo Shinozaki; Hideya Yoshida; Kazuyoshi Takeda; Yukiko Yamazaki; Matthieu Conte; Yuji Kohara

doi:10.1093/dnares/dsn034

Development of 5006 full-length CDNAs in barley: A tool for accessing cereal genomics resources

Kazuhiro Sato, Tadasu Shin-I, Motoaki Seki, Kazuo Shinozaki, Hideya Yoshida, Kazuyoshi Takeda, Yukiko Yamazaki, Matthieu Conte, Yuji Kohara

Institute of Plant Science and Resources

Research output: Contribution to journal › Article › peer-review

78 Citations (Scopus)

Abstract

A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60 of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81) and the wheat gene index (84). The high homology between FLcDNAs (27) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species.

Original language	English
Pages (from-to)	81-89
Number of pages	9
Journal	DNA Research
Volume	16
Issue number	2
DOIs	https://doi.org/10.1093/dnares/dsn034
Publication status	Published - Apr 2009

Keywords

Full-length cDNA
Gene ontology
Hordeum vulgare
MRNA

ASJC Scopus subject areas

Molecular Biology
Genetics

Access to Document

10.1093/dnares/dsn034

Cite this

@article{96ca7b71c4fe402d895923a85cf48150,

title = "Development of 5006 full-length CDNAs in barley: A tool for accessing cereal genomics resources",

abstract = "A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60 of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81) and the wheat gene index (84). The high homology between FLcDNAs (27) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species.",

keywords = "Full-length cDNA, Gene ontology, Hordeum vulgare, MRNA",

author = "Kazuhiro Sato and Tadasu Shin-I and Motoaki Seki and Kazuo Shinozaki and Hideya Yoshida and Kazuyoshi Takeda and Yukiko Yamazaki and Matthieu Conte and Yuji Kohara",

year = "2009",

month = apr,

doi = "10.1093/dnares/dsn034",

language = "English",

volume = "16",

pages = "81--89",

journal = "DNA Research",

issn = "1340-2838",

publisher = "Oxford University Press",

number = "2",

}

TY - JOUR

T1 - Development of 5006 full-length CDNAs in barley

T2 - A tool for accessing cereal genomics resources

AU - Sato, Kazuhiro

AU - Shin-I, Tadasu

AU - Seki, Motoaki

AU - Shinozaki, Kazuo

AU - Yoshida, Hideya

AU - Takeda, Kazuyoshi

AU - Yamazaki, Yukiko

AU - Conte, Matthieu

AU - Kohara, Yuji

PY - 2009/4

Y1 - 2009/4

N2 - A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60 of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81) and the wheat gene index (84). The high homology between FLcDNAs (27) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species.

AB - A collection of 5006 full-length (FL) cDNA sequences was developed in barley. Fifteen mRNA samples from various organs and treatments were pooled to develop a cDNA library using the CAP trapper method. More than 60 of the clones were confirmed to have complete coding sequences, based on comparison with rice amino acid and UniProt sequences. Blastn homologies (E<1E-5) to rice genes and Arabidopsis genes were 89 and 47, respectively. Of the 5028 possible amino acid sequences derived from the 5006 FLcDNAs, 4032 (80.2) were classified into 1678 GreenPhyl multigenic families. There were 555 cDNAs showing low homology to both rice and Arabidopsis. Gene ontology annotation by InterProScan indicated that many of these cDNAs (71) have no known molecular functions and may be unique to barley. The cDNAs showed high homology to Barley 1 GeneChip oligo probes (81) and the wheat gene index (84). The high homology between FLcDNAs (27) and mapped barley expressed sequence tag enabled assigning linkage map positions to 151-233 FLcDNAs on each of the seven barley chromosomes. These comprehensive barley FLcDNAs provide strong platform to connect pre-existing genomic and genetic resources and accelerate gene identification and genome analysis in barley and related species.

KW - Full-length cDNA

KW - Gene ontology

KW - Hordeum vulgare

KW - MRNA

UR - http://www.scopus.com/inward/record.url?scp=67650140201&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67650140201&partnerID=8YFLogxK

U2 - 10.1093/dnares/dsn034

DO - 10.1093/dnares/dsn034

M3 - Article

C2 - 19150987

AN - SCOPUS:67650140201

SN - 1340-2838

VL - 16

SP - 81

EP - 89

JO - DNA Research

JF - DNA Research

IS - 2

ER -

Development of 5006 full-length CDNAs in barley: A tool for accessing cereal genomics resources

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this