Comprehensive Sequence Analysis of 24,783 Barley Full-Length cDNAs Derived from 12 Clone Libraries

被引：171

作者：

Matsumoto, Takashi ^{[1
]}

Tanaka, Tsuyoshi ^{[1
]}

Sakai, Hiroaki ^{[1
]}

Amano, Naoki ^{[1
]}

Kanamori, Hiroyuki ^{[2
]}

Kurita, Kanako ^{[2
]}

Kikuta, Ari ^{[2
]}

Kamiya, Kozue ^{[2
]}

Yamamoto, Mayu ^{[2
]}

Ikawa, Hiroshi ^{[2
]}

Fujii, Nobuyuki ^{[3
]}

Hori, Kiyosumi ^{[1
,4
]}

Itoh, Takeshi ^{[1
]}

Sato, Kazuhiro ^{[4
]}

机构：

[1] Natl Inst Agrobiol Sci, Tsukuba, Ibaraki 3058602, Japan

[2] Inst Soc Techno Innovat Agr Forestry & Fisheries, Tsukuba, Ibaraki 3050854, Japan

[3] Hitachi Govt & Publ Corp Syst Engn Ltd, Koto Ku, Tokyo 1358633, Japan

[4] Okayama Univ, Inst Plant Sci & Resources, Okayama 7100046, Japan

来源：

PLANT PHYSIOLOGY | 2011年 / 156卷 / 01期

关键词：

GENE-EXPRESSION; FUNCTIONAL ANNOTATION; CEREAL GENOMICS; DROUGHT STRESS; DATABASE; CONSTRUCTION; RESOURCE; RICE; TRANSCRIPTS; MATURATION;

D O I：

10.1104/pp.110.171579

中图分类号：

Q94 [植物学];

学科分类号：

071001 [植物学];

摘要：

Full-length cDNA (FLcDNA) libraries consisting of 172,000 clones were constructed from a two-row malting barley cultivar (Hordeum vulgare 'Haruna Nijo') under normal and stressed conditions. After sequencing the clones from both ends and clustering the sequences, a total of 24,783 complete sequences were produced. By removing duplicates between these and publicly available sequences, 22,651 representative sequences were obtained: 17,773 were novel barley FLcDNAs, and 1,699 were barley specific. Highly conserved genes were found in the barley FLcDNA sequences for 721 of 881 rice (Oryza sativa) trait genes with 50% or greater identity. These FLcDNA resources from our Haruna Nijo cDNA libraries and the full-length sequences of representative clones will improve our understanding of the biological functions of genes in barley, which is the cereal crop with the fourth highest production in the world, and will provide a powerful tool for annotating the barley genome sequences that will become available in the near future.

引用

页码：20 / 28

页数：9

共 55 条

[1]

Features of Arabidopsis genes and genome discovered using full-length cDNAs [J].

Alexandrov, NN ;

Troukhan, ME ;

Brover, VV ;

Tatarinova, T ;

Flavell, RB ;

Feldmann, KA .

PLANT MOLECULAR BIOLOGY, 2006, 60 (01) :69-85

[2]

BASIC LOCAL ALIGNMENT SEARCH TOOL [J].

ALTSCHUL, SF ;

GISH, W ;

MILLER, W ;

MYERS, EW ;

LIPMAN, DJ .

JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) :403-410

[3]

Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics [J].

Aoki, Koh ;

Yano, Kentaro ;

Suzuki, Ayako ;

Kawamura, Shingo ;

Sakurai, Nozomu ;

Suda, Kunihiro ;

Kurabayashi, Atsushi ;

Suzuki, Tatsuya ;

Tsugane, Taneaki ;

Watanabe, Manabu ;

Ooga, Kazuhide ;

Torii, Maiko ;

Narita, Takanori ;

Shin-i, Tadasu ;

Kohara, Yuji ;

Yamamoto, Naoki ;

Takahashi, Hideki ;

Watanabe, Yuichiro ;

Egusa, Mayumi ;

Kodama, Motoichiro ;

Ichinose, Yuki ;

Kikuchi, Mari ;

Fukushima, Sumire ;

Okabe, Akiko ;

Arie, Tsutomu ;

Sato, Yuko ;

Yazawa, Katsumi ;

Satoh, Shinobu ;

Omura, Toshikazu ;

Ezura, Hiroshi ;

Shibata, Daisuke .

BMC GENOMICS, 2010, 11

[4]

The Universal Protein Resource (UniProt) 2009 [J].

Bairoch, Amos ;

Consortium, UniProt ;

Bougueleret, Lydie ;

Altairac, Severine ;

Amendolia, Valeria ;

Auchincloss, Andrea ;

Argoud-Puy, Ghislaine ;

Axelsen, Kristian ;

Baratin, Delphine ;

Blatter, Marie-Claude ;

Boeckmann, Brigitte ;

Bolleman, Jerven ;

Bollondi, Laurent ;

Boutet, Emmanuel ;

Quintaje, Silvia Braconi ;

Breuza, Lionel ;

Bridge, Alan ;

deCastro, Edouard ;

Ciapina, Luciane ;

Coral, Danielle ;

Coudert, Elisabeth ;

Cusin, Isabelle ;

Delbard, Gwennaelle ;

Dornevil, Dolnide ;

Roggli, Paula Duek ;

Duvaud, Severine ;

Estreicher, Anne ;

Famiglietti, Livia ;

Feuermann, Marc ;

Gehant, Sebastian ;

Farriol-Mathis, Nathalie ;

Ferro, Serenella ;

Gasteiger, Elisabeth ;

Gateau, Alain ;

Gerritsen, Vivienne ;

Gos, Arnaud ;

Gruaz-Gumowski, Nadine ;

Hinz, Ursula ;

Hulo, Chantal ;

Hulo, Nicolas ;

James, Janet ;

Jimenez, Silvia ;

Jungo, Florence ;

Junker, Vivien ;

Kappler, Thomas ;

Keller, Guillaume ;

Lachaize, Corinne ;

Lane-Guermonprez, Lydie ;

Langendijk-Genevaux, Petra ;

Lara, Vicente .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D169-D174

[5]

The GOA database in 2009-an integrated Gene Ontology Annotation resource [J].

Barrell, Daniel ;

Dimmer, Emily ;

Huntley, Rachael P. ;

Binns, David ;

O'Donovan, Claire ;

Apweiler, Rolf .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D396-D403

[6]

Consistent over-estimation of gene number in complex plant genomes [J].

Bennetzen, JL ;

Coleman, C ;

Liu, RY ;

Ma, JX ;

Ramakrishna, W .

CURRENT OPINION IN PLANT BIOLOGY, 2004, 7 (06) :732-736

[7]

Normalization and subtraction of cap-trapper-selected cDNAs to prepare full-length cDNA libraries for rapid discovery of new genes [J].

Carninci, P ;

Shibata, Y ;

Hayatsu, N ;

Sugahara, Y ;

Shibata, K ;

Itoh, M ;

Konno, H ;

Okazaki, Y ;

Muramatsu, M ;

Hayashizaki, Y .

GENOME RESEARCH, 2000, 10 (10) :1617-1630

[8]

High-efficiency full-length cDNA cloning by biotinylated CAP trapper [J].

Carninci, P ;

Kvam, C ;

Kitamura, A ;

Ohsumi, T ;

Okazaki, Y ;

Itoh, M ;

Kamiya, M ;

Shibata, K ;

Sasaki, N ;

Izawa, M ;

Muramatsu, M ;

Hayashizaki, Y ;

Schneider, C .

GENOMICS, 1996, 37 (03) :327-336

[9]

A new resource for cereal genomics: 22K barley GeneChip comes of age [J].

Close, TJ ;

Wanamaker, SI ;

Caldo, RA ;

Turner, SM ;

Ashlock, DA ;

Dickerson, JA ;

Wing, RA ;

Muehlbauer, GJ ;

Kleinhofs, A ;

Wise, RP .

PLANT PHYSIOLOGY, 2004, 134 (03) :960-968

[10]

Incorrectly predicted genes in rice? [J].

Cruveiller, S ;

Jabbari, K ;

Clay, O ;

Bernardi, G .

GENE, 2004, 333 :187-188

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