Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.
Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics.
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DOI：
10.1186/1471-2164-11-210
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发表时间：
2010-03-30
期刊：
影响因子：
4.4
通讯作者：
Shibata D
中科院分区：
文献类型：
--
作者：
Aoki K;Yano K;Suzuki A;Kawamura S;Sakurai N;Suda K;Kurabayashi A;Suzuki T;Tsugane T;Watanabe M;Ooga K;Torii M;Narita T;Shin-I T;Kohara Y;Yamamoto N;Takahashi H;Watanabe Y;Egusa M;Kodama M;Ichinose Y;Kikuchi M;Fukushima S;Okabe A;Arie T;Sato Y;Yazawa K;Satoh S;Omura T;Ezura H;Shibata D
茄科包括几种经济上重要的蔬菜作物。番茄（Solanum lycopersicum）被认为是茄科（Solanaceae）的模式植物。最近，一些番茄资源已被开发与正在进行的番茄基因组测序计划并行。特别是微型栽培品种Micro-Tom被认为是番茄基因组学的模式系统，并且国际联盟已经建立了Micro-Tom背景下的许多基因组学资源，如EST和诱变品系。为了加快番茄基因组学的进展，我们开发了一个完整测序的13，227个Micro-Tom全长cDNA的集合。通过检查冗余序列、编码序列和嵌合序列，产生了一组11，502个非冗余全长cDNA（nrFLcDNA）。对非翻译区的分析表明，番茄的5 '和3'非翻译区比水稻以外的大多数植物都长。从编码序列预测的蛋白质的功能分类表明，nrFLcDNA涵盖了广泛的功能。nrFLcDNA与16种植物基因的比较有助于鉴定在其他植物中未发现的番茄基因，其中大多数没有已知的蛋白质结构域。将nrFLcDNA映射到目前可用的番茄基因组序列上有助于预测外显子-内含子结构。番茄基因的内含子比拟南芥和水稻基因的内含子长。根据nrFLcDNA和番茄基因组序列之间的外显子序列的比较，Micro-Tom和基因组测序品种（海因茨1706）之间的外显子中的核苷酸错配频率估计为0.061%。本研究中所获得的Micro-Tom nrFLcDNA集将为植物生物学家弥合基础研究和应用研究之间的差距提供有价值的基因组工具。nrFLcDNA序列将有助于番茄全基因组序列的注释，并有助于番茄功能基因组学和分子育种。全长cDNA序列及其注释通过国家生物资源计划番茄网站（http://www.pgb.kazusa.or.jp/kaftom/http://tomato.nbrp.jp中提供。
The Solanaceae family includes several economically important vegetable crops. The tomato (Solanum lycopersicum) is regarded as a model plant of the Solanaceae family. Recently, a number of tomato resources have been developed in parallel with the ongoing tomato genome sequencing project. In particular, a miniature cultivar, Micro-Tom, is regarded as a model system in tomato genomics, and a number of genomics resources in the Micro-Tom-background, such as ESTs and mutagenized lines, have been established by an international alliance. To accelerate the progress in tomato genomics, we developed a collection of fully-sequenced 13,227 Micro-Tom full-length cDNAs. By checking redundant sequences, coding sequences, and chimeric sequences, a set of 11,502 non-redundant full-length cDNAs (nrFLcDNAs) was generated. Analysis of untranslated regions demonstrated that tomato has longer 5'- and 3'-untranslated regions than most other plants but rice. Classification of functions of proteins predicted from the coding sequences demonstrated that nrFLcDNAs covered a broad range of functions. A comparison of nrFLcDNAs with genes of sixteen plants facilitated the identification of tomato genes that are not found in other plants, most of which did not have known protein domains. Mapping of the nrFLcDNAs onto currently available tomato genome sequences facilitated prediction of exon-intron structure. Introns of tomato genes were longer than those of Arabidopsis and rice. According to a comparison of exon sequences between the nrFLcDNAs and the tomato genome sequences, the frequency of nucleotide mismatch in exons between Micro-Tom and the genome-sequencing cultivar (Heinz 1706) was estimated to be 0.061%. The collection of Micro-Tom nrFLcDNAs generated in this study will serve as a valuable genomic tool for plant biologists to bridge the gap between basic and applied studies. The nrFLcDNA sequences will help annotation of the tomato whole-genome sequence and aid in tomato functional genomics and molecular breeding. Full-length cDNA sequences and their annotations are provided in the database KaFTom http://www.pgb.kazusa.or.jp/kaftom/ via the website of the National Bioresource Project Tomato http://tomato.nbrp.jp.
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影响因子：
2.9
作者：
CHOMCZYNSKI, P;SACCHI, N
通讯作者：
SACCHI, N
影响因子：
5.1
作者：
Alexandrov, NN;Troukhan, ME;Feldmann, KA
通讯作者：
Feldmann, KA
影响因子：
14.9
作者：
Barrell D;Dimmer E;Huntley RP;Binns D;O'Donovan C;Apweiler R
通讯作者：
Apweiler R
影响因子：
4.4
作者：
Carninci, P;Kvam, C;Schneider, C
通讯作者：
Schneider, C
源自大规模cDNA测序的玉米基因的见解。
影响因子：
5.1
作者：
Alexandrov, Nickolai N.;Brover, Vyacheslav V.;Freidin, Stanislav;Troukhan, Maxim E.;Tatarinova, Tatiana V.;Zhang, Hongyu;Swaller, Timothy J.;Lu, Yu-Ping;Bouck, John;Flavell, Richard B.;Feldmann, Kenneth A.
通讯作者：
Feldmann, Kenneth A.