Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
Identifieur interne : 001A68 ( Main/Merge ); précédent : 001A67; suivant : 001A69Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics
Auteurs : Koh Aoki [Japon] ; Kentaro Yano [Japon] ; Ayako Suzuki [Japon] ; Shingo Kawamura [Japon] ; Nozomu Sakurai [Japon] ; Kunihiro Suda [Japon] ; Atsushi Kurabayashi [Japon] ; Tatsuya Suzuki [Japon] ; Taneaki Tsugane [Japon] ; Manabu Watanabe [Japon] ; Kazuhide Ooga [Japon] ; Maiko Torii [Japon] ; Takanori Narita [Japon] ; Tadasu Shin-I [Japon] ; Yuji Kohara [Japon] ; Naoki Yamamoto [Japon] ; Hideki Takahashi [Japon] ; Yuichiro Watanabe [Japon] ; Mayumi Egusa [Japon] ; Motoichiro Kodama [Japon] ; Yuki Ichinose [Japon] ; Mari Kikuchi [Japon] ; Sumire Fukushima [Japon] ; Akiko Okabe [Japon] ; Tsutomu Arie [Japon] ; Yuko Sato [Japon] ; Katsumi Yazawa [Japon] ; Shinobu Satoh [Japon] ; Toshikazu Omura [Japon] ; Hiroshi Ezura [Japon] ; Daisuke Shibata [Japon]Source :
- BMC Genomics [ 1471-2164 ] ; 2010.
Abstract
The Solanaceae family includes several economically important vegetable crops. The tomato (
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
Url:
DOI: 10.1186/1471-2164-11-210
PubMed: 20350329
PubMed Central: 2859864
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000E11
- to stream Pmc, to step Curation: 000E10
- to stream Pmc, to step Checkpoint: 000F38
- to stream Ncbi, to step Merge: 000B47
- to stream Ncbi, to step Curation: 000B47
- to stream Ncbi, to step Checkpoint: 000B47
Links to Exploration step
PMC:2859864Le document en format XML
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Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006</wicri:regionArea><wicri:noRegion>266-0006</wicri:noRegion></affiliation></author><author><name sortKey="Ooga, Kazuhide" sort="Ooga, Kazuhide" uniqKey="Ooga K" first="Kazuhide" last="Ooga">Kazuhide Ooga</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Torii, Maiko" sort="Torii, Maiko" uniqKey="Torii M" first="Maiko" last="Torii">Maiko Torii</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country 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xml:lang="fr">Japon</country><wicri:regionArea>The University of Tokyo, Komaba, Meguro-ku, 153-8902</wicri:regionArea><wicri:noRegion>153-8902</wicri:noRegion></affiliation></author><author><name sortKey="Egusa, Mayumi" sort="Egusa, Mayumi" uniqKey="Egusa M" first="Mayumi" last="Egusa">Mayumi Egusa</name><affiliation wicri:level="1"><nlm:aff id="I7">Tottori University, 4-101 Koyama-minami, Tottori, 680-8553, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tottori University, 4-101 Koyama-minami, Tottori, 680-8553</wicri:regionArea><wicri:noRegion>680-8553</wicri:noRegion></affiliation></author><author><name sortKey="Kodama, Motoichiro" sort="Kodama, Motoichiro" uniqKey="Kodama M" first="Motoichiro" last="Kodama">Motoichiro Kodama</name><affiliation wicri:level="1"><nlm:aff id="I7">Tottori University, 4-101 Koyama-minami, Tottori, 680-8553, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tottori University, 4-101 Koyama-minami, Tottori, 680-8553</wicri:regionArea><wicri:noRegion>680-8553</wicri:noRegion></affiliation></author><author><name sortKey="Ichinose, Yuki" sort="Ichinose, Yuki" uniqKey="Ichinose Y" first="Yuki" last="Ichinose">Yuki Ichinose</name><affiliation wicri:level="1"><nlm:aff id="I8">Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530</wicri:regionArea><wicri:noRegion>700-8530</wicri:noRegion></affiliation></author><author><name sortKey="Kikuchi, Mari" sort="Kikuchi, Mari" uniqKey="Kikuchi M" first="Mari" last="Kikuchi">Mari Kikuchi</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Fukushima, Sumire" sort="Fukushima, Sumire" uniqKey="Fukushima S" first="Sumire" last="Fukushima">Sumire Fukushima</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Okabe, Akiko" sort="Okabe, Akiko" uniqKey="Okabe A" first="Akiko" last="Okabe">Akiko Okabe</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Arie, Tsutomu" sort="Arie, Tsutomu" uniqKey="Arie T" first="Tsutomu" last="Arie">Tsutomu Arie</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Sato, Yuko" sort="Sato, Yuko" uniqKey="Sato Y" first="Yuko" last="Sato">Yuko Sato</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Yazawa, Katsumi" sort="Yazawa, Katsumi" uniqKey="Yazawa K" first="Katsumi" last="Yazawa">Katsumi Yazawa</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Satoh, Shinobu" sort="Satoh, Shinobu" uniqKey="Satoh S" first="Shinobu" last="Satoh">Shinobu Satoh</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Omura, Toshikazu" sort="Omura, Toshikazu" uniqKey="Omura T" first="Toshikazu" last="Omura">Toshikazu Omura</name><affiliation wicri:level="1"><nlm:aff id="I11">Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Ezura, Hiroshi" sort="Ezura, Hiroshi" uniqKey="Ezura H" first="Hiroshi" last="Ezura">Hiroshi Ezura</name><affiliation wicri:level="1"><nlm:aff id="I11">Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Shibata, Daisuke" sort="Shibata, Daisuke" uniqKey="Shibata D" first="Daisuke" last="Shibata">Daisuke Shibata</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20350329</idno><idno type="pmc">2859864</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859864</idno><idno type="RBID">PMC:2859864</idno><idno type="doi">10.1186/1471-2164-11-210</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000E11</idno><idno type="wicri:Area/Pmc/Curation">000E10</idno><idno type="wicri:Area/Pmc/Checkpoint">000F38</idno><idno type="wicri:Area/Ncbi/Merge">000B47</idno><idno type="wicri:Area/Ncbi/Curation">000B47</idno><idno type="wicri:Area/Ncbi/Checkpoint">000B47</idno><idno type="wicri:Area/Main/Merge">001A68</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Large-scale analysis of full-length cDNAs from the tomato (<italic>Solanum lycopersicum</italic>) cultivar Micro-Tom, a reference system for the Solanaceae genomics</title><author><name sortKey="Aoki, Koh" sort="Aoki, Koh" uniqKey="Aoki K" first="Koh" last="Aoki">Koh Aoki</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Yano, Kentaro" sort="Yano, Kentaro" uniqKey="Yano K" first="Kentaro" last="Yano">Kentaro Yano</name><affiliation wicri:level="1"><nlm:aff id="I2">Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571</wicri:regionArea><wicri:noRegion>214-8571</wicri:noRegion></affiliation></author><author><name sortKey="Suzuki, Ayako" sort="Suzuki, Ayako" uniqKey="Suzuki A" first="Ayako" last="Suzuki">Ayako Suzuki</name><affiliation wicri:level="1"><nlm:aff id="I2">Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571</wicri:regionArea><wicri:noRegion>214-8571</wicri:noRegion></affiliation></author><author><name sortKey="Kawamura, Shingo" sort="Kawamura, Shingo" uniqKey="Kawamura S" first="Shingo" last="Kawamura">Shingo Kawamura</name><affiliation wicri:level="1"><nlm:aff id="I2">Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571</wicri:regionArea><wicri:noRegion>214-8571</wicri:noRegion></affiliation></author><author><name sortKey="Sakurai, Nozomu" sort="Sakurai, Nozomu" uniqKey="Sakurai N" first="Nozomu" last="Sakurai">Nozomu Sakurai</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Suda, Kunihiro" sort="Suda, Kunihiro" uniqKey="Suda K" first="Kunihiro" last="Suda">Kunihiro Suda</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Kurabayashi, Atsushi" sort="Kurabayashi, Atsushi" uniqKey="Kurabayashi A" first="Atsushi" last="Kurabayashi">Atsushi Kurabayashi</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Suzuki, Tatsuya" sort="Suzuki, Tatsuya" uniqKey="Suzuki T" first="Tatsuya" last="Suzuki">Tatsuya Suzuki</name><affiliation wicri:level="1"><nlm:aff id="I3">Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006</wicri:regionArea><wicri:noRegion>266-0006</wicri:noRegion></affiliation></author><author><name sortKey="Tsugane, Taneaki" sort="Tsugane, Taneaki" uniqKey="Tsugane T" first="Taneaki" last="Tsugane">Taneaki Tsugane</name><affiliation wicri:level="1"><nlm:aff id="I3">Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006</wicri:regionArea><wicri:noRegion>266-0006</wicri:noRegion></affiliation></author><author><name sortKey="Watanabe, Manabu" sort="Watanabe, Manabu" uniqKey="Watanabe M" first="Manabu" last="Watanabe">Manabu Watanabe</name><affiliation wicri:level="1"><nlm:aff id="I3">Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Chiba Prefectural Agriculture and Forestry Research Center, 808 Daizenno-cho, Midori-ku, Chiba, 266-0006</wicri:regionArea><wicri:noRegion>266-0006</wicri:noRegion></affiliation></author><author><name sortKey="Ooga, Kazuhide" sort="Ooga, Kazuhide" uniqKey="Ooga K" first="Kazuhide" last="Ooga">Kazuhide Ooga</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Torii, Maiko" sort="Torii, Maiko" uniqKey="Torii M" first="Maiko" last="Torii">Maiko Torii</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author><author><name sortKey="Narita, Takanori" sort="Narita, Takanori" uniqKey="Narita T" first="Takanori" last="Narita">Takanori Narita</name><affiliation wicri:level="1"><nlm:aff id="I4">National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>National Institute of Genetics, Yata 1111, Mishima, 411-8540</wicri:regionArea><wicri:noRegion>411-8540</wicri:noRegion></affiliation></author><author><name sortKey="Shin I, Tadasu" sort="Shin I, Tadasu" uniqKey="Shin I T" first="Tadasu" last="Shin-I">Tadasu Shin-I</name><affiliation wicri:level="1"><nlm:aff id="I4">National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>National Institute of Genetics, Yata 1111, Mishima, 411-8540</wicri:regionArea><wicri:noRegion>411-8540</wicri:noRegion></affiliation></author><author><name sortKey="Kohara, Yuji" sort="Kohara, Yuji" uniqKey="Kohara Y" first="Yuji" last="Kohara">Yuji Kohara</name><affiliation wicri:level="1"><nlm:aff id="I4">National Institute of Genetics, Yata 1111, Mishima, 411-8540, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>National Institute of Genetics, Yata 1111, Mishima, 411-8540</wicri:regionArea><wicri:noRegion>411-8540</wicri:noRegion></affiliation></author><author><name sortKey="Yamamoto, Naoki" sort="Yamamoto, Naoki" uniqKey="Yamamoto N" first="Naoki" last="Yamamoto">Naoki Yamamoto</name><affiliation wicri:level="1"><nlm:aff id="I2">Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Meiji University, 1-1-1 Higashi-mita, Tama-ku, Kawasaki, 214-8571</wicri:regionArea><wicri:noRegion>214-8571</wicri:noRegion></affiliation></author><author><name sortKey="Takahashi, Hideki" sort="Takahashi, Hideki" uniqKey="Takahashi H" first="Hideki" last="Takahashi">Hideki Takahashi</name><affiliation wicri:level="4"><nlm:aff id="I5">Tohoku University, 1-1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981-8555, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tohoku University, 1-1 Amamiya-machi, Tsutsumidori, Aoba-ku, Sendai, 981-8555</wicri:regionArea><orgName type="university">Université du Tōhoku</orgName><placeName><settlement type="city">Sendai</settlement><region type="province">Région de Tōhoku</region></placeName></affiliation></author><author><name sortKey="Watanabe, Yuichiro" sort="Watanabe, Yuichiro" uniqKey="Watanabe Y" first="Yuichiro" last="Watanabe">Yuichiro Watanabe</name><affiliation wicri:level="1"><nlm:aff id="I6">The University of Tokyo, Komaba, Meguro-ku, 153-8902, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>The University of Tokyo, Komaba, Meguro-ku, 153-8902</wicri:regionArea><wicri:noRegion>153-8902</wicri:noRegion></affiliation></author><author><name sortKey="Egusa, Mayumi" sort="Egusa, Mayumi" uniqKey="Egusa M" first="Mayumi" last="Egusa">Mayumi Egusa</name><affiliation wicri:level="1"><nlm:aff id="I7">Tottori University, 4-101 Koyama-minami, Tottori, 680-8553, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tottori University, 4-101 Koyama-minami, Tottori, 680-8553</wicri:regionArea><wicri:noRegion>680-8553</wicri:noRegion></affiliation></author><author><name sortKey="Kodama, Motoichiro" sort="Kodama, Motoichiro" uniqKey="Kodama M" first="Motoichiro" last="Kodama">Motoichiro Kodama</name><affiliation wicri:level="1"><nlm:aff id="I7">Tottori University, 4-101 Koyama-minami, Tottori, 680-8553, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tottori University, 4-101 Koyama-minami, Tottori, 680-8553</wicri:regionArea><wicri:noRegion>680-8553</wicri:noRegion></affiliation></author><author><name sortKey="Ichinose, Yuki" sort="Ichinose, Yuki" uniqKey="Ichinose Y" first="Yuki" last="Ichinose">Yuki Ichinose</name><affiliation wicri:level="1"><nlm:aff id="I8">Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530</wicri:regionArea><wicri:noRegion>700-8530</wicri:noRegion></affiliation></author><author><name sortKey="Kikuchi, Mari" sort="Kikuchi, Mari" uniqKey="Kikuchi M" first="Mari" last="Kikuchi">Mari Kikuchi</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Fukushima, Sumire" sort="Fukushima, Sumire" uniqKey="Fukushima S" first="Sumire" last="Fukushima">Sumire Fukushima</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Okabe, Akiko" sort="Okabe, Akiko" uniqKey="Okabe A" first="Akiko" last="Okabe">Akiko Okabe</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Arie, Tsutomu" sort="Arie, Tsutomu" uniqKey="Arie T" first="Tsutomu" last="Arie">Tsutomu Arie</name><affiliation wicri:level="1"><nlm:aff id="I9">Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, 183-8509</wicri:regionArea><wicri:noRegion>183-8509</wicri:noRegion></affiliation></author><author><name sortKey="Sato, Yuko" sort="Sato, Yuko" uniqKey="Sato Y" first="Yuko" last="Sato">Yuko Sato</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Yazawa, Katsumi" sort="Yazawa, Katsumi" uniqKey="Yazawa K" first="Katsumi" last="Yazawa">Katsumi Yazawa</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Satoh, Shinobu" sort="Satoh, Shinobu" uniqKey="Satoh S" first="Shinobu" last="Satoh">Shinobu Satoh</name><affiliation wicri:level="1"><nlm:aff id="I10">Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Institute of Biological Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Omura, Toshikazu" sort="Omura, Toshikazu" uniqKey="Omura T" first="Toshikazu" last="Omura">Toshikazu Omura</name><affiliation wicri:level="1"><nlm:aff id="I11">Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Ezura, Hiroshi" sort="Ezura, Hiroshi" uniqKey="Ezura H" first="Hiroshi" last="Ezura">Hiroshi Ezura</name><affiliation wicri:level="1"><nlm:aff id="I11">Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8571</wicri:regionArea><wicri:noRegion>305-8571</wicri:noRegion></affiliation></author><author><name sortKey="Shibata, Daisuke" sort="Shibata, Daisuke" uniqKey="Shibata D" first="Daisuke" last="Shibata">Daisuke Shibata</name><affiliation wicri:level="1"><nlm:aff id="I1">Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818, Japan</nlm:aff><country xml:lang="fr">Japon</country><wicri:regionArea>Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, 292-0818</wicri:regionArea><wicri:noRegion>292-0818</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The Solanaceae family includes several economically important vegetable crops. The tomato (<italic>Solanum lycopersicum</italic>) 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.</p></sec><sec><title>Results</title><p>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%.</p></sec><sec><title>Conclusion</title><p>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 <ext-link ext-link-type="uri" xlink:href="http://www.pgb.kazusa.or.jp/kaftom/">http://www.pgb.kazusa.or.jp/kaftom/</ext-link> via the website of the National Bioresource Project Tomato <ext-link ext-link-type="uri" xlink:href="http://tomato.nbrp.jp">http://tomato.nbrp.jp</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Knapp, S" uniqKey="Knapp S">S Knapp</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Giovannoni, Jj" uniqKey="Giovannoni J">JJ Giovannoni</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pedley, Kf" uniqKey="Pedley K">KF Pedley</name></author><author><name sortKey="Martin, Gb" uniqKey="Martin G">GB Martin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mueller, La" uniqKey="Mueller L">LA 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