Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.
Large scale full-length cDNA sequencing reveals a unique genomic landscape in a lepidopteran model insect, Bombyx mori.
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DOI：
10.1534/g3.113.006239
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发表时间：
2013-09-04
期刊：
影响因子：
--
通讯作者：
Mita K
中科院分区：
文献类型：
--
作者：
Suetsugu Y;Futahashi R;Kanamori H;Kadono-Okuda K;Sasanuma S;Narukawa J;Ajimura M;Jouraku A;Namiki N;Shimomura M;Sezutsu H;Osanai-Futahashi M;Suzuki MG;Daimon T;Shinoda T;Taniai K;Asaoka K;Niwa R;Kawaoka S;Katsuma S;Tamura T;Noda H;Kasahara M;Sugano S;Suzuki Y;Fujiwara H;Kataoka H;Arunkumar KP;Tomar A;Nagaraju J;Goldsmith MR;Feng Q;Xia Q;Yamamoto K;Shimada T;Mita K
鳞翅目模式种家蚕全基因组序列的建立，为家蚕功能基因组学研究奠定了基础。更完整的基因组注释将有利于功能和比较研究，并加速该昆虫的广泛工业应用。为了实现这些目标，我们开始从来自家蚕14种组织的21个全长cDNA文库中大规模收集全长cDNA，并通过引物步移对11，104个全长cDNA进行全测序。大的平均内含子大小为1904 bp，这是由于转座子的高积累。使用GLEAN预测的基因模型和已发表的mRNA，我们在家蚕基因组组装上鉴定了16，823个基因位点。对11种昆虫共153个物种的同源性分析表明，在帝王蝶和蝎尾蝶等3种鳞翅目昆虫中，403个最大的家蚕特异性基因主要由保护性免疫蛋白、家蚕相关蛋白和特征性结构蛋白组成。睾丸/卵巢特异性基因的分析揭示了性二态性的独特特征，包括与睾丸特异性基因的富集相反的Z染色体上卵巢特异性基因的耗尽。超过40%的基因在特定组织中表达，定位在组织特异性染色体簇中。新获得的FL-cDNA序列使我们能够更准确地注释该鳞翅目模式昆虫的基因组，增强鳞翅目昆虫的基因组和功能研究以及与其他昆虫目的比较分析，并对鳞翅目特有基因的进化和组织产生新的见解。
The establishment of a complete genomic sequence of silkworm, the model species of Lepidoptera, laid a foundation for its functional genomics. A more complete annotation of the genome will benefit functional and comparative studies and accelerate extensive industrial applications for this insect. To realize these goals, we embarked upon a large-scale full-length cDNA collection from 21 full-length cDNA libraries derived from 14 tissues of the domesticated silkworm and performed full sequencing by primer walking for 11,104 full-length cDNAs. The large average intron size was 1904 bp, resulting from a high accumulation of transposons. Using gene models predicted by GLEAN and published mRNAs, we identified 16,823 gene loci on the silkworm genome assembly. Orthology analysis of 153 species, including 11 insects, revealed that among three Lepidoptera including Monarch and Heliconius butterflies, the 403 largest silkworm-specific genes were composed mainly of protective immunity, hormone-related, and characteristic structural proteins. Analysis of testis-/ovary-specific genes revealed distinctive features of sexual dimorphism, including depletion of ovary-specific genes on the Z chromosome in contrast to an enrichment of testis-specific genes. More than 40% of genes expressed in specific tissues mapped in tissue-specific chromosomal clusters. The newly obtained FL-cDNA sequences enabled us to annotate the genome of this lepidopteran model insect more accurately, enhancing genomic and functional studies of Lepidoptera and comparative analyses with other insect orders, and yielding new insights into the evolution and organization of lepidopteran-specific genes.
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影响因子：
64.8
作者：
Dasmahapatra, Kanchon K.;Walters, James R.;Briscoe, Adriana D.;Davey, John W.;Whibley, Annabel;Nadeau, Nicola J.;Zimin, Aleksey V.;Hughes, Daniel S. T.;Ferguson, Laura C.;Martin, Simon H.;Salazar, Camilo;Lewis, James J.;Adler, Sebastian;Ahn, Seung-Joon;Baker, Dean A.;Baxter, Simon W.;Chamberlain, Nicola L.;Chauhan, Ritika;Counterman, Brian A.;Dalmay, Tamas;Gilbert, Lawrence E.;Gordon, Karl;Heckel, David G.;Hines, Heather M.;Hoff, Katharina J.;Holland, Peter W. H.;Jacquin-Joly, Emmanuelle;Jiggins, Francis M.;Jones, Robert T.;Kapan, Durrell D.;Kersey, Paul;Lamas, Gerardo;Lawson, Daniel;Mapleson, Daniel;Maroja, Luana S.;Martin, Arnaud;Moxon, Simon;Palmer, William J.;Papa, Riccardo;Papanicolaou, Alexie;Pauchet, Yannick;Ray, David A.;Rosser, Neil;Salzberg, Steven L.;Supple, Megan A.;Surridge, Alison;Tenger-Trolander, Ayse;Vogel, Heiko;Wilkinson, Paul A.;Wilson, Derek;Yorke, James A.;Yuan, Furong;Balmuth, Alexi L.;Eland, Cathlene;Gharbi, Karim;Thomson, Marian;Gibbs, Richard A.;Han, Yi;Jayaseelan, Joy C.;Kovar, Christie;Mathew, Tittu;Muzny, Donna M.;Ongeri, Fiona;Pu, Ling-Ling;Qu, Jiaxin;Thornton, Rebecca L.;Worley, Kim C.;Wu, Yuan-Qing;Linares, Mauricio;Blaxter, Mark L.;Ffrench-Constant, Richard H.;Joron, Mathieu;Kronforst, Marcus R.;Mullen, Sean P.;Reed, Robert D.;Scherer, Steven E.;Richards, Stephen;Mallet, James;McMillan, W. Owen;Jiggins, Chris D.
通讯作者：
Jiggins, Chris D.
影响因子：
4.5
作者：
Gahan LJ;Pauchet Y;Vogel H;Heckel DG
通讯作者：
Heckel DG
影响因子：
3.8
作者：
Osanai-Futahashi, Mizuko;Suetsugu, Yoshitaka;Fujiwara, Haruhiko
通讯作者：
Fujiwara, Haruhiko
影响因子：
1.7
作者：
Abe, H;Mita, K;Shimada, T
通讯作者：
Shimada, T
影响因子：
11.8
作者：
Maeshima, K;Laemmli, UK
通讯作者：
Laemmli, UK