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Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori

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...

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Autores principales: Suetsugu, Yoshitaka, Futahashi, Ryo, Kanamori, Hiroyuki, Kadono-Okuda, Keiko, Sasanuma, Shun-ichi, Narukawa, Junko, Ajimura, Masahiro, Jouraku, Akiya, Namiki, Nobukazu, Shimomura, Michihiko, Sezutsu, Hideki, Osanai-Futahashi, Mizuko, Suzuki, Masataka G, Daimon, Takaaki, Shinoda, Tetsuro, Taniai, Kiyoko, Asaoka, Kiyoshi, Niwa, Ryusuke, Kawaoka, Shinpei, Katsuma, Susumu, Tamura, Toshiki, Noda, Hiroaki, Kasahara, Masahiro, Sugano, Sumio, Suzuki, Yutaka, Fujiwara, Haruhiko, Kataoka, Hiroshi, Arunkumar, Kallare P., Tomar, Archana, Nagaraju, Javaregowda, Goldsmith, Marian R., Feng, Qili, Xia, Qingyou, Yamamoto, Kimiko, Shimada, Toru, Mita, Kazuei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755909/
https://www.ncbi.nlm.nih.gov/pubmed/23821615
http://dx.doi.org/10.1534/g3.113.006239
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author Suetsugu, Yoshitaka
Futahashi, Ryo
Kanamori, Hiroyuki
Kadono-Okuda, Keiko
Sasanuma, Shun-ichi
Narukawa, Junko
Ajimura, Masahiro
Jouraku, Akiya
Namiki, Nobukazu
Shimomura, Michihiko
Sezutsu, Hideki
Osanai-Futahashi, Mizuko
Suzuki, Masataka G
Daimon, Takaaki
Shinoda, Tetsuro
Taniai, Kiyoko
Asaoka, Kiyoshi
Niwa, Ryusuke
Kawaoka, Shinpei
Katsuma, Susumu
Tamura, Toshiki
Noda, Hiroaki
Kasahara, Masahiro
Sugano, Sumio
Suzuki, Yutaka
Fujiwara, Haruhiko
Kataoka, Hiroshi
Arunkumar, Kallare P.
Tomar, Archana
Nagaraju, Javaregowda
Goldsmith, Marian R.
Feng, Qili
Xia, Qingyou
Yamamoto, Kimiko
Shimada, Toru
Mita, Kazuei
author_facet Suetsugu, Yoshitaka
Futahashi, Ryo
Kanamori, Hiroyuki
Kadono-Okuda, Keiko
Sasanuma, Shun-ichi
Narukawa, Junko
Ajimura, Masahiro
Jouraku, Akiya
Namiki, Nobukazu
Shimomura, Michihiko
Sezutsu, Hideki
Osanai-Futahashi, Mizuko
Suzuki, Masataka G
Daimon, Takaaki
Shinoda, Tetsuro
Taniai, Kiyoko
Asaoka, Kiyoshi
Niwa, Ryusuke
Kawaoka, Shinpei
Katsuma, Susumu
Tamura, Toshiki
Noda, Hiroaki
Kasahara, Masahiro
Sugano, Sumio
Suzuki, Yutaka
Fujiwara, Haruhiko
Kataoka, Hiroshi
Arunkumar, Kallare P.
Tomar, Archana
Nagaraju, Javaregowda
Goldsmith, Marian R.
Feng, Qili
Xia, Qingyou
Yamamoto, Kimiko
Shimada, Toru
Mita, Kazuei
author_sort Suetsugu, Yoshitaka
collection PubMed
description 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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spelling pubmed-37559092013-09-01 Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori Suetsugu, Yoshitaka Futahashi, Ryo Kanamori, Hiroyuki Kadono-Okuda, Keiko Sasanuma, Shun-ichi Narukawa, Junko Ajimura, Masahiro Jouraku, Akiya Namiki, Nobukazu Shimomura, Michihiko Sezutsu, Hideki Osanai-Futahashi, Mizuko Suzuki, Masataka G Daimon, Takaaki Shinoda, Tetsuro Taniai, Kiyoko Asaoka, Kiyoshi Niwa, Ryusuke Kawaoka, Shinpei Katsuma, Susumu Tamura, Toshiki Noda, Hiroaki Kasahara, Masahiro Sugano, Sumio Suzuki, Yutaka Fujiwara, Haruhiko Kataoka, Hiroshi Arunkumar, Kallare P. Tomar, Archana Nagaraju, Javaregowda Goldsmith, Marian R. Feng, Qili Xia, Qingyou Yamamoto, Kimiko Shimada, Toru Mita, Kazuei G3 (Bethesda) Investigations 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. Genetics Society of America 2013-09-01 /pmc/articles/PMC3755909/ /pubmed/23821615 http://dx.doi.org/10.1534/g3.113.006239 Text en Copyright © 2013 Suetsugu et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Investigations
Suetsugu, Yoshitaka
Futahashi, Ryo
Kanamori, Hiroyuki
Kadono-Okuda, Keiko
Sasanuma, Shun-ichi
Narukawa, Junko
Ajimura, Masahiro
Jouraku, Akiya
Namiki, Nobukazu
Shimomura, Michihiko
Sezutsu, Hideki
Osanai-Futahashi, Mizuko
Suzuki, Masataka G
Daimon, Takaaki
Shinoda, Tetsuro
Taniai, Kiyoko
Asaoka, Kiyoshi
Niwa, Ryusuke
Kawaoka, Shinpei
Katsuma, Susumu
Tamura, Toshiki
Noda, Hiroaki
Kasahara, Masahiro
Sugano, Sumio
Suzuki, Yutaka
Fujiwara, Haruhiko
Kataoka, Hiroshi
Arunkumar, Kallare P.
Tomar, Archana
Nagaraju, Javaregowda
Goldsmith, Marian R.
Feng, Qili
Xia, Qingyou
Yamamoto, Kimiko
Shimada, Toru
Mita, Kazuei
Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title_full Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title_fullStr Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title_full_unstemmed Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title_short Large Scale Full-Length cDNA Sequencing Reveals a Unique Genomic Landscape in a Lepidopteran Model Insect, Bombyx mori
title_sort large scale full-length cdna sequencing reveals a unique genomic landscape in a lepidopteran model insect, bombyx mori
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3755909/
https://www.ncbi.nlm.nih.gov/pubmed/23821615
http://dx.doi.org/10.1534/g3.113.006239
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