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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2013
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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. |
format | Online Article Text |
id | pubmed-3755909 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
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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