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Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing

The domestic silkworm, Bombyx mori, is a model insect with important economic value for silk production that also acts as a bioreactor for biomaterial production. The functional complexity of the silkworm transcriptome has not yet been fully elucidated, although genomic sequencing and other tools ha...

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Detalles Bibliográficos
Autores principales: Li, Yinü, Wang, Guozeng, Tian, Jian, Liu, Huifen, Yang, Huipeng, Yi, Yongzhu, Wang, Jinhui, Shi, Xiaofeng, Jiang, Feng, Yao, Bin, Zhang, Zhifang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426547/
https://www.ncbi.nlm.nih.gov/pubmed/22928022
http://dx.doi.org/10.1371/journal.pone.0043713
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author Li, Yinü
Wang, Guozeng
Tian, Jian
Liu, Huifen
Yang, Huipeng
Yi, Yongzhu
Wang, Jinhui
Shi, Xiaofeng
Jiang, Feng
Yao, Bin
Zhang, Zhifang
author_facet Li, Yinü
Wang, Guozeng
Tian, Jian
Liu, Huifen
Yang, Huipeng
Yi, Yongzhu
Wang, Jinhui
Shi, Xiaofeng
Jiang, Feng
Yao, Bin
Zhang, Zhifang
author_sort Li, Yinü
collection PubMed
description The domestic silkworm, Bombyx mori, is a model insect with important economic value for silk production that also acts as a bioreactor for biomaterial production. The functional complexity of the silkworm transcriptome has not yet been fully elucidated, although genomic sequencing and other tools have been widely used in its study. We explored the transcriptome of silkworm at different developmental stages using high-throughput paired-end RNA sequencing. A total of about 3.3 gigabases (Gb) of sequence was obtained, representing about a 7-fold coverage of the B. mori genome. From the reads that were mapped to the genome sequence; 23,461 transcripts were obtained, 5,428 of them were novel. Of the 14,623 predicted protein-coding genes in the silkworm genome database, 11,884 of them were found to be expressed in the silkworm transcriptome, giving a coverage of 81.3%. A total of 13,195 new exons were detected, of which, 5,911 were found in the annotated genes in the Silkworm Genome Database (SilkDB). An analysis of alternative splicing in the transcriptome revealed that 3,247 genes had undergone alternative splicing. To help with the data analysis, a transcriptome database that integrates our transcriptome data with the silkworm genome data was constructed and is publicly available at http://124.17.27.136/gbrowse2/. To our knowledge, this is the first study to elucidate the silkworm transcriptome using high-throughput RNA sequencing technology. Our data indicate that the transcriptome of silkworm is much more complex than previously anticipated. This work provides tools and resources for the identification of new functional elements and paves the way for future functional genomics studies.
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spelling pubmed-34265472012-08-27 Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing Li, Yinü Wang, Guozeng Tian, Jian Liu, Huifen Yang, Huipeng Yi, Yongzhu Wang, Jinhui Shi, Xiaofeng Jiang, Feng Yao, Bin Zhang, Zhifang PLoS One Research Article The domestic silkworm, Bombyx mori, is a model insect with important economic value for silk production that also acts as a bioreactor for biomaterial production. The functional complexity of the silkworm transcriptome has not yet been fully elucidated, although genomic sequencing and other tools have been widely used in its study. We explored the transcriptome of silkworm at different developmental stages using high-throughput paired-end RNA sequencing. A total of about 3.3 gigabases (Gb) of sequence was obtained, representing about a 7-fold coverage of the B. mori genome. From the reads that were mapped to the genome sequence; 23,461 transcripts were obtained, 5,428 of them were novel. Of the 14,623 predicted protein-coding genes in the silkworm genome database, 11,884 of them were found to be expressed in the silkworm transcriptome, giving a coverage of 81.3%. A total of 13,195 new exons were detected, of which, 5,911 were found in the annotated genes in the Silkworm Genome Database (SilkDB). An analysis of alternative splicing in the transcriptome revealed that 3,247 genes had undergone alternative splicing. To help with the data analysis, a transcriptome database that integrates our transcriptome data with the silkworm genome data was constructed and is publicly available at http://124.17.27.136/gbrowse2/. To our knowledge, this is the first study to elucidate the silkworm transcriptome using high-throughput RNA sequencing technology. Our data indicate that the transcriptome of silkworm is much more complex than previously anticipated. This work provides tools and resources for the identification of new functional elements and paves the way for future functional genomics studies. Public Library of Science 2012-08-23 /pmc/articles/PMC3426547/ /pubmed/22928022 http://dx.doi.org/10.1371/journal.pone.0043713 Text en © 2012 Li et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Li, Yinü
Wang, Guozeng
Tian, Jian
Liu, Huifen
Yang, Huipeng
Yi, Yongzhu
Wang, Jinhui
Shi, Xiaofeng
Jiang, Feng
Yao, Bin
Zhang, Zhifang
Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title_full Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title_fullStr Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title_full_unstemmed Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title_short Transcriptome Analysis of the Silkworm (Bombyx mori) by High-Throughput RNA Sequencing
title_sort transcriptome analysis of the silkworm (bombyx mori) by high-throughput rna sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3426547/
https://www.ncbi.nlm.nih.gov/pubmed/22928022
http://dx.doi.org/10.1371/journal.pone.0043713
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