Abstract
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.
Highlights
The domestic silkworm, Bombyx mori, has been intensively studied for the past several decades for its economic and academic value [1]
Summary of RNA-Seq Data Sets To obtain a global view of the silkworm transcriptome and gene activity at single-nucleotide resolution, we performed highthroughput RNA-Seq experiments using Illumina sequencing technology on poly (A)–enriched RNAs from a pool sample that covered the representative developmental stages of silkworm eggs, larva, pupa, and moth
We mapped the silkworm expressed sequence tags (ESTs) sequences from GenBank’s ESTdb onto the B. mori genome, and found that more than 86.8% of the transcript regions identified from the EST alignments were present in our transcriptome data but more than 39.6% of the transcripts defined using the RNA-Seq reads were not detected by the EST mapping (Figure 1)
Summary
The domestic silkworm, Bombyx mori, has been intensively studied for the past several decades for its economic and academic value [1]. The most important economic value of the silkworm is in the production of silk. In 2010, the production value reached about 30.6 billion dollars in China’s silk industry [2]. Silkworms are used widely as bioreactors for the production of vaccines [3], enzymes [4], proteinaceous drugs [5], and other biomaterials. A variety of methods, such as expressed sequence tags (ESTs) [8,9], serial analysis of gene expression (SAGE) [10,11], and microarrays [11,12], were used to identify and determine the activity of the functional elements in the silkworm genome. Because of limitations of the conventional technical approaches, the functional complexity of the silkworm transcriptome has not yet been fully elucidated
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
