Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina

The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 pla...

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Bibliographic Details
Published in:PloS one 2015-03, Vol.10 (3), p.e0122837-e0122837
Main Authors: Cheng, Tingcai, Fu, Bohua, Wu, Yuqian, Long, Renwen, Liu, Chun, Xia, Qingyou
Format: Article
Language:English
Subjects:
Analysis
Animals
Biochemistry
Bombyx - genetics
Bombyx mandarina
Bombyx mori
Computer programs
Data analysis
Data bases
Data processing
Databases, Genetic
DNA methylation
Domestication
Endocrinology
Evolution & development
Gene expression
Gene sequencing
Genes
Genomes
Genomics
High-Throughput Nucleotide Sequencing
Insects
Laboratories
Molecular biology
Molecular Sequence Annotation
Ontology
Open Reading Frames - genetics
Polymorphism, Single Nucleotide
Positive selection
Proteins
Quality
Sequence Analysis, RNA
Signal transduction
Silk
Silk gland
Silkworms
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Software
Transcriptome
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Summary:The wild silkworm Bombyx mandarina is widely believed to be an ancestor of the domesticated silkworm, Bombyx mori. Silkworms are often used as a model for studying the mechanism of species domestication. Here, we performed transcriptome sequencing of the wild silkworm using an Illumina HiSeq2000 platform. We produced 100,004,078 high-quality reads and assembled them into 50,773 contigs with an N50 length of 1764 bp and a mean length of 941.62 bp. A total of 33,759 unigenes were identified, with 12,805 annotated in the Nr database, 8273 in the Pfam database, and 9093 in the Swiss-Prot database. Expression profile analysis found significant differential expression of 1308 unigenes between the middle silk gland (MSG) and posterior silk gland (PSG). Three sericin genes (sericin 1, sericin 2, and sericin 3) were expressed specifically in the MSG and three fibroin genes (fibroin-H, fibroin-L, and fibroin/P25) were expressed specifically in the PSG. In addition, 32,297 Single-nucleotide polymorphisms (SNPs) and 361 insertion-deletions (INDELs) were detected. Comparison with the domesticated silkworm p50/Dazao identified 5,295 orthologous genes, among which 400 might have experienced or to be experiencing positive selection by Ka/Ks analysis. These data and analyses presented here provide insights into silkworm domestication and an invaluable resource for wild silkworm genomics research.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0122837