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Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

Cheng T, Fu B, Wu Y, Long R, Liu C, Xia Q - PLoS ONE (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.

ABSTRACT
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.

No MeSH data available.


Distribution of Ka and Ks values.Above the black line, orthologous pairs with Ka/Ks ratio >1; between black and gray lines, pairs with Ka/Ks ratio 0.5–1.
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pone.0122837.g003: Distribution of Ka and Ks values.Above the black line, orthologous pairs with Ka/Ks ratio >1; between black and gray lines, pairs with Ka/Ks ratio 0.5–1.

Mentions: A total of 83 (2.96%) pairs of orthologs had a Ka/Ks > 1 showing genes that might have experienced strong positive selection (Fig 3). A Ka/Ks ratio of 0.5 was considered as a useful cut-off to identify genes under positive selection [27], for 317 (11.30%) pairs of orthologs with a Ka/Ks ratio between 0.5 and 1 (Fig 3). Thus, 400 (Ka/Ks > 0.5) pairs were considered likely to have experienced or be experiencing positive selection. Comparing with 354 candidate domestic genes in genomic regions of selective signals (GROSS) from resequencing data [1], 13 genes were common between Ka/Ks and GROSS analysis (S5 Table). In addition, two unigenes (Ka/Ks = 0.68, 1.31) encoding cytochrome b-like proteins were considered to be under positive selection. The cytochrome b gene showed a strong signal of positive selection in the domesticated clade [2].


Transcriptome sequencing and positive selected genes analysis of Bombyx mandarina.

Cheng T, Fu B, Wu Y, Long R, Liu C, Xia Q - PLoS ONE (2015)

Distribution of Ka and Ks values.Above the black line, orthologous pairs with Ka/Ks ratio >1; between black and gray lines, pairs with Ka/Ks ratio 0.5–1.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4373670&req=5

pone.0122837.g003: Distribution of Ka and Ks values.Above the black line, orthologous pairs with Ka/Ks ratio >1; between black and gray lines, pairs with Ka/Ks ratio 0.5–1.
Mentions: A total of 83 (2.96%) pairs of orthologs had a Ka/Ks > 1 showing genes that might have experienced strong positive selection (Fig 3). A Ka/Ks ratio of 0.5 was considered as a useful cut-off to identify genes under positive selection [27], for 317 (11.30%) pairs of orthologs with a Ka/Ks ratio between 0.5 and 1 (Fig 3). Thus, 400 (Ka/Ks > 0.5) pairs were considered likely to have experienced or be experiencing positive selection. Comparing with 354 candidate domestic genes in genomic regions of selective signals (GROSS) from resequencing data [1], 13 genes were common between Ka/Ks and GROSS analysis (S5 Table). In addition, two unigenes (Ka/Ks = 0.68, 1.31) encoding cytochrome b-like proteins were considered to be under positive selection. The cytochrome b gene showed a strong signal of positive selection in the domesticated clade [2].

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.

ABSTRACT
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.

No MeSH data available.