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Data released on November 12, 2011

Resequencing data from 40 varieties of wild and domesticated silkworms.

Becquet, C; Cao, J; Cheng, D; Cheng, T; Dai, F; Fan, W; Guo, Y; Hellmann, I; Jensen, J; Jiang, L; Jiang, T; Li, D; Li, J; Li, R; Li, Y; Li, Z; Lin, Y; Liu, C; Shen, Y; Tang, S; Xia, Q; Xu, H; Xu, X; Xuan, Z; Yu, C; Zha, X; Zhang, G; Zhang, Z; Zhao, P; He, N; Liu, S; Zhou, Y; Liu, H; Zhao, J; Du, Z; Ye, C; Pan, G; Zhao, A; Shao, H; Zeng, W; Wu, P; Li, C; Pan, M; Li, J; Yin, X; Li, D; Wang, J; Zheng, H; Wang, W; Zhang, X; Li, S; Yang, H; Lu, C; Nielsen, R; Zhou, Z; Wang, J; Xiang, Z; Wang, J (2011): Resequencing data from 40 varieties of wild and domesticated silkworms. GigaScience. http://dx.doi.org/10.5524/100024 RIS BibTeX Text

Here we present whole-genome resequencing data of 40 domesticated and wild silkworms (Bombyx). The domesticated silkworm (Bombyx mori) is of great economic interest and has been domesticated for more the 5,000 years. An organism with a mid-range genome size (~432 Mb), it often serves as a model insect for the order Lepidoptera. A number of wild varieties of silkworms exist as well, including the Chinese wild silkworm (Bombyx mandarina) from which the domesticated silkworm originated. Each of the silkworm varieties was sequenced to ~3X coverage, representing 99.88% of the genome. These sequences were then used to create a single-base pair resolution genetic variation map of the silkworm. SNP sets were obtained separately for the pool of 29 domesticated strains and the pool of 11 wild varieties. The number of SNPs in the domestic versus wild varieties was approximately 14 million and 13 million, respectively. In addition to SNPs, approximately 0.33 million small insertion-deletions (indels) and 35 thousand structural variants (SVs) were identified among the 40 varieties. Over three-fourths of the SVs overlapped with transposable elements. A total of 1,041 candidate regions Genomic Regions of Selective Signals (GROSS) were identified. These regions cover 12.5 Mb (2.9%) of the genome and may reflect genomic footprints left by artificial selection during domestication, as they include 354 protein-coding genes that were identified as good candidates for domestication genes. We observed that 159 genes from GROSS were expressed in on different B. mori tissues on day 3 of the fifth larval instar as a reference strain, and were enriched in tissues of silk gland, midgut, and testis. The genes expressed in silk gland are involved in the synthesis of silk proteins, including fibroin and sericin. Midgut-enriched genes are related to the metabolism of carbohydrates, amino acids and lipids. And genes enriched in the testis are annotated as having binding, catalytic, and motor activity related to reproduction. The reference genome for this project was the Japanese wild silkworm (NCBI Accession Number NC_003395).

Contact Submitter

Related manuscripts:

doi:10.1126/science.1176620 (PubMed: 19713493)

Additional information:

http://silkworm.genomics.org.cn/silkdb/doc/download.html

Accessions (data not in GigaDB):

SRA: SRP001012

Genomic, Epigenomic

http://gigadb.org/images/data/cropped/100024_Bombyx_mori.jpg

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Silkworms7090Silkworm Bombyx
Displaying 1-1 of 1 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
SilkwormsReadmeTEXT0.33 KB2011-11-12
SilkwormsCoding sequenceFASTA5.38 MB2011-11-12
SilkwormsSequence assemblyFASTA125.69 MB2011-11-12
SilkwormsAnnotationGFF1012 KB2011-11-12
SilkwormsMethylome dataTSV1.03 GB2011-11-12
SilkwormsProtein sequenceFASTA3.45 MB2011-11-12
Displaying 1-6 of 6 File(s).

History:

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