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Originally published in Science Express on 27 August 2009
Science 16 October 2009:
Vol. 326. no. 5951, pp. 433 - 436
DOI: 10.1126/science.1176620
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Reports

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)

Qingyou Xia,1,2,* Yiran Guo,3,* Ze Zhang,1,2,* Dong Li,1,3,* Zhaoling Xuan,3,* Zhuo Li,3,* Fangyin Dai,1 Yingrui Li,3 Daojun Cheng,1 Ruiqiang Li,3,4 Tingcai Cheng,1,2 Tao Jiang,3 Celine Becquet,5,{dagger} Xun Xu,3 Chun Liu,1 Xingfu Zha,1 Wei Fan,3 Ying Lin,1 Yihong Shen,1 Lan Jiang,3 Jeffrey Jensen,5 Ines Hellmann,5 Si Tang,5 Ping Zhao,1 Hanfu Xu,1 Chang Yu,3 Guojie Zhang,3 Jun Li,3 Jianjun Cao,3 Shiping Liu,1 Ningjia He,1 Yan Zhou,3 Hui Liu,3 Jing Zhao,3 Chen Ye,3 Zhouhe Du,1 Guoqing Pan,1 Aichun Zhao,1 Haojing Shao,3,7 Wei Zeng,3 Ping Wu,3 Chunfeng Li,1 Minhui Pan,1 Jingjing Li,3 Xuyang Yin,3 Dawei Li,3 Juan Wang,3 Huisong Zheng,3 Wen Wang,3 Xiuqing Zhang,3 Songgang Li,3 Huanming Yang,3 Cheng Lu,1 Rasmus Nielsen,4,5 Zeyang Zhou,1,6 Jian Wang,3 Zhonghuai Xiang,1,{ddagger} Jun Wang3,4,{ddagger}

A single–base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.

1 The Key Sericultural Laboratory of Agricultural Ministry, College of Biotechnology, Southwest University, Chongqing 400715, China.
2 Institute of Agronomy and Life Sciences, Chongqing University, Chongqing 400044, China.
3 BGI-Shenzhen, Shenzhen 518083, China.
4 Department of Biology, University of Copenhagen, Universitetsparken 15, 2100 Kbh Ø, Denmark.
5 Departments of Integrative Biology and Statistics, University of California Berkeley, Berkeley, CA 94720, USA.
6 Chongqing Normal University, Chongqing 400047, China.
7 Innovative Program for Undergraduate Students, South China University of Technology, Guangzhou 510006, China.

* These authors contributed equally to this work.

{dagger} Present address: Institute for Human Genetics, University of California San Francisco, San Francisco, CA 94143–0794, USA.

{ddagger} To whom correspondence should be addressed. E-mail: wangj{at}genomics.org.cn (J.W.); xbxzh{at}swu.edu.cn (Z.X.)

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