Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

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

doi:10.1126/science.1176620

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

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

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Abstract

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.

Original language	English (US)
Pages (from-to)	433-436
Number of pages	4
Journal	Science
Volume	326
Issue number	5951
DOIs	https://doi.org/10.1126/science.1176620
State	Published - Oct 16 2009
Externally published	Yes

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Xia, Q, Guo, Y, Zhang, Z, Li, D, Xuan, Z, Li, Z, Dai, F, Li, Y, Cheng, D, Li, R, Cheng, T, Jiang, T, Becquet, C, Xu, X, Liu, C, Zha, X, Fan, W, Lin, Y, Shen, Y, Jiang, L, Jensen, J, Hellmann, I, Tang, S, Zhao, P, Xu, H, Yu, C, Zhang, G, Li, J, Cao, J, Liu, S, He, N, Zhou, Y, Liu, H, Zhao, J, Ye, C, Du, Z, 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 2009, 'Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)', Science, vol. 326, no. 5951, pp. 433-436. https://doi.org/10.1126/science.1176620

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title = "Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)",

abstract = "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.",

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

year = "2009",

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doi = "10.1126/science.1176620",

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T1 - Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

AU - Xia, Qingyou

AU - Guo, Yiran

AU - Zhang, Ze

AU - Li, Dong

AU - Xuan, Zhaoling

AU - Li, Zhuo

AU - Dai, Fangyin

AU - Li, Yingrui

AU - Cheng, Daojun

AU - Li, Ruiqiang

AU - Cheng, Tingcai

AU - Jiang, Tao

AU - Becquet, Celine

AU - Xu, Xun

AU - Liu, Chun

AU - Zha, Xingfu

AU - Fan, Wei

AU - Lin, Ying

AU - Shen, Yihong

AU - Jiang, Lan

AU - Jensen, Jeffrey

AU - Hellmann, Ines

AU - Tang, Si

AU - Zhao, Ping

AU - Xu, Hanfu

AU - Yu, Chang

AU - Zhang, Guojie

AU - Li, Jun

AU - Cao, Jianjun

AU - Liu, Shiping

AU - He, Ningjia

AU - Zhou, Yan

AU - Liu, Hui

AU - Zhao, Jing

AU - Ye, Chen

AU - Du, Zhouhe

AU - Pan, Guoqing

AU - Zhao, Aichun

AU - Shao, Haojing

AU - Zeng, Wei

AU - Wu, Ping

AU - Li, Chunfeng

AU - Pan, Minimi

AU - Li, Jingjing

AU - Yin, Xuyang

AU - Li, Dawei

AU - Wang, Juan

AU - Zheng, Huisong

AU - Wang, Wen

AU - Zhang, Xiuqing

AU - Li, Songgang

AU - Yang, Huanming

AU - Lu, Cheng

AU - Nielsen, Rasmus

AU - Zhou, Zeyang

AU - Wang, Jian

AU - Xiang, Zhonghuai

AU - Wang, Jun

PY - 2009/10/16

Y1 - 2009/10/16

N2 - 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.

AB - 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.

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DO - 10.1126/science.1176620

M3 - Article

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AN - SCOPUS:70350134644

SN - 0036-8075

VL - 326

SP - 433

EP - 436

JO - Science

JF - Science

IS - 5951

ER -

Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

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