High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation

Xiaoling Tong (), Min-Jin Han, Kunpeng Lu, Shuaishuai Tai, Shubo Liang, Yucheng Liu, Hai Hu, Jianghong Shen, Anxing Long, Chengyu Zhan, Xin Ding, Shuo Liu, Qiang Gao, Bili Zhang, Linli Zhou, Duan Tan, Yajie Yuan, Nangkuo Guo, Yan-Hong Li, Zhangyan Wu, Lulu Liu, Chunlin Li, Yaru Lu, Tingting Gai, Yahui Zhang, Renkui Yang, Heying Qian, Yanqun Liu, Jiangwen Luo, Lu Zheng, Jinghou Lou, Yunwu Peng, Weidong Zuo, Jiangbo Song, Songzhen He, Songyuan Wu, Yunlong Zou, Lei Zhou, Lan Cheng, Yuxia Tang, Guotao Cheng, Lianwei Yuan, Weiming He, Jiabao Xu, Tao Fu, Yang Xiao, Ting Lei, Anying Xu, Ye Yin, Jian Wang, Antónia Monteiro, Eric Westhof, Cheng Lu (), Zhixi Tian (), Wen Wang (), Zhonghuai Xiang () and Fangyin Dai ()
Additional contact information
Xiaoling Tong: Southwest University
Min-Jin Han: Southwest University
Kunpeng Lu: Southwest University
Shuaishuai Tai: BGI Genomics, BGI-Shenzhen
Shubo Liang: Southwest University
Yucheng Liu: Chinese Academy of Sciences
Hai Hu: Southwest University
Jianghong Shen: Southwest University
Anxing Long: Southwest University
Chengyu Zhan: Southwest University
Xin Ding: Southwest University
Shuo Liu: Southwest University
Qiang Gao: Southwest University
Bili Zhang: Southwest University
Linli Zhou: Southwest University
Duan Tan: Southwest University
Yajie Yuan: Southwest University
Nangkuo Guo: Southwest University
Yan-Hong Li: BGI Genomics, BGI-Shenzhen
Zhangyan Wu: BGI Genomics, BGI-Shenzhen
Lulu Liu: Southwest University
Chunlin Li: Southwest University
Yaru Lu: Southwest University
Tingting Gai: Southwest University
Yahui Zhang: Southwest University
Renkui Yang: Chongqing Sericulture Science and Technology Research Institute
Heying Qian: Jiangsu University of Science and Technology
Yanqun Liu: Shenyang Agricultural University
Jiangwen Luo: Southwest University
Lu Zheng: Southwest University
Jinghou Lou: Southwest University
Yunwu Peng: Ankang University
Weidong Zuo: Southwest University
Jiangbo Song: Southwest University
Songzhen He: Southwest University
Songyuan Wu: Southwest University
Yunlong Zou: Southwest University
Lei Zhou: Southwest University
Lan Cheng: Southwest University
Yuxia Tang: Southwest University
Guotao Cheng: Southwest University
Lianwei Yuan: Southwest University
Weiming He: BGI Genomics, BGI-Shenzhen
Jiabao Xu: BGI Genomics, BGI-Shenzhen
Tao Fu: BGI Genomics, BGI-Shenzhen
Yang Xiao: Guangdong Academy of Agricultural Sciences
Ting Lei: Chongqing Sericulture Science and Technology Research Institute
Anying Xu: Jiangsu University of Science and Technology
Ye Yin: BGI Genomics, BGI-Shenzhen
Jian Wang: BGI-Shenzhen
Antónia Monteiro: National University of Singapore
Eric Westhof: Southwest University
Cheng Lu: Southwest University
Zhixi Tian: Chinese Academy of Sciences
Wen Wang: Northwestern Polytechnical University
Zhonghuai Xiang: Southwest University
Fangyin Dai: Southwest University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.

Date: 2022
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DOI: 10.1038/s41467-022-33366-x

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