High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation
Xiaoling Tong, Minjin Han, Kunpeng Lu, Shuaishuai Tai, Shubo Liang, Yucheng Liu, Hai Hu, Jianghong Shen, Anxing Long, Chengyu Zhan, Xin Shun Ding, Shuo Liu, Qiang Gao, Bili Zhang, Linli Zhou, Duan Tan, Yajie Yuan, Nangkuo Guo, Yanhong Li, Zhangyan Wu, Lulu Liu, Chunlin Li, Yaru Lu, Tingting Gai, Yahui Zhang, Renkui Yang, Heying Qian, Yan‐Qun 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, Éric Westhof, Cheng Lu, Zhixi Tian, Wen Wang, Zhonghuai Xiang, Fangyin Dai
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.