Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships

Xiaoling Tong; Minjin Han; Kunpeng Lu; Shuaishuai Tai; Shubo Liang; Yucheng Liu; Hai Hu; Jianghong Shen; Anxing Long; Chengyu Zhan; Xin Shun Ding; Qiang Gao; Bili Zhang; 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

doi:10.1101/2021.09.28.462073

GenomicsbioRxivSep 28, 2021

Preprint

Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships

Xiaoling Tong iD, Minjin Han iD, Kunpeng Lu iD, Shuaishuai Tai iD, Shubo Liang iD, Yucheng Liu iD, Hai Hu iD, Jianghong Shen, Anxing Long, Chengyu Zhan, Xin Shun Ding iD, Qiang Gao iD, Bili Zhang iD, Duan Tan, Yajie Yuan, Nangkuo Guo, Yanhong Li iD, Zhangyan Wu, Lulu Liu iD, Chunlin Li iD, Yaru Lu iD, Tingting Gai, Yahui Zhang iD, Renkui Yang, Heying Qian iD, , Fangyin Dai iD

Abstract

The silkworm Bombyx mori is a domestic insect for silk production and a lepidopteran model. The currently available genomes limit a full understanding of its genetic and phenotypic diversity. Here we assembled long-read genomes of 545 domestic and wild silkworms and constructed a high-resolution pan-genome dataset. We found that the silkworm population harbors extremely variable genomes containing 7,308 new gene families, 4,260 (22%) core gene families, and 3,432,266 non-redundant SVs. We deciphered a series of causal genes and variants associated with domestication, breeding, and ecological adaptation traits, and experimentally validated two of those genes using CRISPR-Cas9 or RNA interference. This unprecedented large-scale genomic resource allows for high-throughput screening of interesting traits for functional genomic research and breeding improvement of silkworms and may serve as a guideline for traits decoding in other species.

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