Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships
Tong, X.; Han, M.-j.; Lu, K.; Tai, S.; Liang, S.; Liu, Y.; Hu, H.; Shen, J.; Long, A.; Zhan, C.; Ding, X.; Gao, Q.; Zhang, B.; Tan, D.; Yuan, Y.; Guo, N.; Li, Y.; Wu, Z.; Liu, L.; Li, C.; Lu, Y.; Gai, T.; Zhang, Y.; Yang, R.; Qian, H.; Liu, Y.; Luo, J.; Zheng, L.; Lou, J.; Peng, Y.; Zuo, W.; Song, J.; He, S.; Wu, S.; Zou, Y.; Zhou, L.; Zhou, L.; Cheng, L.; Tang, Y.; Cheng, G.; Yuan, L.; He, W.; Xu, J.; Fu, T.; Xiao, Y.; Lei, T.; Xu, A.; Yin, Y.; Wang, J.; Monteiro, A.; Westhof, E.; Lu, C.; Tian, Z.; Wang, W.; Xiang, Z.; Dai, F.
Show 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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