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

作者：Tong, Xiaoling; Han, Min-Jin; Lu, Kunpeng; Tai, Shuaishuai; Liang, Shubo; Liu, Yucheng; Hu, Hai; Shen, Jianghong; Long, Anxing; Zhan, Chengyu; Ding, Xin; Liu, Shuo; Gao, Qiang; Zhang, Bili; Zhou, Linli; Tan, Duan; Yuan, Yajie; Guo, Nangkuo; Li, Yan-Hong; Wu, Zhangyan; Liu, Lulu; Li, Chunlin; Lu, Yaru; Gai, Tingting; Zhang, Yahui; Yang, Renkui; Qian, Heying; Liu, Yanqun; Luo, Jiangwen; Zheng, Lu; Lou, Jinghou; Peng, Yunwu; Zuo, Weidong; Song, Jiangbo; He, Songzhen; Wu, Songyuan; Zou, Yunlong

来源：Nature Communications, 2022, 13(1): 5619.

DOI：10.1038/s41467-022-33366-x

• STRUCTURAL VARIATION
• READ ALIGNMENT
• RNA
• ACCURATE
• SEQUENCE
• ANNOTATION
• DIFFERENTIATION
• EVOLUTION
• MUTATION
• PROGRAM

Tong et al. describe a super pangenome assembled from long-read sequences of 545 wild and domesticated silkworms. Naturally selected (diapause, aposemantic coloration) or artificially selected (silk yield and fineness) sets of genes are delineated. @@@ 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.

• 单位
  中国科学院; 广东省农业科学院; 西北工业大学; 西南大学; 中国科学院研究生院; 深圳华大基因研究院; 江苏科技大学