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

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.

142 telomere-to-telomere assemblies reveal the genome structural landscape inSaccharomyces cerevisiae

“…3 times lower than in S. cerevisiae. In other eukaryotes that benefit from pangenome data, the SV density scales from 1 SV/90 kb in Drosophila (Chakraborty et al ., 2019), 1 SV/38 kb in soybean (Liu et al ., 2020), 1 SV/17 kb in rice (Qin et al ., 2021) and up to 1 SV/4 kb in silkworm (Tong et al ., 2022). We also found a clear positive correlation between the numbers of SVs and SNVs/INDELs accumulating within genomes.…”

“…These advancements in the ease of producing more contiguous, reference-like assemblies, has allowed few species to have multiple contiguous genomes. As expected, classical model organisms and species of anthropocentric and economic importance such as Escherichia coli (Wang et al ., 2021), Drosophila melanogaster (Rech et al ., 2022; Kim et al ., 2021), Solanum lycopersicum (tomato) (Alonge et al ., 2020), Glycine max (soybean) (Liu et al ., 2020), Oryza sativa (rice) (Qin et al ., 2021; Zhang et al ., 2022), Bombyx mori (silkworm) (Tong et al ., 2022) and humans (Audano et al ., 2019; Beyter et al ., 2021; Wong et al ., 2018) already have several contiguous genomes within each species. As has often been the case in genetics and genomics, the baker’s yeast, Saccharomyces cerevisiae , is at the forefront of the field currently totaling 68 long-read genome assemblies of non-reference strains (Abou Saada et al ., 2021; Bendixsen et al ., 2021; Berlin et al ., 2015; Czaja et al ., 2020; Istace et al ., 2017; Jenjaroenpun et al ., 2018; Lee et al ., 2022; Shao et al ., 2018; Yue et al ., 2017; Zhang and Emerson, 2019; Heasley and Argueso, 2022).…”

The Loci of Insect Phenotypic Evolution

“…In another case, the suspected mutation (A301S in the rdl gene) did not confer measurable resistance when introduced in Plutella xylostella , suggesting that insecticide resistance is not due to this mutation alone [20]. In a tour de force association study in Bombyx mori , four genes were found to contribute to coloration, egg diapause and two silk traits, respectively, and the phenotypic effect of three of these genes was confirmed by CRISPR/Cas9 [21].…”

Highly accurate genome assembly of an improved high-yielding silkworm strain, Nichi01

“…This new reference genome with an accurate structure provides a solid research foundation for further genomics and breeding. For example, an alignment-based scaffolding using a reference genome is one of the standard methods for correction and anchoring contigs to chromosome-scale assembly; the recently published genome assembly of over 500 silkworm strains was based on the method using the p50T genome assembly (Tong et al 2022). In such cases, the new Nichi01 genome assembly can serve as a better structural model.…”