Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx)

Abstract

A single-base pair resolution silkworm genetic variation map was constructed from 40 domesticated and wild silkworms, each sequenced to approximately threefold coverage, representing 99.88% of the genome. We identified ~16 million single-nucleotide polymorphisms, many indels, and structural variations. We find that the domesticated silkworms are clearly genetically differentiated from the wild ones, but they have maintained large levels of genetic variability, suggesting a short domestication event involving a large number of individuals. We also identified signals of selection at 354 candidate genes that may have been important during domestication, some of which have enriched expression in the silk gland, midgut, and testis. These data add to our understanding of the domestication processes and may have applications in devising pest control strategies and advancing the use of silkworms as efficient bioreactors.

Fig. 1

Silkworm phylogeny and population structure from PCA. (A) A neighbor-joining tree from genomic SNPs, bootstrapped with 1000 replicates (bootstrap values less than 100 are shown on arcs; those equal to 100 are not shown): green for all wild varieties; others are domesticated strains separated into three groups (purple, red, and yellow). Domesticated strains are denoted by a combination of symbols representing silkworm systems (hollow circles, Chinese; stars, Japanese; triangles, tropical; squares, European; filled circles, mutant system) and sample IDs (D01 to D29 and P50-ref for the reference genome of Dazao). Wild varieties are indicated by their IDs (W01 to W11). Scale bar, frequencies of base-pair differences. (B) PCA results of the first four statistically significant components (Tracy-Wisdom, P < 0.05). (Top) The first eigenvector separates domesticated and wild varieties, and the second divides the domesticated strains into subgroups. (Bottom) The third eigenvector separates the high-silk production Japanese domesticated strains D01 and D03 from the other domesticated strains, and the fourth separates the wild varieties W01 and W04 from the other wild varieties.

Fig. 2

GROSS. (A) Two-dimensional distribution for θ_{π,domesticated}^/θ_π,wild and Tajima's D for domesticated silkworms. 5-kb windows, data points of which locate to the left of the vertical red line (corresponding to Z test P < 0.005) and below the horizontal red line (also Z test P < 0.005), were picked out as building blocks of GROSS. (B) LD in GROSS. For domesticated silkworms, LD decays much more slowly in GROSS than in the whole genome, whereas for wild varieties, no obvious change in the pattern was observed. (C) Distribution of divergence between domesticated and wild groups in GROSS versus the whole genome (F_st) (7).