Genetic diversity, molecular phylogeny and selection evidence of the silkworm mitochondria implicated by complete resequencing of 41 genomes

Abstract

BackgroundMitochondria are a valuable resource for studying the evolutionary process and deducing phylogeny. A few mitochondria genomes have been sequenced, but a comprehensive picture of the domestication event for silkworm mitochondria remains to be established. In this study, we integrate the extant data, and perform a whole genome resequencing of Japanese wild silkworm to obtain breakthrough results in silkworm mitochondrial (mt) population, and finally use these to deduce a more comprehensive phylogeny of the Bombycidae.ResultsWe identified 347 single nucleotide polymorphisms (SNPs) in the mt genome, but found no past recombination event to have occurred in the silkworm progenitor. A phylogeny inferred from these whole genome SNPs resulted in a well-classified tree, confirming that the domesticated silkworm, Bombyx mori, most recently diverged from the Chinese wild silkworm, rather than from the Japanese wild silkworm. We showed that the population sizes of the domesticated and Chinese wild silkworms both experience neither expansion nor contraction. We also discovered that one mt gene, named cytochrome b, shows a strong signal of positive selection in the domesticated clade. This gene is related to energy metabolism, and may have played an important role during silkworm domestication.ConclusionsWe present a comparative analysis on 41 mt genomes of B. mori and B. mandarina from China and Japan. With these, we obtain a much clearer picture of the evolution history of the silkworm. The data and analyses presented here aid our understanding of the silkworm in general, and provide a crucial insight into silkworm phylogeny.

The complete mitochondrial genome of the wild silkworm moth, Actias selene

“…We also identified a macrosatellite (AT)n element in the A + T-rich region of A. selene mitogenomes. The presence of multiple tandem repeat elements is a characteristic of the insect A + T-rich region, however the repeat element is variable, even within the same species (Hu et al, 2010a(Hu et al, , 2010bLi et al, 2010;Vila and Björklund, 2004). The A. melete and Artogeia napi mitogenome contains a duplicate 36 bp repeat element comprising a 26 bp core sequence flanked by 10 bp perfectly inverted repeats Vila and Björklund, 2004).…”

Accumulation of slightly deleterious mutations in the mitochondrial genome: A hallmark of animal domestication

“…Although some studies have claimed evidence of positive selection on mt protein-coding genes (Bazin et al; Li et al 2010; Mishmar et al 2006) and RNA-encoding genes (Ruiz-Pesini and Wallace 2006), the methods used in these analyses are of questionable validity (Hughes 2007); Hughes and Friedman 2008; Hughes et al 2008). Moreover, these studies have at best merely reported statistical patterns allegedly consistent with positive selection.…”

Little gene flow between domestic silkmoth <i>Bombyx mori</i> and its wild relative <i>Bombyx mandarina</i> in Japan, and possible artificial selection on the <i>CAD</i> gene of <i>B. mori</i>

“…Both mitochondrial gene-based relationships clearly showed that the clade (including B. mori) was separate from that of Japanese B. mandarina. The tree presented by Li et al (2010) also demonstrated that the Chinese B. mandarina was located in a clade different from that of B. mori. In contrast, our deduced network showed that the two B. mori haplotypes belonged to a clade including most of the Chinese B. mandarina CAD haplotypes.…”

“…When compared with the mitochondrial DNA-based phylogenetic tree (Li et al, 2010) and the COI-based maximum parsimony network (Yukuhiro et al, 2011), the network of 18 CAD haplotype sequences in Fig. 2 formed a different network shape.…”