Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes

Abstract

BackgroundPine moths (Lepidoptera; Bombycoidea; Lasiocampidae: Dendrolimus spp.) are among the most serious insect pests of forests, especially in southern China. Although COI barcodes (a standardized portion of the mitochondrial cytochrome c oxidase subunit I gene) can distinguish some members of this genus, the evolutionary relationships of the three morphospecies Dendrolimus punctatus, D. tabulaeformis and D. spectabilis have remained largely unresolved. We sequenced whole mitochondrial genomes of eight specimens, including D. punctatuswenshanensis. This is an unambiguous subspecies of D. punctatus, and was used as a reference for inferring the relationships of the other two morphospecies of the D. punctatus complex. We constructed phylogenetic trees from this data, including twelve published mitochondrial genomes of other Bombycoidea species, and examined the relationships of the Dendrolimus taxa using these trees and the genomic features of the mitochondrial genome.ResultsThe eight fully sequenced mitochondrial genomes from the three morphospecies displayed similar genome structures as other Bombycoidea species in terms of gene content, base composition, level of overall AT-bias and codon usage. However, the Dendrolimus genomes possess a unique feature in the large ribosomal 16S RNA subunits (rrnL), which are more than 60 bp longer than other members of the superfamily and have a higher AC proportion. The eight mitochondrial genomes of Dendrolimus were highly conservative in many aspects, for example with identical stop codons and overlapping regions. But there were many differences in start codons, intergenic spacers, and numbers of mismatched base pairs of tRNA (transfer RNA genes).Our results, based on phylogenetic trees, genetic distances, species delimitation and genomic features (such as intergenic spacers) of the mitochondrial genome, indicated that D. tabulaeformis is as close to D. punctatus as is D. punctatus wenshanensis, whereas D. spectabilis evolved independently from D. tabulaeformis and D. punctatus. Whole mitochondrial DNA phylogenies showed that D. spectabilis formed a well-supported monophyletic clade, with a clear species boundary separating it from the other congeners examined here. However, D. tabulaeformis often clustered with D. punctatus and with the subspecies D. punctatus wenshanensis. Genetic distance analyses showed that the distance between D. tabulaeformis and D. punctatus is generally less than the intraspecific distance of D. punctatus and its subspecies D. punctatus wenshanensis. In the species delimitation analysis of Poisson Tree Processes (PTP), D. tabulaeformis, D. punctatus and D. punctatus wenshanensis clustered into a putative species separated from D. spectabilis. In comparison with D. spectabilis, D. tabulaeformis and D. punctatus also exhibit a similar structure in intergenic spacer characterization. These different types of evidence suggest that D. tabulaeformis is very close to D. punctatus and its subspecies D. punctatus wenshanensis, and is likely to be another...

Genetic diversity among eight Dendrolimus species in Eurasia (Lepidoptera: Lasiocampidae) inferred from mitochondrial COI and COII, and nuclear ITS2 markers

“…A similar pattern of relationships between species of the SPT cluster has been shown by a series of other molecular barcoding methods [36]. Furthermore, recent studies of mitochondrial genomes of these species provide an analogous results [33]. …”

“…3, 4 and 5). In contrast, D. tabulaeformis is not distinguishable from the D. punctatus on the all COI and ITS2 phylogenetic trees supporting its subspecies status [33]. In concordance with the ITS2 tree, SPT cluster looks more homogeneous due to the lower resolution of nuclear markers (Fig.…”

“…Sequences of Odontopus sanguinolens and Odontopus nigricomis were chosen for COII. For uniformity to analyses of the mitochondrial markers COI the regions from complete mitochondrial genomes of Biston panterinaria and Phthonandria atrilineata were used as outgroup [33]. …”

A Review of the Mitogenomic Phylogeny of the Chondrichthyes

“…However, the analysis of the complete mtDNA genome may provide a much richer source of genetic information for phylogenetic inferences in comparison with the more traditional approach, based on the analysis of single or multiple genes [32]. In this context, the principal objective of the present study was to provide phylogenetic inferences on the Chondrichthyes based on the complete mitochondrial genome, and a more comprehensive understanding of the relationships among the species of sharks and rays.…”

“…[6]. More recently, however, improvements in the speed and accuracy of new generation sequencing (NGS), and the reduction of laboratory costs, have provided a large number of molecular markers, amplifying considerably the analytical perspectives in the fields of phylogenetic and phylogenetic research, and the potential for the study of molecular ecology in a wide range of organisms [30][31][32]. In 2015 and 2016 alone, around 21 new elasmobranch genomes were made available in GenBank.…”