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

Qin et al. BMC Genomics (2015) 16:428 DOI 10.1186/s12864-015-1566-5 RESEARCH ARTICLE Open Access Mitochondrial phylogenomics and genetic relationships of closely related pine moth (Lasiocampidae: Dendrolimus) species in China, using whole mitochondrial genomes Jie Qin1, Yanzhou Zhang2*, Xin Zhou3, Xiangbo Kong4, Shujun Wei5, Robert D Ward6 and Ai-bing Zhang1,7* Abstract Background: Pine 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. punctatus wenshanensis. 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. Results: The 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 (Continued on next page) * Correspondence: ; 2 Institute of Zoology, Chinese Academy of Sciences, 1 Beichen West Road, Chaoyang District, Beijing 100101, P.R. China 1 College of Life Sciences, Capital Normal University, Beijing 100048, China Full list of author information is available at the end of the article © 2015 Qin et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Qin et al. BMC Genomics (2015) 16:428 Page 2 of 12 (Continued from previous page) 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 subspecies of D. punctatus. Conclusions: Whole mitochondrial genomes possess relatively rich genetic information compared with the traditional use of single or multiple genes for phylogenetic purposes. They can be used to better infer phylogenetic relationships and degrees of relatedness of taxonomic groups, at least from the aspect of maternal lineage: caution should be taken due to the maternal-only inheritance of this genome. Our results indicate that D. spectabilis is an independent lineage, while D. tabulaeformis shows an extremely close relationship to D. punctatus. Keywords: Mitochondrial genome, Dendrolimus punctatus, D. tabulaeformis, D. spectabilis, Subspecies Background Insect mitochondrial genomes are usually a closed-circular molecule 14-20 kilo base pairs (kbp) in size [1]. They contain 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and a large non-coding region called the control region (CR, or the AT-rich region) which includes the essential regulatory elements for transcription and replication [1,2]. Due to their unique characters, which include small genome size, easily accessible nature, faster nucleotide substitution rates and the presence of strictly orthologous genes, mitochondrial genomes have been widely used as molecular markers for phylogenetic analyses and the investigation of questions concerning comparative and evolutionary genomics [3-10]. Whole mitochondrial genomes provide not only more general genetic information than shorter sequences of individual genes such as the COI gene, but also sets of genome-level characters, such as the relative position of different genes, structural genomic features and compositional features [1,2,11,12]. Whole mitochondrial genomes are widely used to infer phylogenetic relationships at different taxonomic levels [7,13-18]. Furthermore, mitochondrial genomes often evolve faster through higher mutation rates than nuclear genomes, especially in intergenic regions [19,20], and can be powerful markers for the inference of phylogenetic relationships among closely related taxa [9,21-24]. Dendrolimus species (Lepidoptera, Lasiocampidae) are the most serious phytophagous pests worldwide. Dendrolimus pini causes destructive damage of the Scots pine (Pinus sylvestris) in Europe [25], and Dendrolimus moths cause extensive forest damage in China [26-31]. The occurrence of different species of these pine moths and the existence of natural hybrids leads to heterosis and strong tolerance to pesticides, giving high survival rates and making them difficult to eradicate [27]. The need for improved biological pest (...truncated)