Comparative Mitogenomics And Phylogeny Of The Microgastrinae (Hymenoptera:Braconidae)

The mitochondrial genomes are widely used in phylogenetic and evolutionary studies because of the unique characteristics, such as the small genome size, stable gene organization, maternally inheritance and accelerated rate of nucleotide substitution. The development of the sequencing technologies and phylogenetic analysis methods has resulted in extensive phylogenetic studies based on mitochondrial genomes. Most of these researches are focused on the higher-level phylogeny, although many pitfalls of the mitochondrial genomes have been reported, such as the nucleotide substitution saturation, long-branch attraction, long-branch like effects, among-site rate heterogeneity and difficulty in determination of partitioning schemes. The mitochondrial genomes have showed high potential in the studies of lower-level phylogeney in several groups.The Microgastrinae is an important subfamily of the Braconidae. It includes the most important groups of natural enemies that parasitize larvae of almost all the families of the Lepidoptera, usually the major pests in agriculture, except for the Hepialidae and some primitive moths. The phylogenetic relationships within the Microgastrinae are confused with huge controversies. Due to the difficulties insequencing of the mitochondrial genomes in the Microgastrinae caused by the high frequency of gene rearrangement and high A+T content, as well as the difficulty in the identification of the species, only one mitochondrial genomes have been sequenced before this study in contrast with its large number of species in this subfamily (more than 2200 species). Therefore, the sequencing and analysis of the mitochondrial genomes from different groups of the Microgastrinae will contribute to the development of phylogenetic markers from the mitochondrial genomes and the reconstruction of the phylogenetic relationships within the Microgastrinae. The results will shed light on the revealing of the evolutionary history and promoting the utilization of the natural enemies of the Microgastrinae.In this study we sequenced and analyzed the mitochondrial genomes of Microgastrine, and then we explored phylogenetic relationship of Microgastrinae. The points are as follows:(1) We sequenced mitochondrial genomes of 15 species representing 5 tribes and 9genera of Microgastrinae and analysed features of the genomes, including genome organization, gene contents, overlapping and intergenic regions and codon usage of the protein-coding genes. The length of the sequenced mitochondrial genomes of Microgastrinae ranges from 5996-14137 bp and A+T% content ranges from 77.64%-86.09%。All start codons of protein-coding genes in the sequenced mitochondrial genomesare ATN and the most frequently used stop codon is TAA. The overlapping and intergenic regions in microgastrine mitogenomes are usually short but with exceptions. The rearranged genes mainly are tRNA genes. The rearrangement hot-spots are located in the tRNA clusters trnH-trnD-trnK and trnA-trnR-trnN-trnS2-trnE-trnF. Rearrangement of protein coding genes were found in two species, i.e. Apanteles sp., Pholetesor sp. and one previously reported species Cotesia vestalis, representing 2 tribes and 3 genera of the Microgastrinae. We found that there is no correlation between the rearrangements in the species. Most used amino acids are Leu, Ile and Phe. Most used anti-codons are TTA (Leu), ATT (Ile) and TTT (Phe). Secondary structure of tRNA genes is clover-like.(2) In the sequenced mitochondrial genomes of Microgastrinae, most of species have a negative AT-skew and a positive GC-skew. However, Pholetesor sp. is the exception with positive AT-skew and GC-skew.(3) The phylogeny of the Microgastrinae is reconstructed based on the mitochondrial genomes and we reported the results based on the nucleotide sequences of protein coding genes and RNA genes. The topologies are the same between the Bayesian (BI) and Most Likelihood (ML) trees. The results support the monophyly of the Microgastrinae and the Forniciini is at the base of this subfamily. The relationship among the subfamilies of the Microgastrinae is ((((Apantelini+Cotesiini)+Microgastrini))+Choeras grammatitergitus)))+Microplitini))))+ Forniciini. Our results supported the frame of Mason (1981) and confirm the relationships of some genera. But some questions need further discussion, for instance, Choeras may not be monophyletic, and the species of this subgenus need further examination. The results support van Achterberg’opinion that some species of Diolcogaster sp. should belong to Forniciini from the molecular level and there should be more discussion of this genus.