Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications

Abstract

The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.

A Compositional Heterogeneity Analysis of Mitochondrial Phylogenomics in Chalcidoidea Involving Two Newly Sequenced Mitogenomes of Eupelminae (Hymenoptera: Chalcidoidea)

“…In summary, with the exception of the BI trees and ML trees constructed from the AA datasets under the homogenous model that did not place Trichogrammatidae closer to the base, the topological trees constructed from our datasets suggested that Chalcididae and Trichogrammatidae may have an earlier origin, a finding consistent with previous studies [ 3 , 43 ]. Comparing the results obtained from our homogeneity and heterogeneity models, we found some inconsistency concerning the classification status of Eupelmidae.…”

The complete mitochondrial genome of Exoristobia philippinensis (Hymenoptera: Chalcidoidea: Encyrtidae) and phylogenetic analysis

“…The following sequences were used: Haltichella nipponensis NC060544 (Zhao et al. 2021 ), Metaphycus eriococci NC_056349 (Zhou et al. 2021 ), Aenasius arizonensis NC_045852 (Ma et al.…”

“…One species from Chalcididae, Haltichella nipponensis (GenBank accession number NC_060544), was used as an outgroup (Zhao et al. 2021 ) ( Table S1 ). To investigate the phylogeny of Exoristobia in Encyrtidae, the family-level relationships within Chalcidoidea were reconstructed by using 13 PCGs with two inference methods (BI and ML).…”