Comparative Analysis of the Complete Mitochondrial Genomes of Five Species of Ricaniidae (Hemiptera: Fulgoromorpha) and Phylogenetic Implications

Ricaniidae is a relatively small planthopper family with about 69 genera and 442 species worldwide. Members of this family occur throughout the warm temperate and tropical regions. Some species cause devastating damage to major agricultural and economic plants. However, the relationship between Ricaniidae and other families of Fulgoroidea needs to be further explored. The morphological definitions of the two biggest genera, Pochazia Amyot & Serville, 1843 and Ricania Germar, 1818 (the type genus of Ricaniidae) remain controversial. In this study, mitogenomes of five representatives in these two genera were decoded using the next-generation sequence method and genome assembly. Results showed that their complete mitogenomes are circular DNA molecules with 15,457 to 16,411 bp. All protein-coding genes (PCGs) begin with the start codon ATN, GTG or TTG and end with TAA, TAG, an incomplete stop codon single T or an incomplete stop codon single A. A lost DHU arm was discovered in the trnS gene of the five mitogenomes and the trnV gene within Pochaziaconfusa, Pochazia guttifera and Ricania simulans. The remnant tRNAs folded into clover-leaf structures. The sliding window, genetic distance, and Ka/Ks analyses indicated that the cox1 gene is the slowest evolving and is relatively conserved. The phylogenetic tree topologies support (Delphacidae + (((Issidae + (Lophopidae + Caliscelidae)) + (Flatidae + Ricaniidae)) + (Achilidae + (Dictyopharidae + Fulgoridae)))) as the best topology, as recognized by both PhyloBayes, RAxML and MrBayes based on four data sets (PCG, PCGRNA, PCG12, PCG12RNA). The monophyly of Ricaniidae and the sister group status of two families Flatidae and Ricaniidae are supported, but all analyses failed to support the monophyly of Pochazia and Ricania. The diagnoses between these two genera cannot be resolved until more evidence is acquired.

Characterization, Comparison of Four New Mitogenomes of Centrotinae (Hemiptera: Membracidae) and Phylogenetic Implications Supports New Synonymy

To explore the phylogenetic relationships of the subfamily Centrotinae from the mitochondrial genome data, four complete mitogenomes (Anchon lineatus, Anchon yunnanensis, Gargara genistae and Tricentrus longivalvulatus) were sequenced and analyzed. All the newly sequenced mitogenomes contain 37 genes. Among the 13 protein-coding genes (PCGs) of the Centrotinae mitogenomes, a sliding window analysis and the ratio of Ka/Ks suggest that atp8 is a relatively fast evolving gene, while cox1 is the slowest. All PCGs start with ATN, except for nad5 (start with TTG), and stop with TAA or the incomplete stop codon T, except for nad2 and cytb (terminate with TAG). All tRNAs can fold into the typical cloverleaf secondary structure, except for trnS1, which lacks the dihydrouridine (DHU) arm. The BI and ML phylogenetic analyses of concatenated alignments of 13 mitochondrial PCGs among the major lineages produce a well-resolved framework. Phylogenetic analyses show that Membracoidea, Smiliinae and Centrotinae, together with tribes Centrotypini and Leptobelini are recovered as well-supported monophyletic groups. The tribe Gargarini (sensu Wallace et al.) and its monophyly are supported.

Complete mitochondrial genome of Manis pentadactyla pentadactyla (Mammalia: Pholidota), an endemic subspecies of Chinese pangolin: mitogenome characterisation and phylogenetic implications

The Chinese pangolin Manis pentadactyla is critically endangered because of over-exploitation and illegal trafficking and includes three subspecies. However, the taxonomic status of the three subspecies of the Chinese pangolin has not been well resolved, which impedes regional conservation and illegal trade traces. In this study, the complete mitogenome sequence of M. p. pentadactyla, an endemic subspecies of the Chinese pangolin in Taiwan, was determined. The complete mitogenome of M. p. pentadactyla is 16,570 base pairs (bp) in length with 13 protein-coding genes (PCG), 23 transfer RNAs (tRNAs), two ribosomal RNAs and a 1164 bp control region. The overall base composition of the genome showed a slight A + T bias (59.9%), positive AT skew (0.1515) and negative GC skew (-0.3406), which is similar to that of other pangolins. All PCGs started with a typical ATN codon and all tRNAs were typical cloverleaf-shaped secondary structures, except for tRNA-Ser(GCU). Phylogenetic analysis indicated a monophyletic relationship for M. p. pentadactyla and M. p. aurita and was monophyletic for M. p. pentadactyla, but paraphyletic for M. p. aurita. The paraphyly of M. p. aurita resulted from an incomplete lineage sorting. This study enriched the mitogenome database of the Chinese pangolin and the molecular information obtained should be very useful for future research on mitogenome evolution and genetic diversification in M. pentadactyla.

New family-level characters for Platygastroidea

Platygastridae (Hymenoptera) is a diverse family of parasitoid wasps for which few studies of internal morphology have been conducted. The monophyly of the group is undisputed based on recently published molecular data, but based on morphology, the family is diagnosable from other platygastroids only by a combination of character reductions. In the present study we explored the mesosoma of Platygastroidea and found two new synapomorphies for Platygastridae: an externally visible anterior mesofurcal pit, which corresponds to an invagination that connects to the anterior portion of the mesofurca, and internally, a posteriorly shifted origin of the first wing flexors. The absence of a mesofurcal bridge and the exclusively mesopectal origin of the fore wing flexors are treated as synapomorphies for Platygastridae+Janzenellidae. Phylogenetic implications and evolutionary hypotheses regarding these traits are discussed.

Novel Gene Rearrangement in the Mitochondrial Genome of Anastatus Fulloi (Hymenoptera Chalcidoidea) and Phylogenetic Implications for Chalcidoidea

The genus Anastatus comprises a large group of parasitoids, including several biological control agents in agricultural and forest systems. The taxonomy and phylogeny of these species remain controversial. In this study, the mitogenome of A. fulloi Sheng and Wang was sequenced and characterized. The nearly full-length mitogenome of A. fulloi was 15,692 bp, compromising 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes and a control region (CR). The total A + T contents were 83.83%, 82.18%, 87.58%, 87.27%, and 82.13% in the whole mitogenome, 13 PCGs, 22 tRNA genes, 2 rRNA genes, and CR, respectively. The mitogenome presented negative AT skews and positive GC skews, except for the CR. Most PCGs were encoded on the majority strand, started with ATN codons, and ended with TAA codons. Among the 3736 amino acid-encoding codons, TTA (Leu1), CGA (Arg), TCA (Ser2), and TCT (Ser2) were predominant. Most tRNAs had cloverleaf secondary structures, except trnS1, with the absence of a dihydrouridine (DHU) arm. Compared with mitogenomes of the ancestral insect and another parasitoid within Eupelmidae, large-scale rearrangements were found in the mitogenome of A. fulloi, especially inversions and inverse transpositions of tRNA genes. The gene arrangements of parasitoid mitogenomes within Chalcidoidea were variable. A novel gene arrangement was presented in the mitogenome of A. fulloi. Phylogenetic analyses based on the 13 protein-coding genes of 20 parasitoids indicated that the phylogenetic relationship of 6 superfamilies could be presented as Mymaridae + (Eupelmidae + (Encyrtidae + (Trichogrammatidae + (Pteromalidae + Eulophidae)))). This study presents the first complete mitogenome of the Anastatus genus and offers insights into the identification, taxonomy, and phylogeny of these parasitoids.

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

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.