The mitogenomes of three beetles (Coleoptera: Polyphaga: Cucujiformia): New gene rearrangement and phylogeny

The complete mitochondrial genome of Trifida elongate and comparative analysis of 43 leafhoppers

In this study, the mitochondrial genome of Trifida elongate was sequenced, and comparative analysis of T. elongate and other 43 leafhoppers was performed based on the mitochondrial genome. The mitochondrial genome sequence length of T. elongate was 14,924 bp. It comprised 13 protein-coding genes, 2 ribosomal RNA (rRNA) genes, 22 transport RNA (tRNA) genes, and 1 non-coding control region. The control region is located between the rrnS and trnI genes, is characterized by two tandem repeats and three simple sequence repeats. Phylogenetic analysis showed that T. elongate is closely related with Bolanusoides shaanxiensis and Limassolla lingchuanensis (bootstrap value = 92% and posterior probabilities = 1). Analysis of synonymous and non-synonymous nucleotide substitutions showed that Ka/Ks value of the 13 protein-coding genes of 8 subfamily leafhoppers were less than 1 ranging from 0.0315 to 0.9928. atp8 had the highest Ka/Ks value whereas cox1 had the lowest Ka/Ks value. This study provides information on the structure and sequence characteristics of the mitochondrial genome of T. elongata. Typhlocybinae is clustered with (Cicadellinae+(Idiocerinae+(Mileewinae+(Nirvaninae+(Evacanthinae+Ledrinae))))).

Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia

The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.

The mitochondrial genomes of two walnut pests, Gastrolina depressa depressa and G. depressa thoracica (Coleoptera: Chrysomelidae), and phylogenetic analyses

In this study, the mitochondrial genomes (mitogenomes) of two walnut leaf insect pests, Gastrolina depressa depressa and G. depressa thoracica, were sequenced by Sanger sequencing technology. The mitogenome of G. depressa thoracica was complete at 16,109 bp in length, while the mitogenome of G. depressa depressa (14,277 bp) was partial. The genomic analyses indicated that both mitogenomes have the typical gene content and arrangement. The formerly identified elements, 'TAGTA' between trnSer(UCN) and nad2, and 'ATGATAA' between atp8 and atp6, were more conserved than that between nad4L and nad4, which was 'ATGTTAA' in Coleoptera excluding Polyphaga. Phylogenetic analyses of the 13 protein-coding genes from 36 coleopteran species well supported a close affinity between the subfamily Chrysomelinae including G. depressa thoracica and G. depressa depressa and Galerucinae, as well as a sister relationship of ((Eumolpinae + Cryptocephalinae) + Cassidinae) within Chrysomelidae.

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Animal mitogenomes are generally thought of as being economic and optimized for rapid replication and transcription. We use long-read sequencing technology to assemble the remarkable mitogenomes of four species of seed beetles. These are the largest circular mitogenomes ever assembled in insects, ranging from 24,496 to 26,613 bp in total length, and are exceptional in that some 40% consists of non-coding DNA. The size expansion is due to two very long intergenic spacers (LIGSs), rich in tandem repeats. The two LIGSs are present in all species but vary greatly in length (114-10,408 bp), show very low sequence similarity, divergent tandem repeat motifs, a very high AT content and concerted length evolution. The LIGSs have been retained for at least some 45 my but must have undergone repeated reductions and expansions, despite strong purifying selection on protein coding mtDNA genes. The LIGSs are located in two intergenic sites where a few recent studies of insects have also reported shorter LIGSs (>200 bp). These sites may represent spaces that tolerate neutral repeat array expansions or, alternatively, the LIGSs may function to allow a more economic translational machinery. Mitochondrial respiration in adult seed beetles is based almost exclusively on fatty acids, which reduces the need for building complex I of the oxidative phosphorylation pathway (NADH dehydrogenase). One possibility is thus that the LIGSs may allow depressed transcription of NAD genes. RNA sequencing showed that LIGSs are partly transcribed and transcriptional profiling suggested that all seven mtDNA NAD genes indeed show low levels of transcription and co-regulation of transcription across sexes and tissues.

Characterization of the complete mitochondrial genome of Acanthoscelides obtectus (Coleoptera: Chrysomelidae: Bruchinae) with phylogenetic analysis

Acanthoscelides obtectus is a common species of the subfamily Bruchinae and a worldwide-distributed seed-feeding beetle. The complete mitochondrial genome of A. obtectus is 16,130 bp in length with an A + T content of 76.4%. It contains a positive AT skew and a negative GC skew. The mitogenome of A. obtectus contains 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes and a non-coding region (D-loop). All PCGs start with an ATN codon, and seven (ND3, ATP6, COIII, ND3, ND4L, ND6, and Cytb) of them terminate with TAA, while the remaining five (COI, COII, ND1, ND4, and ND5) terminate with a single T, ATP8 terminates with TGA. Except tRNA ^Ser , the secondary structures of 21 tRNAs that can be folded into a typical clover-leaf structure were identified. The secondary structures of lrRNA and srRNA were also predicted in this study. There are six domains with 48 helices in lrRNA and three domains with 32 helices in srRNA. The control region of A. obtectus is 1354 bp in size with the highest A + T content (83.5%) in a mitochondrial gene. Thirteen PCGs in 19 species have been used to infer their phylogenetic relationships. Our results show that A. obtectus belongs to the family Chrysomelidae (subfamily-Bruchinae). This is the first study on phylogenetic analyses involving the mitochondrial genes of A. obtectus and could provide basic data for future studies of mitochondrial genome diversities and the evolution of related insect lineages.

The complete mitochondrial genome of Euproctis similis (Lepidoptera: Noctuoidea: Erebidae) and phylogenetic analysis

The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We sequenced, annotated, and characterized the mitogenome of Euproctis similis. The complete mitogenome is 15,437bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a control region (A+T-rich region). The A+T content in the mitogenome was 80.16%. All PCGs use standard ATN as a start codon, with the exception of cytochrome c coxidase 1 (cox1) with CGA. A gene rearrangement (trnM) was found. All transfer RNA (tRNA) genes have a typical clover-leaf structure except for trnS1 (AGN). Phylogenetic analysis was performed using Bayesian Inference and Maximum Likelihood based on the amino acid and nucleotide sequences of 13 mitochondrial PCGs. The well-supported phylogenetic relationships can be generally described as: Notodontidae+(Erebidae+(Nolidae+(Euteliidae+Noctuidae))). The tree support that E. similis shares a close ancestry with Erebidae insects. Our results indicate that Erebidae is a sister group to the other families (Euteliidae, Nolidae, and Noctuidae).