Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications

Abstract

A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and −0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.

The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships

“…Total mitogenomes were obtained by next-generation sequencing (NGS) with the whole-genome shotgun (WGS) strategy on the Illumina MiSeq platform [19]. The reads of sequences were cleaned to remove the adaptor sequences and low-quality reads with ambiguous sequences [19].…”

“…Total mitogenomes were obtained by next-generation sequencing (NGS) with the whole-genome shotgun (WGS) strategy on the Illumina MiSeq platform [19]. The reads of sequences were cleaned to remove the adaptor sequences and low-quality reads with ambiguous sequences [19]. The high-quality second-generation sequences were de novo assembled to obtain contigs and scaffolds using A5-miseq v20150522 [25] and SPAdes v3.9.0 [26].…”

“…The incomplete stop codons (TA/T) may be converted to the complete stop codon (TAA) through RNA polyadenylation [31,44,45]. Incomplete stop codons are common in animal mitochondrial genomes [19,46,47].…”

“…Mitochondrial genomes have many advantages in evolutionary analyses, including a small size, a high copy number, a wide range of evolutionary rates, maternal inheritance, a lack of recombination and high mutation rates [15][16][17][18]. Therefore, mitogenomes have been widely adopted in molecular phylogenetics, evolutionary ecology, population genetics and phylogeography [11,19]. Moreover, combinations of the above 37 genes in a mitogenome might improve phylogenetic resolution [19].…”

“…Therefore, mitogenomes have been widely adopted in molecular phylogenetics, evolutionary ecology, population genetics and phylogeography [11,19]. Moreover, combinations of the above 37 genes in a mitogenome might improve phylogenetic resolution [19].…”