The complete mitochondrial genomes of five Agrilinae (Coleoptera, Buprestidae) species and phylogenetic implications

Abstract

Five complete mitochondrial genomes of five species from the subfamily Agrilinae were sequenced and annotated, including Coraebus diminutus Gebhardt, 1928 (15,499 bp), Coraebus cloueti Théry, 1893 (15,514 bp), Meliboeus sinae Obenberger, 1935 (16,108 bp), Agrilus sichuanus Jendek, 2011 (16,521 bp), and Sambus femoralis Kerremans, 1892 (15,367 bp). These mitogenomes ranged from 15,367 to 16,521 bp in length and encoded 37 typical mitochondrial genes: 13 protein-coding genes (13 PCGs), 2 ribosomal RNA genes (2 rRNAs), 22 transfer RNA genes (22 tRNAs), and a control region (CR). Most of PCGs had typical ATN start codons and terminated with TAR or an incomplete stop codon T–. Among these five mitogenomes, Leu2, Ile, Phe, Ser2, Gly, Met, and Val were the seven most frequently encoded amino acids. Interestingly, in A. sichuanus, a 774 bp insertion was present at trnW and trnC junction, which is unusual in Buprestidae. Additionally, phylogenetic analyses were performed based on three kinds of nucleotide matrixes (13 PCGs, 2 rRNAs, and 13 PCGs + 2 rRNAs) using Bayesian inference and maximum-likelihood methods. The results showed that the clade of Buprestidae was well separated from outgroups and all Agrilinae species formed to a single highly supported clade. The tribe Coraebini was polyphyletic, as the genus Meliboeus (Coraebini) clustered with the genus Trachys (Tracheini). The rRNA genes had important impact for the tree topology of Agrilinae. Compared to the tribes Tracheini and Agrilini, the tribe Coraebini is a younger group.

First mitochondrial genome of subfamily Julodinae (Coleoptera, Buprestidae) with its phylogenetic implications

“…The rRNA genes were located between the A + T-rich region and trnL1, and separated by trnV, which is consistent with previous studies (Duan et al 2017;Cao and Wang 2019a, b;Xiao et al 2019;Sun et al 2020;Chen et al 2021;Peng et al 2021;Huang et al 2022;Wei 2022;Weng et al 2022). The total length of rRNA genes ranged from 2035 bp (C. japonica) to 2093 bp (J. variolaris), of which the length of 16S gene ranged from 1299 bp (C. japonica and P. chinensis) to 1301 bp (J. variolaris).…”

“…In these three mitogenome, the N-strand encoded the sense-strand of 14 genes (nad1, nad4L, nad4, nad5, trnQ, trnV, trnL1, trnP, trnH, trnF, trnY, trnC, rrnL, and rrnS), while the J-strand encoded the sense-strand of the remaining 23 genes (Table 2), which was consistent with the known buprestid species (Cao and Wang 2019a, b;Xiao et al 2019;Chen et al 2021;Peng et al 2021;Huang et al 2022;Wei 2022;Weng et al 2022).…”

“…The UG mismatches were detected in some tRNAs (Suppl. material 1: figs S2-S4), which also appeared in other buprestid species (Sun et al 2020;Chen et al 2021;Huang et al 2022;Wei 2022;Weng et al 2022).…”

“…The majority of PCGs directly used ATN as the start codon, but the exceptions were nad1 (J. variolaris, P. chinensis, and C. japonica), nad4L (C. japonica), and nad5 (C. japonica) genes which started with TTG, GTG, and GTG, respectively. The unusual start codon TTG was also reported in Agrilinae (Wei 2022) and Buprestinae (Huang et al 2022). The start codon of the cox1 gene in these three mitogenomes was not determined, which may use non-canonical start codons (Friedrich and Muquim 2003;Fenn et al 2007;Yang et al 2013;Wang et al 2021;Wu et al 2022).…”

“…This region, containing regulatory elements correlated with the regulation of replication and transcription (Zhang et al 1995), plays a very important role in molecular evolution (Zhang and Hewitt 1997). The length of A + T-rich region ranged from 1080 bp (C. japonica) to 1510 bp (J. variolaris), which are of medium length in the Buprestidae (Sun et al 2020;Huang et al 2022;Wei 2022). The A + T content of the A + T-rich region of C. japonica (75.93%) and P. chinensis (78.38%) was found to be higher than that of the whole genome (67.97%, 67.00%), PCGs (66.46%, 64.55%), rRNAs (71.50%, 72.51%), and tRNAs (68.82%, 71.46%), whereas the A + T content of J. variolaris (72.85%) was lower than that of whole genome (70.43%), PCGs (68.82%), rRNAs (74.30%), and tRNAs (74.79%).…”