Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

Abstract

Mitochondrial genomes of twelve species of Trigonopterus weevils are presented, ten of them complete. We describe their gene order and molecular features and test their potential for reconstructing the phylogeny of this hyperdiverse genus comprising > 1,000 species. The complete mitochondrial genomes examined herein ranged from 16,501 bp to 21,007 bp in length, with an average AT content of 64.2% to 69.7%. Composition frequencies and skews were generally lower across species for atp6, cox1-3, and cob genes, while atp8 and genes coded on the minus strand showed much higher divergence at both nucleotide and amino acid levels. Most variation within genes was found at the codon level with high variation at third codon sites across species, and with lesser degree at the coding strand level. Two large non-coding regions were found, CR1 (between rrnS and trnI genes) and CR2 (between trnI and trnQ), but both with large variability in length; this peculiar structure of the non-coding region may be a derived character of Curculionoidea. The nad1 and cob genes exhibited an unusually high interspecific length variation of up to 24 bp near the 3′ end. This pattern was probably caused by a single evolutionary event since both genes are only separated by trnS2 and length variation is extremely rare in mitochondrial protein coding genes. We inferred phylogenetic trees using protein coding gene sequences implementing both maximum likelihood and Bayesian approaches, each for both nucleotide and amino acid sequences. While some clades could be retrieved from all reconstructions with high confidence, there were also a number of differences and relatively low support for some basal nodes. The best partition scheme of the 13 protein coding sequences obtained by IQTREE suggested that phylogenetic signal is more accurate by splitting sequence variation at the codon site level as well as coding strand, rather than at the gene level. This result corroborated the different patterns found in Trigonopterus regarding to A+T frequencies and AT and GC skews that also greatly diverge at the codon site and coding strand levels.

Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence

“…More specifically, vertebrates A and C are found in the most frequent nucleotides at the third codon position [ 169 ], and in this clade most of the genes are located on the L strand, the one that in fact mostly accumulates A and C. In Bivalvia, where the strand asymmetry is reversed, the most used codons end with T and G [ 170 ]. Several works report that in Arthropoda and Nematoda mitogenomes, the most used codons end with A and T [ 171 , 172 , 173 ]. As detailed above, these phyla show the highest A+T content among Eukaryota; the neutral accumulation of A and T is confirmed by the highest frequency at the third codon position compared to the first and the second one [ 174 ].…”

Comparative Mitogenomics in Hyalella (Amphipoda: Crustacea)

“…Nucleotide, amino acid, and codon compositional analyses at both complete mitogenome and single gene sequences were performed using the Python script from Narakusumo et al [ 39 ] and plotted with the Python package matplotlib [ 40 ] and the R [ 41 ] packages ggplot [ 42 ] and heatmap [ 43 ]. We used CREx [ 44 ] to analyze mtDNA gene rearrangements and the molecular mechanism driving them.…”

Twenty-eight new species of Trigonopterus Fauvel (Coleoptera, Curculionidae) from Central Sulawesi

“…nov. was coded as “ Trigonopterus sp. 1114” ( Narakusumo et al 2020 ). The species belongs to the T. satyrus -group and is closely related to T. rosichoni sp.…”

“…nov. was coded as “ Trigonopterus sp. 1188” ( Narakusumo et al 2020 ). This species belongs to the T. impressicollis -group.…”

“…Sulawesi is geologically complex ( Hall 2009 ; Stelbrink et al 2012 ) and its biogeography is currently the subject of a detailed study by us utilizing, among other taxa, the genus Trigonopterus . The purpose of this paper is to provide names to these species, especially as some of them had been part of an earlier study on mitogenomes ( Narakusumo et. al.…”