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Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils

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 gen...

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Autores principales: Narakusumo, Raden Pramesa, Riedel, Alexander, Pons, Joan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566755/
https://www.ncbi.nlm.nih.gov/pubmed/33083123
http://dx.doi.org/10.7717/peerj.10017
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author Narakusumo, Raden Pramesa
Riedel, Alexander
Pons, Joan
author_facet Narakusumo, Raden Pramesa
Riedel, Alexander
Pons, Joan
author_sort Narakusumo, Raden Pramesa
collection PubMed
description 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.
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spelling pubmed-75667552020-10-19 Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils Narakusumo, Raden Pramesa Riedel, Alexander Pons, Joan PeerJ Entomology 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. PeerJ Inc. 2020-10-13 /pmc/articles/PMC7566755/ /pubmed/33083123 http://dx.doi.org/10.7717/peerj.10017 Text en ©2020 Narakusumo et al. https://creativecommons.org/licenses/by-nc/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by-nc/4.0/) , which permits using, remixing, and building upon the work non-commercially, as long as it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Entomology
Narakusumo, Raden Pramesa
Riedel, Alexander
Pons, Joan
Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title_full Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title_fullStr Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title_full_unstemmed Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title_short Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils
title_sort mitochondrial genomes of twelve species of hyperdiverse trigonopterus weevils
topic Entomology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7566755/
https://www.ncbi.nlm.nih.gov/pubmed/33083123
http://dx.doi.org/10.7717/peerj.10017
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