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...
| Main Authors: | , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
PeerJ Inc.
2020-10-01
|
| Series: | PeerJ |
| Subjects: | |
| Online Access: | https://peerj.com/articles/10017.pdf |
| _version_ | 1797418499821273088 |
|---|---|
| author | Raden Pramesa Narakusumo Alexander Riedel Joan Pons |
| author_facet | Raden Pramesa Narakusumo Alexander Riedel Joan Pons |
| author_sort | Raden Pramesa Narakusumo |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-09T06:33:34Z |
| format | Article |
| id | doaj.art-fb68284e4adc4806a7ea2ee112a7bf50 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:33:34Z |
| publishDate | 2020-10-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-fb68284e4adc4806a7ea2ee112a7bf502023-12-03T11:01:45ZengPeerJ Inc.PeerJ2167-83592020-10-018e1001710.7717/peerj.10017Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevilsRaden Pramesa Narakusumo0Alexander Riedel1Joan Pons2State Museum of Natural History Karlsruhe, Karlsruhe, GermanyState Museum of Natural History Karlsruhe, Karlsruhe, GermanyDiversidad Animal y Microbiana, Instituto Mediterráneo de Estudios Avanzados IMEDEA (CSIC-UIB), Esporles, Balearic Islands, SpainMitochondrial 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.https://peerj.com/articles/10017.pdfCryptorhynchinaeCurculionidaeMitochondrial genomesNext generation sequencingPhylogenetic analysis |
| spellingShingle | Raden Pramesa Narakusumo Alexander Riedel Joan Pons Mitochondrial genomes of twelve species of hyperdiverse Trigonopterus weevils PeerJ Cryptorhynchinae Curculionidae Mitochondrial genomes Next generation sequencing Phylogenetic analysis |
| 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 | Cryptorhynchinae Curculionidae Mitochondrial genomes Next generation sequencing Phylogenetic analysis |
| url | https://peerj.com/articles/10017.pdf |
| work_keys_str_mv | AT radenpramesanarakusumo mitochondrialgenomesoftwelvespeciesofhyperdiversetrigonopterusweevils AT alexanderriedel mitochondrialgenomesoftwelvespeciesofhyperdiversetrigonopterusweevils AT joanpons mitochondrialgenomesoftwelvespeciesofhyperdiversetrigonopterusweevils |