Dataset Information

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

ABSTRACT: Coleoptera is the most diverse group of insects with over 360,000 described species divided into four suborders: Adephaga, Archostemata, Myxophaga, and Polyphaga. In this study, we present six new complete mitochondrial genome (mtgenome) descriptions, including a representative of each suborder, and analyze the evolution of mtgenomes from a comparative framework using all available coleopteran mtgenomes. We propose a modification of atypical cox1 start codons based on sequence alignment to better reflect the conservation observed across species as well as findings of TTG start codons in other genes. We also analyze tRNA-Ser(AGN) anticodons, usually GCU in arthropods, and report a conserved UCU anticodon as a possible synapomorphy across Polyphaga. We further analyze the secondary structure of tRNA-Ser(AGN) and present a consensus structure and an updated covariance model that allows tRNAscan-SE (via the COVE software package) to locate and fold these atypical tRNAs with much greater consistency. We also report secondary structure predictions for both rRNA genes based on conserved stems. All six species of beetle have the same gene order as the ancestral insect. We report noncoding DNA regions, including a small gap region of about 20 bp between tRNA-Ser(UCN) and nad1 that is present in all six genomes, and present results of a base composition analysis.

SUBMITTER: Sheffield NC

PROVIDER: S-EPMC2568038 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:Insect mitochondrial genomes (mitogenomes) exhibit high diversity in some lineages. The gene rearrangement and large intergenic spacer (IGS) have been reported in several Coleopteran species, although very little is known about mitogenomes of Meloidae.We determined complete or nearly complete mitogenomes of seven meloid species. The circular genomes encode 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs) and two ribosomal RNAs (rRNAs), and contain a control region, with gene arrangement identical to the ancestral type for insects. The evolutionary rates of all PCGs indicate that their evolution is based on purifying selection. The comparison of tRNA secondary structures indicates diverse substitution patterns in Meloidae. Remarkably, all mitogenomes of the three studied Hycleus species contain two large intergenic spacers (IGSs). IGS1 is located between trnW and trnC, including a 9 bp consensus motif. IGS2 is located between trnS2 (UCN) and nad1, containing discontinuous repeats of a pentanucleotide motif and two 18-bp repeat units in both ends. To date, IGS2 is found only in genera Hycleus across all published Coleopteran mitogenomes. The duplication/random loss model and slipped-strand mispairing are proposed as evolutionary mechanisms for the two IGSs (IGS1, IGS2). The phylogenetic analyses using MrBayes, RAxML, and PhyloBayes methods based on nucleotide and amino acid datasets of 13 PCGs from all published mitogenomes of Tenebrionoids, consistently recover the monophylies of Meloidae and Tenebrionidae. Within Meloidae, the genus Lytta clusters with Epicauta rather than with Mylabris. Although data collected thus far could not resolve the phylogenetic relationships within Meloidae, this study will assist in future mapping of the Meloidae phylogeny.This study presents mitogenomes of seven meloid beetles. New mitogenomes retain the genomic architecture of the Coleopteran ancestor, but contain two IGSs in the three studied Hycleus species. Comparative analyses of two IGSs suggest that their evolutionary mechanisms are duplication/random loss model and slipped-strand mispairing.

Project description:A taxonomic review of the known Taiwanese taxa of the pericaline Lebiini, this paper includes a key to the genera, keys to species, descriptions, and redescriptions of all species, illustrations, geographic range maps, re-rankings, and new synonymies. In total 34 species are treated, nine of which are described as new. A new genus and new species are as follows: Bellavalentis gen. n., (type species Dolichoctiskuzugamii Shibata, 1967); Amphimenesabsensacidus sp. n.; Amphimenesbeichatiensis sp. n.; Amphimenescarinacaulis sp. n.; Catascopus(s. str.)asahartisp. n.; Catascopus(s. str.)viridiorchissp. n.; Coptodera (Coptoderina) occultasp. n.; Dolichoctisbadiadorsis sp. n.; Dolichoctisdilatata sp. n.; Moctherusobscurabasis sp. n. After close examination of the type material of several species, we were able to determine that Coptoderinachaudoirianguilipennis (Nakane and Okhura) is a junior synonym of Coptodera (Coptoderina) chaudoiri Andrewes, syn. n. and Coptoderanobilis Jedli?ka is also a junior synonym of C.chaudoiri, syn. n. Dolichoctisstriatusformosanus Habu is a junior synonym of Dolichoctisrotundata (Schmidt-Goebel), syn. n.Dolichoctis (Mochtherus) uenoi Habu is a junior synonym of Mochtherusluctuosus Putzeys, syn. n. Pericalusformosanus Dupuis was recently ranked as a subspecies of Pericalusornatusformosanus Dupuis. After consideration of the several consistent taxonomic characteristics and also considering its allopatric distribution with all other species of Pericalus, we believe Pericalusformosanus Dupuis to be a valid species, stat. resurr. The monobasic genus Pseudomenarus (type species Pseudomenarusflavomaculatus Shibata, 1964) is established as conspecific with members of the genus Formosiella Jedli?ka, 1951, comb. n. Species previously recorded from Taiwan that are not present here include: Amphimenespiceolus Bates; Catascopusaequatus Dejean; Catascopusfacialis (Wiedemann) Coptoderainterrupta Schmidt-Goebel Coptoderaflexuosa Schmidt-Goebel and Peripristusater (Laporte). The pericaline taxa of Taiwan are arranged in 14 genera, five subgenera, and 34 currently known species. Notes on collecting circumstances, habits, and habitat are included when known.

Project description:BackgroundNucleotide sequences and the gene arrangements of mitochondrial genomes are effective tools for resolving phylogenetic problems. Hemipteroid insects are known to possess highly reorganized mitochondrial genomes, but in the suborder Heteroptera (Insecta: Hemiptera), there was only one complete mitochondrial genome sequenced without gene rearrangement and the phylogeny of infraorder Pentatomomorpha in Heteroptera was still uncertain.ResultsFifteen mitochondrial genomes of the suborder Heteroptera were sequenced. Gene rearrangements were found as follows: 1) tRNA-I and tRNA-Q switched positions in Aradidae, 2) tRNA-T and tRNA-P switched positions in Largidae and Pyrrhocoridae. Two recombination events were found in Alydidae and Malcidae. The other mt-genomes were organized in the same way as observed in Drosophila yakuba. The phylogenetic analyses of infraorder Pentatomomorpha based on the nucleotide sequence raised the hypothesis of (Aradoidea + (Pentatomoidea + (Pyrrhocoroidea + (Lygaeoidea + Coreoidea)))). The rearrangement of tRNA-T and tRNA-P also linked Largidae and Pyrrhocoridae together. Furthermore, the conserved sequence block in the unusual intergenic spacers between tRNA-H and ND4 favored the monophyly of Lygaeoidea. Tetranucleotide ATCA was inferred to be the initiation codon of ND2 in Cydnidae. No correlation was found between the rates of nucleotide substitution and gene rearrangement. CG content was significantly correlated with the nucleotide substitution rate of each gene. For ND1, there was a positive correlation (P < 0.01) between amino acids variations and hydrophobicity, but a negative correlation (P < 0.01) for ND6. No conserved sequence was found among the control regions and these regions were not always the most AT-rich region of the mt-genome.ConclusionHeteropteran insects are extremely complex groups worthy of further study because of the unusual tetranucleotide initiation codon and their great mt-genomic diversity, including gene rearrangements and recombinations. The mt-genome is a powerful molecular marker for resolving phylogeny at the level of the superfamily and family. Gene rearrangements were not correlated with nucleotide substitution rates. CG content variation caused the different evolutionary patterns among genes. For ND1, in many polar or nonpolar regions the specific identity of the amino acid residues might be more important than maintaining the polarity of these regions, while the opposite is true for ND6. Most sequences of the control regions did not appear to be important for regulatory functions. Finally, we suggest that the term "AT-rich regions" should not be used.

Dataset Information

A comparative analysis of mitochondrial genomes in Coleoptera (Arthropoda: Insecta) and genome descriptions of six new beetles.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets