Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

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Abstract

The Symphyta is traditionally accepted as a paraphyletic group located in a basal position of the order Hymenoptera. Herein, we conducted a comparative analysis of the mitochondrial genomes in the Symphyta by describing two newly sequenced ones, from Trichiosoma anthracinum, representing the first mitochondrial genome in family Cimbicidae, and Asiemphytus rufocephalus, from family Tenthredinidae. The sequenced lengths of these two mitochondrial genomes were 15,392 and 14,864 bp, respectively. Within the sequenced region, trnC and trnY were rearranged to the upstream of trnI- nad2 in T. anthracinum, while in A. rufocephalus all sequenced genes were arranged in the putative insect ancestral gene arrangement. Rearrangement of the tRNA genes is common in the Symphyta. The rearranged genes are mainly from trnL1 and two tRNA clusters of trnI- trnQ-trnM and trnW-trnC-trnY. The mitochondrial genomes of Symphyta show a biased usage of A and T rather than G and C. Protein-coding genes in Symphyta species show a lower evolutionary rate than those of Apocrita. The Ka/Ks ratios were all less than 1, indicating purifying selection of Symphyta species. Phylogenetic analyses supported the paraphyly and basal position of Symphyta in Hymenoptera. The well-supported phylogenetic relationship in the study is Tenthredinoidea + (Cephoidea + (Orussoidea + Apocrita)).

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DnaSP, DNA polymorphism analyses by the coalescent and other methods.

Julio Rozas, Juan Sánchez-DelBarrio, Xavier Messeguer … (2003)

DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (approximately 5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp

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TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Federico Abascal, Rafael Zardoya, Maximilian J Telford (2010)

We present TranslatorX, a web server designed to align protein-coding nucleotide sequences based on their corresponding amino acid translations. Many comparisons between biological sequences (nucleic acids and proteins) involve the construction of multiple alignments. Alignments represent a statement regarding the homology between individual nucleotides or amino acids within homologous genes. As protein-coding DNA sequences evolve as triplets of nucleotides (codons) and it is known that sequence similarity degrades more rapidly at the DNA than at the amino acid level, alignments are generally more accurate when based on amino acids than on their corresponding nucleotides. TranslatorX novelties include: (i) use of all documented genetic codes and the possibility of assigning different genetic codes for each sequence; (ii) a battery of different multiple alignment programs; (iii) translation of ambiguous codons when possible; (iv) an innovative criterion to clean nucleotide alignments with GBlocks based on protein information; and (v) a rich output, including Jalview-powered graphical visualization of the alignments, codon-based alignments coloured according to the corresponding amino acids, measures of compositional bias and first, second and third codon position specific alignments. The TranslatorX server is freely available at http://translatorx.co.uk.

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Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences.

Alexandre Hassanin, Nelly Léger, Jean Deutsch (2005)

Mitochondrial DNA (mtDNA) sequences are comonly used for inferring phylogenetic relationships. However, the strand-specific bias in the nucleotide composition of the mtDNA, which is thought to reflect assymetric mutational constraints, combined with the important compositional heterogeneity among taxa, are known to be highly problematic for phylogenetic analyses. Here, nucleotide composition was compared across 49 species of Metazoa (34 arthropods, 2 annelids, 2 molluscs, and 11 deuterosomes), and analyzed for a mtDNA fragment including six protein-coding genes, i.e., atp6, atp8, cox1, cox2, cox3, and nad2. The analyses show that most metazoan species present a clear strand assymetry, where one strand is biased in favor of A and C, whereas the other strand has reverse bias, i.e. in favor of T and G. the origin of this strand bias can be related to assymetric mutational constraints involving deaminations of A and C nucleotides during the replication and/or transcription processes. The analyses reveal that six unrelated genera are characterized by a reversal of the usual strand bias, i.e., Argiope (Araneae), Euscorpius (Scorpiones), Tigrioupus (Maxillopoda), Branchiostoma (Cephalochordata) Florometra (Echinodermata), and Katharina (Mollusca). It is proposed that assymetric mutational constraints have been independantly reversed in these six genera, through an inversion of the control region, i.e., the region that contains most regulatory elements for replication and transcription of the mtDNA. We show that reversals of assymetric mutational constraints have dramatic consequences on the phylogenetic analyses, as taxa characterized by reverse strand bias tend to group together due to long-branch attraction artifacts. We propose a new method for limiting this specific problem in tree reconstruction under the Bayesian approach. We apply our method to deal with the question of phylogenetic relationships of the major lineages of Arthropoda, This new approach provides a better congruence with nuclear analyses based on mtDNA sequences, our data suggest that Chelicerata, Crustacea, Myriapoda, Pancrustacea, and Paradoxopoda are monophyletic.

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Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group

ISSN (Electronic): 2045-2322

Publication date (Electronic): 16 February 2016

Publication date Collection: 2016

Volume: 6

Electronic Location Identifier: 20972

Affiliations

[1 ]State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University , Hangzhou 310058, China

[2 ]Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences , Beijing 100097, China

Author notes

[a ] shujun268@ 123456163.com

[b ] xxchen@ 123456zju.edu.cn

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Publisher Item ID: srep20972

DOI: 10.1038/srep20972

PMC ID: 4754708

PubMed ID: 26879745

SO-VID: 7d3ed9a5-88fc-4896-8c11-d7f59f9da3d8

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This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

Comparative and phylogenetic analysis of the mitochondrial genomes in basal hymenopterans

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Hymenoptera

Most cited references 29

DnaSP, DNA polymorphism analyses by the coalescent and other methods.

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of metazoa, and consequences for phylogenetic inferences.

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