Increasing 28 mitogenomes of Ephemeroptera, Odonata and Plecoptera support the Chiastomyaria hypothesis with three different outgroup combinations

Background The phylogenetic relationships of Odonata (dragonflies and damselflies) and Ephemeroptera (mayflies) remain unresolved. Different researchers have supported one of three hypotheses (Palaeoptera, Chiastomyaria or Metapterygota) based on data from different morphological characters and molecular markers, sometimes even re-assessing the same transcriptomes or mitochondrial genomes. The appropriate choice of outgroups and more taxon sampling is thought to eliminate artificial phylogenetic relationships and obtain an accurate phylogeny. Hence, in the current study, we sequenced 28 mt genomes from Ephemeroptera, Odonata and Plecoptera to further investigate phylogenetic relationships, the probability of each of the three hypotheses, and to examine mt gene arrangements in these species. We selected three different combinations of outgroups to analyze how outgroup choice affected the phylogenetic relationships of Odonata and Ephemeroptera. Methods Mitochondrial genomes from 28 species of mayflies, dragonflies, damselflies and stoneflies were sequenced. We used Bayesian inference (BI) and Maximum likelihood (ML) analyses for each dataset to reconstruct an accurate phylogeny of these winged insect orders. The effect of outgroup choice was assessed by separate analyses using three outgroups combinations: (a) four bristletails and three silverfish as outgroups, (b) five bristletails and three silverfish as outgroups, or (c) five diplurans as outgroups. Results Among these sequenced mitogenomes we found the gene arrangement IMQM in Heptageniidae (Ephemeroptera), and an inverted and translocated tRNA-Ile between the 12S RNA gene and the control region in Ephemerellidae (Ephemeroptera). The IMQM gene arrangement in Heptageniidae (Ephemeroptera) can be explained via the tandem-duplication and random loss model, and the transposition and inversion of tRNA-Ile genes in Ephemerellidae can be explained through the recombination and tandem duplication-random loss (TDRL) model. Our phylogenetic analysis strongly supported the Chiastomyaria hypothesis in three different outgroup combinations in BI analyses. The results also show that suitable outgroups are very important to determining phylogenetic relationships in the rapid evolution of insects especially among Ephemeroptera and Odonata. The mt genome is a suitable marker to investigate the phylogeny of inter-order and inter-family relationships of insects but outgroup choice is very important for deriving these relationships among winged insects. Hence, we must carefully choose the correct outgroup in order to discuss the relationships of Ephemeroptera and Odonata.

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Two Complete Mitochondrial Genomes of Mileewinae (Hemiptera: Cicadellidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects12080668 ◽

2021 ◽

Vol 12 (8) ◽

pp. 668

Author(s):

Tinghao Yu ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Strong Support ◽

Intergenic Spacer ◽

Taxonomic Status ◽

Start Codon ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Protein Coding

More studies are using mitochondrial genomes of insects to explore the sequence variability, evolutionary traits, monophyly of groups and phylogenetic relationships. Controversies remain on the classification of the Mileewinae and the phylogenetic relationships between Mileewinae and other subfamilies remain ambiguous. In this study, we present two newly completed mitogenomes of Mileewinae (Mileewa rufivena Cai and Kuoh 1997 and Ujna puerana Yang and Meng 2010) and conduct comparative mitogenomic analyses based on several different factors. These species have quite similar features, including their nucleotide content, codon usage of protein genes and the secondary structure of tRNA. Gene arrangement is identical and conserved, the same as the putative ancestral pattern of insects. All protein-coding genes of U. puerana began with the start codon ATN, while 5 Mileewa species had the abnormal initiation codon TTG in ND5 and ATP8. Moreover, M. rufivena had an intergenic spacer of 17 bp that could not be found in other mileewine species. Phylogenetic analysis based on three datasets (PCG123, PCG12 and AA) with two methods (maximum likelihood and Bayesian inference) recovered the Mileewinae as a monophyletic group with strong support values. All results in our study indicate that Mileewinae has a closer phylogenetic relationship to Typhlocybinae compared to Cicadellinae. Additionally, six species within Mileewini revealed the relationship (U. puerana + (M. ponta + (M. rufivena + M. alara) + (M. albovittata + M. margheritae))) in most of our phylogenetic trees. These results contribute to the study of the taxonomic status and phylogenetic relationships of Mileewinae.

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Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

10.7287/peerj.preprints.27183v2 ◽

2018 ◽

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae). The total length of the S.longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr(CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S.longialata mitogenome was as follows: A=41.0%, T=33.8%, C=15.5%, G=9.7%. Both BI and ML analyse strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

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Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

10.7287/peerj.preprints.27183 ◽

2018 ◽

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

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"Tandem duplication-random loss" is not a real feature of oyster mitochondrial genomes

BMC Genomics ◽

10.1186/1471-2164-10-84 ◽

2009 ◽

Vol 10 (1) ◽

pp. 84 ◽

Cited By ~ 15

Author(s):

Jianfeng Ren ◽

Xiao Liu ◽

Guofan Zhang ◽

Bin Liu ◽

Ximing Guo

Keyword(s):

Tandem Duplication ◽

Mitochondrial Genomes ◽

Random Loss

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Characteristics of the complete mitochondrial genome of Suhpalacsalongialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

10.7287/peerj.preprints.27183v1 ◽

2018 ◽

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

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Characteristics of the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae) and its phylogenetic implications

PeerJ ◽

10.7717/peerj.5914 ◽

2018 ◽

Vol 6 ◽

pp. e5914 ◽

Cited By ~ 4

Author(s):

Xin-Yan Gao ◽

Yin-Yin Cai ◽

Dan-Na Yu ◽

Kenneth B. Storey ◽

Jia-Yong Zhang

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Nucleotide Composition ◽

The Other ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Duplicated Genes ◽

Sister Clade ◽

Phylogenetic Implications

The owlflies (Family Ascalaphidae) belong to the Neuroptera but are often mistaken as dragonflies because of morphological characters. To date, only three mitochondrial genomes of Ascalaphidae, namely Libelloides macaronius; Ascaloptynx appendiculatus; Ascalohybris subjacens, are published in GenBank, meaning that they are greatly under-represented in comparison with the 430 described species reported in this family. In this study, we sequenced and described the complete mitochondrial genome of Suhpalacsa longialata (Neuroptera, Ascalaphidae). The total length of the S. longialata mitogenome was 15,911 bp, which is the longest known to date among the available family members of Ascalaphidae. However, the size of each gene was similar to the other three Ascalaphidae species. The S. longialata mitogenome included a transposition of tRNACys and tRNATrp genes and formed an unusual gene arrangement tRNACys-tRNATrp-tRNATyr (CWY). It is likely that the transposition occurred by a duplication of both genes followed by random loss of partial duplicated genes. The nucleotide composition of the S. longialata mitogenome was as follows: A = 41.0%, T = 33.8%, C = 15.5%, G = 9.7%. Both Bayesian inference and ML analyses strongly supported S. longialata as a sister clade to (Ascalohybris subjacens + L. macaronius), and indicated that Ascalaphidae is not monophyletic.

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TANDEM DUPLICATION RANDOM LOSS EVENTS INFLUENCED TO GENE ORDER CHANGES IN BAIKALIAN AMPHIPODS

MOLECULAR PHYLOGENETICS ◽

10.30826/molphy2018-71 ◽

2018 ◽

Author(s):

E.A. SIROTININA ◽

◽

E.V. ROMANOVA ◽

D. YU. SHERBAKOV ◽

◽

...

Keyword(s):

Gene Order ◽

Tandem Duplication ◽

Random Loss

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Readjustment of the Standard ASUDAS to Encompass Dental Morphological Variations in Plio-Pleistocene Hominins

Bulletins et Mémoires de la Société d anthropologie de Paris ◽

10.3166/bmsap-2018-0002 ◽

2018 ◽

Vol 30 (1-2) ◽

pp. 32-48

Author(s):

M. Louail ◽

S. Prat

Keyword(s):

Phylogenetic Relationships ◽

Homo Sapiens ◽

Initial Study ◽

Morphological Characters ◽

State University ◽

Arizona State University ◽

Dental Anthropology ◽

Morphological Variations ◽

Fossil Hominins ◽

Fossil Hominin

The standard ASUDAS scoring system (Arizona State University Dental Anthropology System) is used to assess dental morphological variations in modern humans. It is also frequently used to study, score, and compare morphological variations in fossil hominin taxa and to examine their phylogenetic relationships. However, using ASUDAS in studies of this type is under debate because it is based on modern Homo sapiens populations and does not appear to cover all variations observed in fossil Plio-Pleistocene homi- nins. Our observations and coding of 178 dentals casts of Plio-Pleistocene specimens based on ASUDAS and from the literature have confirmed the need to adapt the standard system to fossil hominins. In this initial study, we propose that the scoring procedures for some morphological characters need to be readjusted, while others could be standardized following the ASUDAS system.

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Novel gene rearrangement in the mitochondrial genome of Muraenesox cinereus and the phylogenetic relationship of Anguilliformes

Scientific Reports ◽

10.1038/s41598-021-81622-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Kun Zhang ◽

Kehua Zhu ◽

Yifan Liu ◽

Hua Zhang ◽

Li Gong ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Tandem Duplication ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

Protein Coding ◽

Muraenesox Cinereus ◽

Complete Mitogenome ◽

Relationship Of ◽

Rna Genes

AbstractThe structure and gene sequence of the fish mitochondrial genome are generally considered to be conservative. However, two types of gene arrangements are found in the mitochondrial genome of Anguilliformes. In this paper, we report a complete mitogenome of Muraenesox cinereus (Anguilliformes: Muraenesocidae) with rearrangement phenomenon. The total length of the M. cinereus mitogenome was 17,673 bp, and it contained 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNA genes, and two identical control regions (CRs). The mitochondrial genome of M. cinereus was obviously rearranged compared with the mitochondria of typical vertebrates. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The tandem duplication and random loss is most suitable for explaining this mitochondrial gene rearrangement. The Anguilliformes phylogenetic tree constructed based on the whole mitochondrial genome well supports Congridae non-monophyly. These results provide a basis for the future Anguilliformes mitochondrial gene arrangement characteristics and further phylogenetic research.

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Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽

10.3390/genes12081134 ◽

2021 ◽

Vol 12 (8) ◽

pp. 1134

Author(s):

Fei Ye ◽

Hu Li ◽

Qiang Xie

Keyword(s):

Gene Rearrangement ◽

Hot Spot ◽

Phylogenetic Analyses ◽

Mitochondrial Gene ◽

Deep Understanding ◽

Gene Arrangement ◽

Mitochondrial Genomes ◽

Current View ◽

Novel Gene ◽

Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

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