Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae)

Li, Ran; Zhang, Wei; Ma, Zhenxing; Zhou, Chang-Fa

doi:10.1016/j.ijbiomac.2020.10.124

Cited by 21 publications

(25 citation statements)

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“…The accuracy of the existing mitogenome of P. cupulatus sequenced using Sanger technology was verified by our new generated sequence [16]. Most of the genes (9 PCGs and 15 (14) tRNAs) were encoded on the major strand (J-strand), while the remaining genes were on the minor strand (N-strand) ( Figure 2).…”

Section: Genomic Organization and Compositionmentioning

confidence: 77%

“…Across the order Ephemeroptera, several gene rearrangement events have been observed, such as in S. chinensis, A. yixiani and C. fusca [12][13][14]. Comparative analysis of the heptageniid mitogenomes indicates that the trnM duplication is unique to the family.…”

Section: Gene Arrangementmentioning

confidence: 99%

“…Finally, the new gene arrangement of heptageniid mitogenomes (trnI-trnM-trnQ-trnM) was generated ( Figure 6d). It is plausible to hypothesize that the gene arrangement pattern with an extra trnM could be explained through the TDRL model [14,55]. All gene rearrangement events reported in Ephemeroptera are almost focused on the tRNA genes, characterized as minor rearrangement.…”

Section: Gene Arrangementmentioning

confidence: 99%

“…The rearrangement of several tRNAs is found in Alainites yixiani (Baetidae) with a gene cluster of trnI-CR-trnC-trnQ-trnY-trnM-ND2-trnW [13]. Recent studies have also demonstrated that trnI of Ephemerellidae is inverted from the downstream of CR in the H-strand to the upstream of CR in the J-strand, forming an identical gene block (trnI-CR-trnQ-trnM) [14]. In addition, the duplication of trnM gene is always observed in Heptageniidae, except Paegniodes cupulatus [13,15,16].…”

Section: Introductionmentioning

confidence: 99%

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Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Lei

et al. 2021

Insects

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Large intergenic spacers and tRNA gene duplications have been reported in several insect groups, although little is known about mitogenomes of mayflies. Here, we determined complete mitogenomes of ten heptageniid species and systemically analyzed their mitogenomic features. Both a conserved intergenic spacer (IGS) and trnM duplication were detected in those mitogenomes. The IGS, which was observed in heptageniids, could be further folded into a stable stem–loop structure. The tRNA gene duplication was found in almost all analyzed mitogenomes, and a unique gene block trnI-trnM-trnQ-trnM-ND2 was also discovered. Our analysis demonstrates that the heptageniid gene arrangement pattern can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on the nucleotide and amino acid sequence data recovered the genus Epeorus as monophyletic with strong support. Our results provide a better understanding of mitogenomic evolution in Heptageniidae, as well as novel molecular markers for species identification of mayflies.

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Section: Genomic Organization and Compositionmentioning

confidence: 77%

Section: Gene Arrangementmentioning

confidence: 99%

Section: Gene Arrangementmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Lei

et al. 2021

Insects

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“…as well as Ephemerella sp. (Ephemerellidae) ( Tang et al, 2014 ), Cincticostella fusca (Ephemerellidae) ( Li et al, 2020 ) and species of Serratella (Ephemerellidae) ( Xu et al, 2020b ), but three copies of the tRNA-Ile inversion in Ephemerellidae sp. as well as species of Torleya (Ephemerellidae) ( Xu et al, 2020a ; Xu et al, 2020b ) and two copies of the tRNA-Ile in Uracanthella sp.…”

Section: Discussionmentioning

confidence: 99%

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

Zhang

et al. 2021

PeerJ

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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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Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

Zuo

Zhang

Shen

2022

Ecology and Evolution

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The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS‐2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT‐skew (−0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome‐scale duplication + (non‐random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.

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Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae)

Cited by 21 publications

References 68 publications

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

Comparative Mitogenomic Analysis of Heptageniid Mayflies (Insecta: Ephemeroptera): Conserved Intergenic Spacer and tRNA Gene Duplication

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

Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS‐2019 and phylogenetic analysis of the Myriapoda

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