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

The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda and Pauropoda), but very little work has been done to explore their phylogenetic relationships. 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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The mitochondrial genome of Leuctra sp. (Plecoptera: Leuctridae) and its performance in phylogenetic analyses

Zootaxa ◽

10.11646/zootaxa.4671.4.8 ◽

2019 ◽

Vol 4671 (4) ◽

pp. 571-580 ◽

Cited By ~ 1

Author(s):

YUE SHEN ◽

YU-ZHOU DU

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

Likelihood Methods ◽

Protein Coding ◽

Maximum Likelihood Methods ◽

Rna Genes ◽

Drosophila Yakuba

The nearly complete mitochondrial genome (mitogenome) of Leuctra sp. (Plecoptera: Leuctridae) was sequenced. The 14,585-bp long mitogenome of L. sp. contained 37 genes including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and a control region (CR). The mitochondrial gene arrangement of L. sp. was identical with other stoneflies and the putative ancestral mitogenome of Drosophila yakuba Burla. Most PCGs used standard ATN start codons and TAN termination codons. Twenty-one of the 22 tRNAs in each mitogenome exhibited the cloverleaf secondary structures, while the dihydrouridine (DHU) arm of trnSer (AGN) was reduced. Phylogenetic analyses using our new Leuctra sp. genome and all other publicly available genomes for Plecoptera and Bayesian inference (BI) and maximum likelihood methods (ML) generated identical topologies, both supporting the monophyly of all stonefly families for which tests were possible and the infraorder Systellognatha. Scopuridae and Gripopterygidae were grouped with the infraorder Euholognatha. The final relationships within Plecoptera were recovered as (((((Perlodidae + Chloroperlidae) + Perlidae) + Pteronarcyidae) + Peltoperlidae) + Styloperlidae) + (((((Capniidae + Taeniopterygidae) + Nemouridae) + Scopuridae) + Leuctridae) + Gripopterygidae).

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The complete mitochondrial genome of the Korean endemic millipede Anaulaciulus koreanus (Verhoeff, 1937), with notes on the gene arrangement of millipede orders

Zootaxa ◽

10.11646/zootaxa.4329.6.3 ◽

2017 ◽

Vol 4329 (6) ◽

pp. 574

Author(s):

HYUNG JIK WOO ◽

ANH D. NGUYEN ◽

KUEM HEE JANG ◽

EUN HWA CHOI ◽

SHI HYUN RYU ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Gene ◽

Gene Arrangement ◽

12S Rrna ◽

Coding Region ◽

Protein Coding ◽

Close Relationship ◽

Relationship Of ◽

Rna Genes

The millipede Anaulaciulus koreanus (Verhoeff, 1937), belonging to the family Julidae, is an endemic species of the Korean fauna. In this study, we sequence and annotate the mitochondrial genome of A. koreanus. The complete mitochondrial genome of this species is 14,916 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes (16S and 12S rRNA), and a large non-coding region. The genome has a very high A+T content (71.1%), less than of the species Brachycybe lecontii Wood, 1864 (order Platydesmida; 76.6%) and Sphaerotheriidae sp. (order Sphaerotheriida; 71.2%). In comparison with the mitochondrial gene arrangement of eight other millipede species, the whole mitochondrial gene arrangement of A. koreanus is most similar to the nemasomatid species, Antrokoreana gracilipes Verhoeff, 1938, but differs from those of the other diplopod orders. The absence of tRNACys between the ND2 and COI regions is unique to the order Polydesmida, whereas the translocation of tRNATyr to between ND2 and COI is exclusive to the Sphaerotheriida. It is also shown that the translocation of tRNAThr between ND4L and ND1 may be a synapomorphy to support a close relationship of two orders Spirobolida and Spirostreptida.

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Morphological and molecular characterization of Megalobatrachonema hainanensis sp. nov. (Nematoda: Ascaridida), with phylogenetic position of Megalobatrachonema in Cosmocercoidea

Journal of Helminthology ◽

10.1017/s0022149x18001086 ◽

2018 ◽

Vol 94 ◽

Author(s):

H.-X. Chen ◽

L.-P. Zhang ◽

L. Li

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Hainan Island ◽

Phylogenetic Position ◽

Phylogenetic Study ◽

Its1 Sequence ◽

Nematode Parasites ◽

Relationship Of ◽

The Relationship

Abstract The genus Megalobatrachonema is a rare group of nematode parasites within Ascaridida. The systematic status of Megalobatrachonema in the superfamily Cosmocercoidea (Ascaridida) has long been controversial. The relationship of Megalobatrachonema and Chabaudgolvania remains unsolved. In the present study, a new species of Megalobatrachonema, M. hainanensis sp. nov., was described based on specimens collected in Amolops hainanensis (Boulenger) and Hylarana spinulosa (Smith) (Amphibia: Anura) from Hainan Island, China. The large ribosomal DNA (28S) and internal transcribed spacer (ITS1-5.8S-ITS2) were also sequenced for molecular identification and phylogenetic study. Phylogenetic analyses using maximum likelihood (ML) inference and Bayesian inference (BI) based on 28S and ITS1 sequence data, respectively, supported that Megalobatrachonema is a member of the family Kathlaniidae. In addition, the genetic comparison and phylogenetic results based on ITS1 sequence data also supported that the genus Chabaudgolvania should be considered as a synonym of Megalobatrachonema.

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The Complete Mitochondrial Genome of endemic giant tarantula, Lyrognathus crotalus (Araneae: Theraphosidae) and comparative analysis

Scientific Reports ◽

10.1038/s41598-019-57065-8 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 2

Author(s):

Vikas Kumar ◽

Kaomud Tyagi ◽

Rajasree Chakraborty ◽

Priya Prasad ◽

Shantanu Kundu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Gene Arrangement ◽

Sister Relationship ◽

Protein Coding ◽

Relationship Of ◽

Rna Genes ◽

Boundary Mapping ◽

Cloverleaf Structure

AbstractThe complete mitochondrial genome of Lyrognathus crotalus is sequenced, annotated and compared with other spider mitogenomes. It is 13,865 bp long and featured by 22 transfer RNA genes (tRNAs), and two ribosomal RNA genes (rRNAs), 13 protein-coding genes (PCGs), and a control region (CR). Most of the PCGs used ATN start codon except cox3, and nad4 with TTG. Comparative studies indicated the use of TTG, TTA, TTT, GTG, CTG, CTA as start codons by few PCGs. Most of the tRNAs were truncated and do not fold into the typical cloverleaf structure. Further, the motif (CATATA) was detected in CR of nine species including L. crotalus. The gene arrangement of L. crotalus compared with ancestral arthropod showed the transposition of five tRNAs and one tandem duplication random loss (TDRL) event. Five plesiomophic gene blocks (A-E) were identified, of which, four (A, B, D, E) retained in all taxa except family Salticidae. However, block C was retained in Mygalomorphae and two families of Araneomorphae (Hypochilidae and Pholcidae). Out of 146 derived gene boundaries in all taxa, 15 synapomorphic gene boundaries were identified. TreeREx analysis also revealed the transposition of trnI, which makes three derived boundaries and congruent with the result of the gene boundary mapping. Maximum likelihood and Bayesian inference showed similar topologies and congruent with morphology, and previously reported multi-gene phylogeny. However, the Gene-Order based phylogeny showed sister relationship of L. crotalus with two Araneomorphae family members (Hypochilidae and Pholcidae) and other Mygalomorphae species.

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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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A new iguanodontian (Dinosauria: Ornithopoda) from the Early Cretaceous of Mongolia

PeerJ ◽

10.7717/peerj.5300 ◽

2018 ◽

Vol 6 ◽

pp. e5300

Author(s):

Terry A. Gates ◽

Khishigjav Tsogtbaatar ◽

Lindsay E. Zanno ◽

Tsogtbaatar Chinzorig ◽

Mahito Watabe

Keyword(s):

Phylogenetic Analysis ◽

Growth Stage ◽

Phylogenetic Analyses ◽

Type Specimen ◽

Sister Taxon ◽

New Taxon ◽

Time Of Death ◽

The North ◽

Unusual Combination ◽

Relationship Of

We describe a new iguanodontian ornithopod,Choyrodon barsboldigen. et sp. nov. from the Albian-aged Khuren Dukh Formation of Mongolia based on several partial skeletons interpreted to represent a subadult growth stage based on osteohistological features. This new taxon is diagnosed by many autapomorphies of the maxilla, nasal, lacrimal, opisthotic, predentary, and surangular.Choyrodondisplays an unusual combination of traits, possessing an open antorbital fenestra (a primitive ornithopod trait) together with derived features such as a downturned dentary and enlarged narial fenestra. Histological imaging suggests that the type specimen ofChoyrodonwould have been a subadult at the time of death. Phylogenetic analysis of two different character matrices do not positChoyrodonto be the sister taxon or to be more primitive than the iguanodontianAltirhinus kurzanovi, which is found in the same formation. The only resolved relationship of this new taxon is that it was hypothesized to be a sister-taxon with the North American speciesEolambia caroljonesa. Though discovered in the same formation andChoyrodonbeing smaller-bodied thanAltirhinus, it does not appear that the former species is an ontogimorph of the latter. Differences in morphology and results of the phylogenetic analyses support their distinction although more specimens of both species will allow better refinement of their uniqueness.

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Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae): morphology, song and 16S rDNA phylogeny

Zootaxa ◽

10.11646/zootaxa.3401.1.4 ◽

2012 ◽

Vol 3401 (1) ◽

pp. 49 ◽

Cited By ~ 1

Author(s):

SARP KAYA ◽

DRAGAN CHOBANOV ◽

BATTAL ÇIPLAK

Keyword(s):

New Species ◽

16S Rdna ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

16S Rdna Sequence ◽

Rdna Sequence Data ◽

Male Calling ◽

Relationship Of ◽

The Relationship

The new species Anterastes davrazensis sp. n. (Orthoptera, Tettigoniidae) is described from south-eastern Turkey. Description, diagnosis and relationships of the new species were studied utilizing morphology, male calling songs and 16S rDNA sequence data from all species in the genus. Morphology and song syllable structure indicate A. davrazensis sp. n. is related to A. uludaghensis. Phylogenetic analyses based on representative haplotypes of 16S rDNA, using Sureyaella bella, Parapholidoptera distincta and Bolua turkiyae as outgroups, also suggested strong support to the relationship of these two species. A. davrazensis sp. n. differs from its closest relative A. uludaghensis by the higher number of stridulatory pegs and the song, consisting of irregular syllable groups.

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Phylogenetic Analysis of Mitogenomic Data Sets Resolves the Relationship of Seven Macropostrongyloides Species from Australian Macropodid and Vombatid Marsupials

Pathogens ◽

10.3390/pathogens9121042 ◽

2020 ◽

Vol 9 (12) ◽

pp. 1042 ◽

Cited By ~ 1

Author(s):

Tanapan Sukee ◽

Anson V. Koehler ◽

Ross Hall ◽

Ian Beveridge ◽

Robin B. Gasser ◽

...

Keyword(s):

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Parasitic Nematodes ◽

Data Sets ◽

Protein Amino Acid ◽

Protein Coding ◽

Relationship Of ◽

The Relationship ◽

Swamp Wallaby

Nematodes of the genus Macropostrongyloides inhabit the large intestines or stomachs of macropodid (kangaroos and wallabies) and vombatid (wombats) marsupials. This study established the relationships of seven species of Macropostrongyloides using mitochondrial (mt) protein amino acid sequence data sets. Phylogenetic analyses revealed that species of Macropostrongyloides (M. lasiorhini, M. baylisi, M. yamagutii, M. spearei, M. mawsonae and M. woodi) from the large intestines of their hosts formed a monophyletic assemblage with strong nodal support to the exclusion of M. dissimilis from the stomach of the swamp wallaby. Furthermore, the mitochondrial protein-coding genes provided greater insights into the diversity and phylogeny of the genus Macropostrongyloides; such data sets could potentially be used to elucidate the relationships among other parasitic nematodes of Australian marsupials.

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Chiridota heheva—the cosmopolitan holothurian

Marine Biodiversity ◽

10.1007/s12526-020-01128-x ◽

2020 ◽

Vol 50 (6) ◽

Author(s):

Elin A. Thomas ◽

Ruoyu Liu ◽

Diva Amon ◽

Jon T. Copley ◽

Adrian G. Glover ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Deep Sea ◽

Species Complex ◽

Hydrothermal Vents ◽

Novel Species ◽

Cold Seeps ◽

Ecological Studies ◽

Chemosynthetic Ecosystems ◽

Relationship Of ◽

The Relationship

AbstractChemosynthetic ecosystems have long been acknowledged as key areas of enrichment for deep-sea life, supporting hundreds of endemic species. Echinoderms are among the most common taxa inhabiting the periphery of chemosynthetic environments, and of these, chiridotid holothurians are often the most frequently observed. Yet, published records of chiridotids in these habitats are often noted only as supplemental information to larger ecological studies and several remain taxonomically unverified. This study therefore aimed to collate and review all known records attributed to Chiridota Eschscholtz, 1829, and to conduct the first phylogenetic analysis into the relationship of these chiridotid holothurians across global chemosynthetic habitats. We show that Chiridota heheva Pawson & Vance, 2004 is a globally widespread, cosmopolitan holothurian that occupies all three types of deep-sea chemosynthetic ecosystem—hydrothermal vents, cold seeps and organic falls—as an organic-enrichment opportunist. Furthermore, we hypothesise that C. heheva may be synonymous with another vent-endemic chiridotid, Chiridota hydrothermica Smirnov et al., 2000, owing to the strong morphological, ecological and biogeographical parallels between the two species, and predict that any chiridotid holothurians subsequently discovered at global reducing environments will belong to this novel species complex. This study highlights the importance of understudied, peripheral taxa, such as holothurians, to provide insights to biogeography, connectivity and speciation at insular deep-sea habitats.

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