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

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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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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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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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 Flavoperla biocellata Chu, 1929 (Plecoptera: Perlidae) and the phylogenetic analyses of Plecoptera

PeerJ ◽

10.7717/peerj.8762 ◽

2020 ◽

Vol 8 ◽

pp. e8762

Author(s):

Yue Shen ◽

Yu-Zhou Du

Keyword(s):

Mitochondrial Genome ◽

Northern Hemisphere ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Trna Genes ◽

Protein Coding ◽

The Family ◽

Maximum Likelihood Methods ◽

Rna Genes

Of the roughly 400 species of Perlidae in the world, most species are widely distributed in the northern hemisphere, but a few can be found in South Africa and South America. There are only five species in the genus Flavoperla of the family Perlidae in China. To gain a better understanding of the architecture and evolution of mitochondrial genome in Flavoperla, the entire mitochondrial genome (mitogenome) of a Chinese Flavoperla biocellata Chu, 1929 from family Perlidae (Insecta: Plecoptera) was sequenced. The 15,805-bp long mitochondrial genome of F. biocellata contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and a putative control region (CR). The gene arrangement of F. biocellata was identical with that of other stoneflies and with the fly Drosophila yakuba. Most PCGs of F. biocellata used the standard ATN start codons and complete TAN termination codons. Twenty-one of the 22 tRNA genes exhibited cloverleaf secondary structures, but the dihydrouridine (DHU) arm of trnSer (AGN) was completely reduced. Phylogenetic analyses with both Bayesian inference (BI) and maximum likelihood methods (ML) generated similar topology, both supporting the monophyly of all stonefly families and the infraorder Systellognatha. The phylogenetic analysis based on mitochondrial genomic data from 30 stonefly species recovered a well-supported tree resolving higher-level relationships within Plecoptera. The northern hemisphere suborder Arctoperlaria divided into two groups, Euholognatha and Systellognatha. The southern hemisphere suborder Antarctoperlaria formed two clades: Eustheniidae+Diamphipnoidae and Austroperlidae+ Gripopterygidae; consistent with relationships proposed based on morphology. The final relationships within Plecoptera were recovered as (((Perlidae+(Perlodidae+Chloroperlidae))+(Pteronarcyidae+(Peltoperlidae+Styloperlidae))) +(Taeniopterygidae+(Capniidae+(Nemouridae+Notonemouridae))))+ (Gripopterygoidae+Eusthenioidae).

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First mitochondrial genome from Yponomeutidae (Lepidoptera, Yponomeutoidea) and the phylogenetic analysis for Lepidoptera

ZooKeys ◽

10.3897/zookeys.879.35101 ◽

2019 ◽

Vol 879 ◽

pp. 137-156

Author(s):

Mingsheng Yang ◽

Bingyi Hu ◽

Lin Zhou ◽

Xiaomeng Liu ◽

Yuxia Shi ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Start Codon ◽

Length Variation ◽

Protein Coding ◽

Conserved Sequence ◽

Protein Coding Genes ◽

The One ◽

Rna Genes

The complete mitochondrial genome (mitogenome) of Yponomeuta montanatus is sequenced and compared with other published yponomeutoid mitogenomes. The mitogenome is circular, 15,349 bp long, and includes the typical metazoan mitochondrial genes (13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes) and an A + T-rich region. All 13 protein-coding genes use a typical start codon ATN, the one exception being cox1, which uses CGA across yponomeutoid mitogenomes. Comparative analyses further show that the secondary structures of tRNAs are conserved, including loss of the Dihydorouidine (DHU) arm in trnS1 (AGN), but remarkable nucleotide variation has occurred mainly in the DHU arms and pseudouridine (TψC) loops. A + T-rich regions exhibit substantial length variation among yponomeutoid mitogenomes, and conserved sequence blocks are recognized but some of them are not present in all species. Multiple phylogenetic analyses confirm the position of Y. montanatus in Yponomeutoidea. However, the superfamily-level relationships in the Macroheterocera clade in Lepidoptera recovered herein show considerable difference with that recovered in previous mitogenomic studies, raising the necessity of extensive phylogenetic investigation when more mitogenomes become available for this clade.

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Complete mitochondrial genome of Echinophyllia aspera (Scleractinia, Lobophylliidae): Mitogenome characterization and phylogenetic positioning

ZooKeys ◽

10.3897/zookeys.793.28977 ◽

2018 ◽

Vol 793 ◽

pp. 1-14

Author(s):

Wentao Niu ◽

Shuangen Yu ◽

Peng Tian ◽

Jiaguang Xiao

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Molecular Data ◽

Start Codon ◽

Gene Arrangement ◽

Protein Coding ◽

Genome Data ◽

Mitogenome Sequence ◽

Complete Mitogenome ◽

First Time

Lack of mitochondrial genome data of Scleractinia is hampering progress across genetic, systematic, phylogenetic, and evolutionary studies concerning this taxon. Therefore, in this study, the complete mitogenome sequence of the stony coralEchinophylliaaspera(Ellis & Solander, 1786), has been decoded for the first time by next generation sequencing and genome assembly. The assembled mitogenome is 17,697 bp in length, containing 13 protein coding genes (PCGs), two transfer RNAs and two ribosomal RNAs. It has the same gene content and gene arrangement as in other Scleractinia. All genes are encoded on the same strand. Most of the PCGs use ATG as the start codon except for ND2, which uses ATT as the start codon. The A+T content of the mitochondrial genome is 65.92% (25.35% A, 40.57% T, 20.65% G, and 13.43% for C). Bayesian and maximum likelihood phylogenetic analysis have been performed using PCGs, and the result shows thatE.asperaclustered closely withSclerophylliamaxima(Sheppard & Salm, 1988), both of which belong to Lobophylliidae, when compared with species belonging to Merulinidae and other scleractinian taxa used as outgroups. The complete mitogenome ofE.asperaprovides essential and important DNA molecular data for further phylogenetic and evolutionary analyses of corals.

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Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia

PLoS ONE ◽

10.1371/journal.pone.0249446 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0249446

Author(s):

Jiantong Feng ◽

Yahong Guo ◽

Chengrui Yan ◽

Yingying Ye ◽

Xiaojun Yan ◽

...

Keyword(s):

Mitochondrial Genome ◽

Gene Rearrangement ◽

Complete Mitochondrial Genome ◽

Gene Arrangement ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Phylogenetic Implications ◽

The Family ◽

Phylogenetic Resolution ◽

Rna Genes

Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.

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The complete mitochondrial genome of Dysgonia stuposa (Lepidoptera: Erebidae) and phylogenetic relationships within Noctuoidea

PeerJ ◽

10.7717/peerj.8780 ◽

2020 ◽

Vol 8 ◽

pp. e8780

Author(s):

Yuxuan Sun ◽

Yeshu Zhu ◽

Chen Chen ◽

Qunshan Zhu ◽

Qianqian Zhu ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Intergenic Spacer ◽

Nucleotide Composition ◽

Start Codon ◽

Phylogenetic Position ◽

Protein Coding ◽

Conserved Sequence ◽

Rna Genes

To determine the Dysgonia stuposa mitochondrial genome (mitogenome) structure and to clarify its phylogenetic position, the entire mitogenome of D. stuposa was sequenced and annotated. The D. stuposa mitogenome is 15,721 bp in size and contains 37 genes (protein-coding genes, transfer RNA genes, ribosomal RNA genes) usually found in lepidopteran mitogenomes. The newly sequenced mitogenome contained some common features reported in other Erebidae species, e.g., an A+T biased nucleotide composition and a non-canonical start codon for cox1 (CGA). Like other insect mitogenomes, the D. stuposa mitogenome had a conserved sequence ‘ATACTAA’ in an intergenic spacer between trnS2 and nad1, and a motif ‘ATAGA’ followed by a 20 bp poly-T stretch in the A+T rich region. Phylogenetic analyses supported D. stuposa as part of the Erebidae family and reconfirmed the monophyly of the subfamilies Arctiinae, Catocalinae and Lymantriinae within Erebidae.

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The complete mitochondrial genome of the jumping grasshopper Sinopodisma pieli (Orthoptera: Acrididae) and the phylogenetic analysis of Melanoplinae

Zootaxa ◽

10.11646/zootaxa.4363.4.3 ◽

2017 ◽

Vol 4363 (4) ◽

pp. 506

Author(s):

HUAXUAN LIU ◽

LIYUN YAN ◽

GUOFANG JIANG

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Genome ◽

Ribosomal Rna ◽

Complete Mitochondrial Genome ◽

Taxonomic Status ◽

Polymerase Chain Reaction Method ◽

Ribosomal Rna Genes ◽

Start Codon ◽

Trna Genes ◽

Rna Genes

In this study, we reported the complete mitochondrial genome (mitogenome) of Sinopodisma pieli by polymerase chain reaction method for the first time, the type species of the genus Sinopodisma. Its mitogenome was a circular DNA molecule of 15,625 bp in length, with 76.0% A+T, and contained 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes and one A+T control region. The overall base composition of the S. pieli mitogenome was 42.8% for A, 33.2% for T, 13.5% for C, and 10.5% for G, respectively. All 13 mitochondrial PCGs shared the start codon ATN. Twelve of the PCGs ended with termination codon TAA and TAG, while cytochrome coxidase subunit 1 (COI) utilized an incomplete T as terminator codon. All tRNA genes could be folded into the typical cloverleaf secondary structure, except trnS(AGN) lacking of dihydrouridine arm. The sizes of the large and small ribosomal RNA genes were 1379 bp and 794 bp, respectively. The A+T rich region was 798 bp in length and contained 88.5% AT content. A phylogenetic analysis based on 13 PCGs by using Bayesian inference (BI) and maximum likelihood (ML) revealed that Sinopodisma is not monophyletic group. We think that the name and taxonomic status of S. tsinlingensis are right, and it should not be moved into the genus Pedopodisma. These data will provide important information for a better understanding of the population genetics and species identification for Sinopodisma.

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Complete mitochondrial genome of Cultellus attenuatus and its phylogenetic implications

10.21203/rs.3.rs-868770/v1 ◽

2021 ◽

Author(s):

Haikun Li ◽

Ruihai Yu ◽

Peizhen Ma ◽

Chunhua Li

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Mitochondrial Genes ◽

Coding Region ◽

Protein Coding ◽

Sinonovacula Constricta ◽

Transfer Rnas ◽

Phylogenetic Implications ◽

Solen Grandis ◽

Relationship Of

Abstract The complete mitochondrial genome of Cultellus attenuates, a new aquaculture species, was sequenced and compared with mitogenomes from seven species of Heterodonta bivalve mollusk in the gene bank. The mitochondrial genome of C. attenuatus is 16888bp in length and contains 36 genes, including 12 protein-coding genes, 2 ribosomal RNAs and 22 transfer RNAs, and all genes are encoded on the same strand. In comparison with C. attenuates, the mitochondrial genes of the Sinonovacula constricta from the same family were not rearranged, but those of six other species from different family were rearranged to different degrees. The largest non-coding region of C. attenuatus is 1173bp in length and with the A + T content of 68.24%, located between nad2 and trnK. The results of phylogenetic analysis show that the C. attenuates and the S. constricta belonging to Cultellidae cluster into one branch while two species of Solenidae ( Solen grandis and Solen strictus) are clustering as their sister taxon. These data not only contribute to the understanding of the phylogenetic relationship of the Heterodonta, but also serve as a resource for the development of the genetic markers in aquaculture.

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