The complete mitochondrial genome of the Emei black chicken (Gallus gallus) and its phylogenetic analyses

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

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Complete mitochondrial genome sequence of Labriocimbex sinicus, a new genus and new species of Cimbicidae (Hymenoptera) from China

PeerJ ◽

10.7717/peerj.7853 ◽

2019 ◽

Vol 7 ◽

pp. e7853 ◽

Cited By ~ 1

Author(s):

Yuchen Yan ◽

Gengyun Niu ◽

Yaoyao Zhang ◽

Qianying Ren ◽

Shiyu Du ◽

...

Keyword(s):

Mitochondrial Genome ◽

New Genus ◽

High Throughput Sequencing ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Sister Group ◽

Morphological Characters ◽

Trna Genes ◽

Sequencing Data ◽

Link Type

Labriocimbex sinicus Yan & Wei gen. et sp. nov. of Cimbicidae is described. The new genus is similar to Praia Andre and Trichiosoma Leach. A key to extant Holarctic genera of Cimbicinae is provided. To identify the phylogenetic placement of Cimbicidae, the mitochondrial genome of L. sinicus was annotated and characterized using high-throughput sequencing data. The complete mitochondrial genome of L. sinicus was obtained with a length of 15,405 bp (GenBank: MH136623; SRA: SRR8270383) and a typical set of 37 genes (22 tRNAs, 13 PCGs, and two rRNAs). The results demonstrated that all PCGs were initiated by ATN codon, and ended with TAA or T stop codons. The study reveals that all tRNA genes have a typical clover-leaf secondary structure, except for trnS1. Remarkably, the secondary structures of the rrnS and rrnL of L. sinicus were much different from those of Corynis lateralis. Phylogenetic analyses verified the monophyly and positions of the three Cimbicidae species within the superfamily Tenthredinoidea and demonstrated a relationship as (Tenthredinidae + Cimbicidae) + (Argidae + Pergidae) with strong nodal supports. Furthermore, we found that the generic relationships of Cimbicidae revealed by the phylogenetic analyses based on COI genes agree quite closely with the systematic arrangement of the genera based on the morphological characters. Phylogenetic tree based on two methods shows that L. sinicus is the sister group of Praia with high support values. We suggest that Labriocimbex belongs to the tribe Trichiosomini of Cimbicinae based on adult morphology and molecular data. Besides, we suggest to promote the subgenus Asitrichiosoma to be a valid genus.

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Phylogenetic relationships and taxonomic position of genus Hyperacrius (Rodentia: Arvicolinae) from Kashmir based on evidences from analysis of mitochondrial genome and study of skull morphology

PeerJ ◽

10.7717/peerj.10364 ◽

2020 ◽

Vol 8 ◽

pp. e10364

Author(s):

Natalia I. Abramson ◽

Fedor N. Golenishchev ◽

Semen Yu. Bodrov ◽

Olga V. Bondareva ◽

Evgeny A. Genelt-Yanovskiy ◽

...

Keyword(s):

Mitochondrial Genome ◽

De Novo ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Morphological Characters ◽

Molecular Data ◽

Phylogenetic Position ◽

Skull Morphology ◽

Protein Coding ◽

Protein Coding Genes

In this article, we present the nearly complete mitochondrial genome of the Subalpine Kashmir vole Hyperacrius fertilis (Arvicolinae, Cricetidae, Rodentia), assembled using data from Illumina next-generation sequencing (NGS) of the DNA from a century-old museum specimen. De novo assembly consisted of 16,341 bp and included all mitogenome protein-coding genes as well as 12S and 16S RNAs, tRNAs and D-loop. Using the alignment of protein-coding genes of 14 previously published Arvicolini tribe mitogenomes, seven Clethrionomyini mitogenomes, and also Ondatra and Dicrostonyx outgroups, we conducted phylogenetic reconstructions based on a dataset of 13 protein-coding genes (PCGs) under maximum likelihood and Bayesian inference. Phylogenetic analyses robustly supported the phylogenetic position of this species within the tribe Arvicolini. Among the Arvicolini, Hyperacrius represents one of the early-diverged lineages. This result of phylogenetic analysis altered the conventional view on phylogenetic relatedness between Hyperacrius and Alticola and prompted the revision of morphological characters underlying the former assumption. Morphological analysis performed here confirmed molecular data and provided additional evidence for taxonomic replacement of the genus Hyperacrius from the tribe Clethrionomyini to the tribe Arvicolini.

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Complete mitochondrial genome sequence of the Himalayan Griffon,Gyps himalayensis(Accipitriformes: Accipitridae): Sequence, structure, and phylogenetic analyses

Ecology and Evolution ◽

10.1002/ece3.5433 ◽

2019 ◽

Vol 9 (15) ◽

pp. 8813-8828 ◽

Cited By ~ 4

Author(s):

Lichun Jiang ◽

Liqing Peng ◽

Min Tang ◽

Zhangqiang You ◽

Min Zhang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Genome Sequence ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Sequence Structure ◽

Mitochondrial Genome Sequence ◽

Complete Mitochondrial Genome Sequence

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Complete mitochondrial genome of the Longsheng Feng chicken (Gallus gallus)

Mitochondrial DNA Part B ◽

10.1080/23802359.2020.1791753 ◽

2020 ◽

Vol 5 (3) ◽

pp. 2911-2912

Author(s):

Jingjing Gu ◽

Sheng Li

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Gallus Gallus

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The complete mitochondrial genome of the Sichuan white goose and its phylogenetic analyses

Mitochondrial DNA Part B ◽

10.1080/23802359.2019.1565967 ◽

2019 ◽

Vol 4 (1) ◽

pp. 754-755

Author(s):

Qian Lin ◽

Gui-Tao Jiang ◽

Qiu-Zhong Dai ◽

Xu Zhang ◽

Xuan Huang ◽

...

Keyword(s):

Mitochondrial Genome ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome

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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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Characterization and Analysis of the Mitochondrial Genome of Common Bean (Phaseolus vulgaris) by Comparative Genomic Approaches

International Journal of Molecular Sciences ◽

10.3390/ijms21113778 ◽

2020 ◽

Vol 21 (11) ◽

pp. 3778

Author(s):

Changwei Bi ◽

Na Lu ◽

Yiqing Xu ◽

Chunpeng He ◽

Zuhong Lu

Keyword(s):

Phaseolus Vulgaris ◽

Mitochondrial Genome ◽

Common Bean ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Rrna Genes ◽

Comparative Genomic ◽

Trna Genes ◽

Leguminous Plants ◽

The Common

The common bean (Phaseolus vulgaris) is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of P. vulgaris, its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes. Among the 31 PCGs, four genes (mttB, nad1, nad4L, and rps10) use ACG as initiation codons, which are altered to standard initiation codons by RNA editing. In addition, the termination codon CGA in the ccmFC gene is converted to UGA. Selective pressure analysis indicates that the ccmB, ccmFC, rps1, rps10, and rps14 genes were under evolutionary positive selection. The proportions of five amino acids (Phe, Leu, Pro, Arg, and Ser) in the whole amino acid profile of the proteins in each mitogenome can be used to distinguish angiosperms from gymnosperms. Phylogenetic analyses show that P. vulgaris is evolutionarily closer to the Glycininae than other leguminous plants. The results of the present study not only provide an important opportunity to conduct further genomic breeding studies in the common bean, they also provide valuable information for future evolutionary and molecular studies of leguminous plants.

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