Mitochondrial genomes of the jungle crow Corvus macrorhynchos (Passeriformes: Corvidae) from shed feathers and a phylogenetic analysis of genus Corvus using mitochondrial protein-coding genes

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

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The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp., and Dicyema japonicum

10.1101/282285 ◽

2018 ◽

Author(s):

Helen. E. Robertson ◽

Philipp. H. Schiffer ◽

Maximilian. J. Telford

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Small Subunit ◽

Mitochondrial Genomes ◽

List Type ◽

Protein Coding ◽

Protein Coding Genes ◽

Cell Layers

AbstractThe Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14,247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a divergent gene order compared to other metazoans. The data we present from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical across the Metazoa. The cox1 gene from dicyemid species has a series of conserved in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.Key FindingsWe report the first almost-complete mitochondrial genome from an orthonectid parasite, Intoshia linei, including 12 protein-coding genes; 20 tRNAs and putative sequences for large and small subunit rRNAs. We find that the I. linei mitochondrial genome is exceptionally AT-rich and has a novel gene order compared to other published metazoan mitochondrial genomes. These findings are indicative of the rapid rate of evolution that has occurred in the I. linei mitochondrial genome.We also report nine and eight protein-coding genes, respectively, from the dicyemid species Dicyema sp. and Dicyema japonicum, and use the cox1 genes from both species for phylogenetic inference of the internal phylogeny of the dicyemids.We find that the cox1 gene from dicyemids has a series of four conserved in-frame deletions which appear to be unique to this group.

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A novel mitogenomic rearrangement for Odorrana schmackeri (Anura: Ranidae) and phylogeny of Ranidae inferred from thirteen mitochondrial protein-coding genes

Amphibia-Reptilia ◽

10.1163/15685381-00002958 ◽

2014 ◽

Vol 35 (3) ◽

pp. 331-343 ◽

Cited By ~ 5

Author(s):

Yongmin Li ◽

Huabin Zhang ◽

Xiaoyou Wu ◽

Hui Xue ◽

Peng Yan ◽

...

Keyword(s):

Nucleotide Sequence ◽

Phylogenetic Relationships ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Mitochondrial Protein ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes

We determined the complete nucleotide sequence of the mitochondrial genome of Odorrana schmackeri (family Ranidae). The O. schmackeri mitogenome (18 302 bp) contained 13 protein-coding genes, 2 rRNA genes, 21 tRNA genes and a single control region (CR). In the new mitogenome, the distinctive feature is the loss of tRNA-His, which could be explained by a hypothesis of gene substitution. The new sequence data was used to assess the phylogenetic relationships among 23 ranid species mostly from China using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic analyses support two families (Ranidae, Dicroglossidae) for Chinese ranids. In Ranidae, we support the genus Amolops should be retained in the subfamily Raninae rather than in a distinct subfamily Amolopinae of its own. Meanwhile, the monophyly of the genus Odorrana was supported. Within Dicroglossidae, four tribes were well supported including Occidozygini, Dicroglossini, Limnonectini and Paini. More mitochondrial genomes and nuclear genes are required to decisively evaluate phylogenetic relationships of ranids.

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The mitochondrial genomes of the mesozoans Intoshia linei, Dicyema sp. and Dicyema japonicum

Parasitology Open ◽

10.1017/pao.2018.12 ◽

2018 ◽

Vol 4 ◽

Cited By ~ 1

Author(s):

Helen E. Robertson ◽

Philipp H. Schiffer ◽

Maximilian J. Telford

Keyword(s):

Mitochondrial Genome ◽

Gene Order ◽

Complete Mitochondrial Genome ◽

Mitochondrial Protein ◽

Mitochondrial Genes ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Protein Coding Genes ◽

Limited Support ◽

Cell Layers

Abstract The Dicyemida and Orthonectida are two groups of tiny, simple, vermiform parasites that have historically been united in a group named the Mesozoa. Both Dicyemida and Orthonectida have just two cell layers and appear to lack any defined tissues. They were initially thought to be evolutionary intermediates between protozoans and metazoans but more recent analyses indicate that they are protostomian metazoans that have undergone secondary simplification from a complex ancestor. Here we describe the first almost complete mitochondrial genome sequence from an orthonectid, Intoshia linei, and describe nine and eight mitochondrial protein-coding genes from Dicyema sp. and Dicyema japonicum, respectively. The 14 247 base pair long I. linei sequence has typical metazoan gene content, but is exceptionally AT-rich, and has a unique gene order. The data we have analysed from the Dicyemida provide very limited support for the suggestion that dicyemid mitochondrial genes are found on discrete mini-circles, as opposed to the large circular mitochondrial genomes that are typical of the Metazoa. The cox1 gene from dicyemid species has a series of conserved, in-frame deletions that is unique to this lineage. Using cox1 genes from across the genus Dicyema, we report the first internal phylogeny of this group.

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Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes

Zoologica Scripta ◽

10.1046/j.1463-6409.2000.00037.x ◽

2000 ◽

Vol 29 (2) ◽

pp. 83-88 ◽

Cited By ~ 21

Author(s):

Bjorn M. Ursing ◽

Kerryn E. Slack ◽

Ulfur Arnason

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Protein ◽

Protein Coding ◽

Protein Coding Genes

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Comparative mitochondrial genomes of four species of Sinopodisma and phylogenetic implications (Orthoptera, Melanoplinae)

ZooKeys ◽

10.3897/zookeys.969.49278 ◽

2020 ◽

Vol 969 ◽

pp. 23-42

Author(s):

Qiu Zhongying ◽

Chang Huihui ◽

Yuan Hao ◽

Huang Yuan ◽

Lu Huimeng ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Bayesian Inference ◽

Mitochondrial Genomes ◽

Rich Region ◽

Stem Loop ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenetic Implications ◽

Relationship Of ◽

Complete Mitochondrial Genomes

In this study, the whole mitochondrial genomes (mitogenomes) from four species were sequenced. The complete mitochondrial genomes of Sinopodisma pieli, S. houshana, S. qinlingensis, and S. wulingshanensis are 15,857 bp, 15,818 bp, 15,843 bp, and 15,872 bp in size, respectively. The 13 protein-coding genes (PCGs) begin with typical ATN codons, except for COXI in S. qinlingensis, which begins with ACC. The highest A+T content in all the sequenced orthopteran mitogenomes is 76.8% (S. qinlingensis), followed by 76.5% (S. wulingshanensis), 76.4% (S. pieli) and 76.4% (S. houshana) (measured on the major strand). The long polythymine stretches (T-stretch) in the A+T-rich region of the four species are not adjacent to the trnI locus but are inside the stem-loop sequences on the major strand. Moreover, several repeated elements are found in the A+T-rich region of the four species. Phylogenetic analysis based on 53 mitochondrial genomes using Bayesian Inference (BI) and Maximum Likelihood (ML) revealed that Melanoplinae (Podismini) was a monophyletic group; however, the monophyly of Sinopodisma was not supported. These data will provide important information for a better understanding of the phylogenetic relationship of Melanoplinae.

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Phylogenetic Analysis Within Tephritidae of Diptera Based on the Concatenated 13 Mitochondrial Protein Coding Genes of mt Genomes

Asian Journal of Animal and Veterinary Advances ◽

10.3923/ajava.2013.542.547 ◽

2013 ◽

Vol 8 (3) ◽

pp. 542-547 ◽

Cited By ~ 1

Author(s):

Qing-Qing Li ◽

Di-Yan Li ◽

Mo-Mo Li ◽

Hui Ye ◽

Wei Shi ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Mitochondrial Protein ◽

Protein Coding ◽

Protein Coding Genes

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The Complete Mitochondrial Genomes of Four Species in the Subfamily Limenitidinae (Lepidoptera, Nymphalidae) and a Phylogenetic Analysis

Insects ◽

10.3390/insects13010016 ◽

2021 ◽

Vol 13 (1) ◽

pp. 16

Author(s):

Ning Liu ◽

Lijun Fang ◽

Yalin Zhang

Keyword(s):

Phylogenetic Analysis ◽

Evolutionary Rate ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Gene Orientation ◽

Likelihood Analysis ◽

The Relationship ◽

Complete Mitochondrial Genomes

The complete mitogenomes of four species, Neptis thisbe, Neptis obscurior, Athyma zeroca, and Aldania raddei, were sequenced with sizes ranging from 15,172 bp (N. obscurior) to 16,348 bp (Al. raddei). All four mitogenomes display similar nucleotide content and codon usage of protein-coding genes (PCGs). Typical cloverleaf secondary structures are identified in 21 tRNA genes, while trnS1 (AGN) lacks the dihydrouridine (DHC) arm. The gene orientation and arrangement of the four mitogenomes are similar to that of other typical mitogenomes of Lepidoptera. The Ka/Ks ratio of 13 PCGs among 58 Limenitidinae species reveals that cox1 had the slowest evolutionary rate, while atp8 and nad6 exhibited a higher evolutionary rate. The phylogenetic analysis reveals that tribe-levels are well-supported monophyletic groups. Additionally, Maximum Likelihood analysis recovered the relationship (Parthenini + ((Chalingini + (Cymothoini + Neptini)) + (Adoliadini + Limenitidini))). However, a Bayesian analysis based on the same dataset recovered the relationship (Parthenini + (Adoliadini + ((Cymothoini + Neptini) + (Chalingini + Limenitidini)))). These results will offer valuable data for the future study of the phylogenetic relationships for Limenitidinae.

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