Two complete mitochondrial genomes of Crocodylus and implications for crocodilians phylogeny

AbstractThe complete mitochondrial (mt) genomes of two crocodilians: Crocodylus palustris and Crocodylus mindorensis, were sequenced in order to examine their gene and genome features. Additionally, we intended to increase the amount of molecular data suitable for phylogenetic analysis. Their gene orders conform to other crocodilians that have been sequenced, except the arrangement of two tRNA genes differ from other vertebrates, showing that the gene order of crocodilians is remarkably conserved. Phylogenetic analyses (maximum likelihood, Bayesian inference) based on the mt protein-coding genes at the nucleotide level were performed among crocodilians for which complete mt genomes were available. The results suggest that the gharial (Gavialis gangeticus) joins the false gharial (Tomistoma schlegelii) on a common branch, that constitutes a sister group to traditional Crocodylidae. In this report, Mecistops cataphractus is evidently most closely related to Osteolaemus tetraspis. They are isolated as sister taxon from the main clades in Crocodylus. Regarding Paleosuchus, it appears as sister group to Caiman within the Alligatoridae. In particular, relationships among species of Crocodylus (true crocodiles) are discussed.

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Three Complete Mitochondrial Genomes of Erotylidae (Coleoptera: Cucujoidea) with Higher Phylogenetic Analysis

Insects ◽

10.3390/insects12060524 ◽

2021 ◽

Vol 12 (6) ◽

pp. 524

Author(s):

Jing Liu ◽

Yuyu Wang ◽

Ruyue Zhang ◽

Chengmin Shi ◽

Weicheng Lu ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Genomic Analysis ◽

Sister Group ◽

Mitochondrial Genomes ◽

Protein Coding ◽

Transfer Rnas ◽

Next Generation Sequencing Technology ◽

The Family ◽

Mt Genome ◽

Complete Mitochondrial Genomes

The family Erotylidae belongs to the superfamily Cucujoidea, which are phytophagous and mycophagous. So far, only two representative complete mitochondrial (mt) genomes of Erotylidae have been sequenced. Mitochondrial genomes of Tritoma metasobrina, Neotriplax arisana, and Episcapha opaca, which all belong to the subfamily Erotylinae, were sequenced using next-generation sequencing technology to better understand the diversity of mt genomes of Erotylidae. A comparative mt genomic analysis was conducted on the three sequenced representatives of Erotylinae and Languriinae sp. (Languriinae). The size of the complete mt genome of the 4 species ranged from 15,581 bp to 16,502 bp in length, including 37 genes (13 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs) and the control region. The arrangements of their mt genomes are highly consistent with other Coleoptera species. The start codons of two PCGs (ND1 and ND5) and the stop codons of one PCG (ATP8) were illustrated differences between Languriinae sp. and the other three species. All tRNAs of these 4 species exhibited cloverleaf secondary structures except that the dihydorouridine (DHU) arm of tRNASer(AGN) was absent. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods all supported that Erotylidae as monophyletic. Erotylinae was monophyletic being the sister group to Xenocelinae. Languriinae was closely related to ‘Erotylinae-Xenocelinae’. Our results recovered Languriinae nested within Erotylidae.

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Three Complete Mitochondrial Genomes of Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis (Insecta: Phasmatodea) and Their Phylogeny

Insects ◽

10.3390/insects12090779 ◽

2021 ◽

Vol 12 (9) ◽

pp. 779 ◽

Cited By ~ 1

Author(s):

Ke-Ke Xu ◽

Qing-Ping Chen ◽

Sam Pedro Galilee Ayivi ◽

Jia-Yin Guan ◽

Kenneth B. Storey ◽

...

Keyword(s):

Sister Group ◽

Recent Common Ancestor ◽

Mitochondrial Genomes ◽

Sister Group Relationship ◽

Protein Coding ◽

Most Recent Common Ancestor ◽

Stick Insects ◽

Long Time ◽

Relationship Of ◽

Complete Mitochondrial Genomes

Insects of the order Phasmatodea are mainly distributed in the tropics and subtropics and are best known for their remarkable camouflage as plants. In this study, we sequenced three complete mitochondrial genomes from three different families: Orestes guangxiensis, Peruphasma schultei, and Phryganistria guangxiensis. The lengths of the three mitochondrial genomes were 15,896 bp, 16,869 bp, and 17,005 bp, respectively, and the gene composition and structure of the three stick insects were identical to those of the most recent common ancestor of insects. The phylogenetic relationships among stick insects have been chaotic for a long time. In order to discuss the intra- and inter-ordinal relationship of Phasmatodea, we used the 13 protein-coding genes (PCGs) of 85 species for maximum likelihood (ML) and Bayesian inference (BI) analyses. Results showed that the internal topological structure of Phasmatodea had a few differences in both ML and BI trees and long-branch attraction (LBA) appeared between Embioptera and Zoraptera, which led to a non-monophyletic Phasmatodea. Consequently, after removal of the Embioptera and Zoraptera species, we re-performed ML and BI analyses with the remaining 81 species, which showed identical topology except for the position of Tectarchus ovobessus (Phasmatodea). We recovered the monophyly of Phasmatodea and the sister-group relationship between Phasmatodea and Mantophasmatodea. Our analyses also recovered the monophyly of Heteropterygidae and the paraphyly of Diapheromeridae, Phasmatidae, Lonchodidae, Lonchodinae, and Clitumninae. In this study, Peruphasma schultei (Pseudophasmatidae), Phraortes sp. YW-2014 (Lonchodidae), and species of Diapheromeridae clustered into the clade of Phasmatidae. Within Heteropterygidae, O. guangxiensis was the sister clade to O. mouhotii belonging to Dataminae, and the relationship of (Heteropteryginae + (Dataminae + Obriminae)) was recovered.

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Mitochondrial Genomes of Hestina persimilis and Hestinalis nama (Lepidoptera, Nymphalidae): Genome Description and Phylogenetic Implications

Insects ◽

10.3390/insects12080754 ◽

2021 ◽

Vol 12 (8) ◽

pp. 754

Author(s):

Yupeng Wu ◽

Hui Fang ◽

Jiping Wen ◽

Juping Wang ◽

Tianwen Cao ◽

...

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Mitochondrial Genomes ◽

Comparative Genomic ◽

Trna Genes ◽

Cox1 Gene ◽

Protein Coding ◽

Phylogenetic Implications ◽

Typical Composition

In this study, the complete mitochondrial genomes (mitogenomes) of Hestina persimilis and Hestinalis nama (Nymphalidae: Apaturinae)were acquired. The mitogenomes of H. persimilis and H. nama are 15,252 bp and 15,208 bp in length, respectively. These two mitogenomes have the typical composition, including 37 genes and a control region. The start codons of the protein-coding genes (PCGs) in the two mitogenomes are the typical codon pattern ATN, exceptCGA in the cox1 gene. Twenty-one tRNA genes show a typical clover leaf structure, however, trnS1(AGN) lacks the dihydrouridine (DHU) stem. The secondary structures of rrnL and rrnS of two species were predicted, and there are several new stem loops near the 5’ of rrnL secondary structure. Based on comparative genomic analysis, four similar conservative structures can be found in the control regions of these two mitogenomes. The phylogenetic analyses were performed on mitogenomes of Nymphalidae. The phylogenetic trees show that the relationships among Nymphalidae are generally identical to previous studies, as follows: Libytheinae\Danainae + ((Calinaginae + Satyrinae) + Danainae\Libytheinae + ((Heliconiinae + Limenitidinae) + (Nymphalinae + (Apaturinae + Biblidinae)))). Hestinalisnama isapart fromHestina, andclosely related to Apatura, forming monophyly.

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The Complete Mitochondrial Genomes of two Flying Fishes, Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii

Indian Journal of Animal Research ◽

10.18805/ijar.b-1119 ◽

2020 ◽

Author(s):

Liyan Qu ◽

Heng Zhang ◽

Fengying Zhang ◽

Wei Wang ◽

Fenghua Tang ◽

...

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Rrna Genes ◽

Phylogenetic Position ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Protein Coding ◽

Protein Coding Genes ◽

Flying Fishes ◽

Complete Mitochondrial Genomes

Background: Genome-scale approaches have played a significant role in the analysis of evolutionary relationships. Because of rich polymorphisms, high evolutionary rate and rare recombination, mitochondrial DNA sequences are commonly considered as effective markers for estimating population genetics, evolutionary and phylogenetic relationships. Flying fishes are important components of epipelagic ecosystems. Up to now, only few complete mitochondrial genomes of flying fishes have been reported. In the present study, the complete mitochondrial DNA sequences of the Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii had been determined. Methods: Based on the published mitogenome of Cheilopogon atrisignis (GenBank: KU360729), fifteen pairs of primers were designed by the software Primer Premier 5.0 to get the complete mitochondrial genomes of two flying fishes. According to the reported data, the phylogenetic position of two flying fishes were detected using the conserved 12 protein-coding genes. Result: The complete mitochondrial genomes of Cheilopogon pinnatibarbatus japonicus and Hirundichthys rondeletii are determined. They are 16532bp and 16525bp in length, respectively. And they both consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The OL regions are conserved in these two flying fishes and might have no function. From the tree topologies, we found C.p. japonicus and H. rondeletii clustered in a group. The findings of the study would contribute to the phylogenetic classification and the genetic conservation management of C.p. japonicus and H. rondeletii.

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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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Comparative Mitogenomic Analysis of the Eurydema Genus in the Context of Representative Pentatomidae (Hemiptera: Heteroptera) Taxa

Journal of Insect Science ◽

10.1093/jisesa/iez122 ◽

2019 ◽

Vol 19 (6) ◽

Cited By ~ 1

Author(s):

Wanqing Zhao ◽

Qing Zhao ◽

Min Li ◽

Jiufeng Wei ◽

Xianhong Zhang ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Sister Group ◽

Mitochondrial Genomes ◽

Rna Structures ◽

Protein Coding ◽

Transfer Rnas ◽

The Family ◽

Maximum Likelihood Methods

Abstract The family Pentatomidae, the largest within the superfamily Pentatomoidae, comprises about 5,000 species; many of which are economically important pests. Although the phylogeny of Pentatomidae species has been studied using various molecular markers, their phylogenetic relationships remain controversial. Recently, mitochondrial genomes (mitogenomes) have been extensively employed to examine the phylogenetics and evolution of different insects, and in this study, we sequenced complete/near-complete mitochondrial genomes from five shield bug species of Eurydema to gain a better understanding of phylogenetic relationships in the Pentatomidae. The five mitogenomes ranged in length from 15,500 to 16,752 bp and comprised 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region. We compared mitogenomic characteristics of the Pentatomidae and constructed phylogenetic trees using Bayesian inference and maximum likelihood methods. Our results showed that gene arrangements, base composition, start/stop codons, gene overlaps, and RNA structures were conserved within the Pentatomidae and that congeneric species shared more characteristics. Saturation and heterogeneity analyses revealed that our PCGs and PCGRNA datasets were valid for phylogenetic analysis. Phylogenetic analyses showed consistent topologies based on BI and ML methods. These analyses strongly supported that Eurydema species belong to the tribe Strachiini, and formed a sister group with Pentatomini. The relationships among Eurydema species were shown to be consistent with their morphological features. (Strachiini + Pentatomini) was found to be a stable sibling of the clade comprising Cappaeini, Graphosomini, and Carpocorini. Furthermore, our results indicated that Graphosoma rubrolineatum (Heteroptera: Pentatomidae) belongs to the Pentatominae and not the Podopinae.

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Mitochondrial DNA Variability withinUromastyx ornata philbyi(Agamidae: Squamata) from Southwestern Saudi Arabia

Comparative and Functional Genomics ◽

10.1155/2012/851379 ◽

2012 ◽

Vol 2012 ◽

pp. 1-8 ◽

Cited By ~ 1

Author(s):

Sayed A. M. Amer ◽

Mohamed M. Ahmed ◽

Thomas M. Wilms ◽

Mohammed Shobrak ◽

Yoshinori Kumazawa

Keyword(s):

Saudi Arabia ◽

Mitochondrial Dna ◽

Sister Group ◽

Molecular Data ◽

Sister Group Relationship ◽

Trna Genes ◽

Loop Structure ◽

Protein Coding ◽

Nadh Dehydrogenase Subunit 2 ◽

The One

Approximately 2.4 kbp of mitochondrial DNA was sequenced from 9 individuals ofUromastyx ornata philbyioriginating from Taif, Namas, Al-Baha, and Jazan in southwestern Saudi Arabia. The sequenced regions cover eight tRNA genes (tRNAGln,tRNAIle,tRNAMet,tRNATrp,tRNAAla,tRNAAsn,tRNACys, andtRNATyr) and two protein-coding genes (NADH dehydrogenase subunit 2 and cytochromeb).U. ornata philbyihad an insertion of 170 bp length betweentRNAGlnandtRNAIlegenes. The first 128 bp of this insertion was similar to the one identified earlier inU. ornata ornataand can be folded into a stem-and-loop structure, which was less stable inU. ornata philbyithan inU. ornata ornata, or the secondtRNAGlngene. The next 42 bp of the insertion was unique inU. ornata philbyiand additionally retained a stable stem-and-loop structure. Most base substitutions found in the sequenced genes were synonymous transitions rather than transversions. Tree analyses supported the sister group relationship between the twoU. ornatasubspecies and dividedU. ornata philbyiinto two groups: Taif+Namas group in the east of Sarawat and Al-Baha+Jazan group in the west of Sarawat. These molecular data are in agreement with current classification ofU. ornata.

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Characterization of the complete mitochondrial genome of Myrmus lateralis (Heteroptera, Rhopalidae) and its implication for phylogenetic analyses

ZooKeys ◽

10.3897/zookeys.1070.72742 ◽

2021 ◽

Vol 1070 ◽

pp. 13-30

Author(s):

Wanqing Zhao ◽

Dajun Liu ◽

Qian Jia ◽

Xin Wu ◽

Hufang Zhang

Keyword(s):

Phylogenetic Trees ◽

Phylogenetic Analyses ◽

Complete Mitochondrial Genome ◽

Purifying Selection ◽

Sister Group ◽

Start Codon ◽

Rrna Genes ◽

Trna Genes ◽

Protein Coding ◽

Inference Methods

Mitochondrial genomes (mitogenomes) are widely used in research studies on phylogenetic relationships and evolutionary history. Here, we sequenced and analyzed the mitogenome of the scentless plant bug Myrmus lateralis Hsiao, 1964 (Heteroptera, Rhopalidae). The complete 17,309 bp genome encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region. The mitogenome revealed a high A+T content (75.8%), a positive AT-skew (0.092), and a negative GC-skew (–0.165). All 13 PCGs were found to start with ATN codons, except for cox1, in which TTG was the start codon. The Ka/Ks ratios of 13 PCGs were all lower than 1, indicating that purifying selection evolved in these genes. All tRNAs could be folded into the typical cloverleaf secondary structure, except for trnS1 and trnV, which lack dihydrouridine arms. Phylogenetic trees were constructed and analyzed based on the PCG+rRNA from 38 mitogenomes, using maximum likelihood and Bayesian inference methods, showed that M. lateralis and Chorosoma macilentum Stål, 1858 grouped together in the tribe Chorosomatini. In addition, Coreoidea and Pyrrhocoroidea were sister groups among the superfamilies of Trichophora, and Rhopalidae was a sister group to Alydidae + Coreidae.

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Ten complete mitochondrial genomes of Gymnocharacini (Stethaprioninae, Characiformes): evolutionary relationships and a repetitive element in the Control Region (D-loop)

10.1101/2020.10.26.355867 ◽

2020 ◽

Author(s):

Rubens Pasa ◽

Fabiano Bezerra Menegídio ◽

Igor Henrique Rodrigues-Oliveira ◽

Iuri Batista da Silva ◽

Matheus Lewi Cruz Bonaccorsi de Campos ◽

...

Keyword(s):

Neotropical Region ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Raw Data ◽

Protein Coding ◽

Protein Coding Genes ◽

Species Complexes ◽

D Loop ◽

Complete Mitochondrial Genomes

AbstractWe are presenting the complete mitogenomes of eight fish species/cytotypes from Neotropical region belonging to the Astyanax and Psalidodon genus: A. aeneus, A. altiparanae, P. fasciatus (from two locations - Upper Paraná and São Francisco river basins), A. lacustris, P. rivularis (two cytotypes) and P. rioparanaibano. We perform the whole-genome sequencing for six of these species in a Novaseq 6000 - by Illumina, meanwhile two genomes were assembled from raw data available in databases. Plus, we reassembled and annotated the mitochondrial genomes for A. mexicanus and P. paranae, both already described and with raw data available online. All the genomes presented the same organization, with 13 protein-coding genes, 22 tRNA genes and two rRNA genes. Aiming to contribute to the understanding of the several cryptic species complexes and phylogeny of the genus, we perform Bayesian analysis using the 13 protein-coding genes from these species, plus Deuterodon giton and using a Brycon species as outgroup.

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The complete mitochondrial genomes of two erythroneurine leafhoppers (Hemiptera, Cicadellidae, Typhlocybinae, Erythroneurini) with assessment of the phylogenetic status and relationships of tribes of Typhlocybinae

ZooKeys ◽

10.3897/zookeys.1037.63671 ◽

2021 ◽

Vol 1037 ◽

pp. 137-159

Author(s):

Xiaoxiao Chen ◽

Can Li ◽

Yuehua Song

Keyword(s):

Nucleotide Diversity ◽

Molecular Data ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Morphological Classification ◽

Protein Coding ◽

Phylogenetic Status ◽

The Relationship ◽

Complete Mitochondrial Genomes

The number and classification of tribes in the leafhopper subfamily Typhlocybinae are not yet fully clear, and molecular data has recently been used to help resolve the problem. In this study, the mitochondrial genomes of Mitjaevia shibingensis Chen, Song & Webb, 2020 and M. dworakowskae Chen, Song & Webb, 2020 of the tribe Erythroneurini (Cicadellidae, Typhlocybinae) were sequenced. Most protein-coding genes (PCGs) start with ATN and end with TAA or TAG, and the AT content of these three codons were found differ from previous results that show that the first codon has the highest incidence. Two rRNA genes are highly conserved, and the AT content in 16S is higher than that of 12S. The nucleotide diversity and genetic distance among 13 PCGs of the four tribes from Typhlocybinae show that Empoascini nucleotide diversity is significantly less than in the other three tribes, and have the largest distance from the others, while Typhlocybini and Zyginellini have the smallest distance, indicating that the relationship between the two is the closest. The nad2, nad4, nad4L, and nad5 genes have greater nucleotide diversity, showing potential for use as the main markers for species identification. The phylogenetic analysis yielded a well-supported topology with most branches receiving maximum support and a few branches pertaining to relationships within Zyginellini and Typhlocybini receiving lower support. The species of these two tribes are intertwined, and it was impossible to resolve them into separate branches. In addition, the tribes Empoascini and Erythroneurini were recovered as monophyletic, and Alebrini was placed at the base of the tree as the most primitive. These results are broadly in line with other molecular phylogenetical studies which differ from traditional morphological classification.

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