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Complete mitochondrial genome of Eurasian Hobby Falco subbuteo (Falconiformes:Falconidae) and phylogenetic analyses.

ABSTRACT: The Eurasian Hobby Falco subbuteo is a Falco bird belonging to the group Falconiformes, and was listed in Appendices II of the Convention on International Trade in Endangered Species of Wild Fauna and Flora and listed as a Class II protected species on China's List of Wildlife under Special State Protection. In this study, the complete mitogenome of F. subbuteo was determined. The mitochondrial DNA is packaged in a compact 17,678 based pair (bp) circular molecule with A + T content of 54.70%. It contains 37 typical mitochondrial genes, including 13 protein-coding genes, 2 rRNAs and 22 tRNAs, and 2 non-coding regions (D-Loop). We reconstructed a phylogenetic tree based on mitogenome sequences of 13 Falconidae species and one outgroup. Phylogenetic analysis indicated that F. subbuteo was a sister taxon to F. cuvierii with node support 100. The new mitogenome data would provide useful information for application in conservation genetics and further clarify the phylogenetic evolution of this species.

SUBMITTER: Gou X

PROVIDER: S-EPMC8008880 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Phylogenetic analyses of complete mitochondrial genome sequences suggest a basal divergence of the enigmatic rodent Anomalurus.

Project description:BACKGROUND: Phylogenetic relationships between Lagomorpha, Rodentia and Primates and their allies (Euarchontoglires) have long been debated. While it is now generally agreed that Rodentia constitutes a monophyletic sister-group of Lagomorpha and that this clade (Glires) is sister to Primates and Dermoptera, higher-level relationships within Rodentia remain contentious. RESULTS: We have sequenced and performed extensive evolutionary analyses on the mitochondrial genome of the scaly-tailed flying squirrel Anomalurus sp., an enigmatic rodent whose phylogenetic affinities have been obscure and extensively debated. Our phylogenetic analyses of the coding regions of available complete mitochondrial genome sequences from Euarchontoglires suggest that Anomalurus is a sister taxon to the Hystricognathi, and that this clade represents the most basal divergence among sampled Rodentia. Bayesian dating methods incorporating a relaxed molecular clock provide divergence-time estimates which are consistently in agreement with the fossil record and which indicate a rapid radiation within Glires around 60 million years ago. CONCLUSION: Taken together, the data presented provide a working hypothesis as to the phylogenetic placement of Anomalurus, underline the utility of mitochondrial sequences in the resolution of even relatively deep divergences and go some way to explaining the difficulty of conclusively resolving higher-level relationships within Glires with available data and methodologies.

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The complete mitochondrial genome of the Dongan black chicken and its phylogenetic analyses.

Project description:Dongan black chicken (Gallus gallus domesticus, DBC) is one of the famous native breed of Hunan province in China. The complete mitochondrial genome sequence plays an important role in the accurate determination of phylogenetic relationships among metazoans. It is the first time that the complete mitochondrial genome sequence of the DBC was reported. The total length of the mtDNA is 16,785?bp, It contains the typical structure, including 22 transfer RNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 non-coding control region (D-loop region). The overall composition of the mtDNA was estimated to be 30.27% for A, 23.78% for T, 32.46% for C, and 13.49% for G. Phylogenetic analyses using N-J computational algorithms showed that the analyzed 21 Galliformes species are divided into four major clades: Phasianidae, Numidiidae, Odontophoridae, and Megapodiidae. In addition, our work confirmed that DBC and Taoyuan chicken (TYC) have a close genetic relationship with fellow tribal members Xuefeng black-boned chicken (XBC) and Huang Lang chicken (HLC). Meanwhile, we also found that DBC and TYC have highly similar genetic relationship. This work will provide an important data set for the study of genetic mechanism of chicken in Hunan province.

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The complete mitochondrial genome of Bothrogonia qiongana (Hemiptera: Cicadellidae) with phylogenetic analyses.

Project description:The species of Bothrogonia qiongana was reported by Yang and Li in 1980. The mitogenome is 15,788 bp in length, including 37 genes and a control region, with an overall A + T content of 76.9%. Most of the PCGs start with ATN (ATA, ATC, ATT, ATG), but ND5 starts with TTG. All PCGs used TAA or TAG as stop codon except COX2 which is using incomplete single T--. The phylogenetic tree was reconstructed based on B. qiongana and 24 reference species, which is consistent with traditional taxonomy.

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Characterization of the Complete Mitochondrial Genome of Harpalus sinicus and Its Implications for Phylogenetic Analyses.

Project description:In this study, we report the complete mitochondrial genome of Harpalus sinicus (occasionally named as the Chinese ground beetle) which is the first mitochondrial genome for Harpalus. The mitogenome is 16,521 bp in length, comprising 37 genes, and a control region. The A + T content of the mitogenome is as high as 80.6%. A mitochondrial origins of light-strand replication (OL)-like region is found firstly in the insect mitogenome, which can form a stem-loop hairpin structure. Thirteen protein-coding genes (PCGs) share high homology, and all of them are under purifying selection. All tRNA genes (tRNAs) can be folded into the classic cloverleaf secondary structures except tRNA-Ser (GCU), which lacks a dihydrouridine (DHU) stem. The secondary structure of two ribosomal RNA genes (rRNAs) is predicted based on previous insect models. Twelve types of tandem repeats and two stem-loop structures are detected in the control region, and two stem-loop structures may be involved in the initiation of replication and transcription. Additionally, phylogenetic analyses based on mitogenomes suggest that Harpalus is an independent lineage in Carabidae, and is closely related to four genera (Abax, Amara, Stomis, and Pterostichus). In general, this study provides meaningful genetic information for Harpalus sinicus and new insights into the phylogenetic relationships within the Carabidae.

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The complete mitochondrial genome of the Kaloula verrucosa (Anura: Microhylidae) and phylogenetic analyses.

Project description:The first complete mitochondrial genome of a Kaloula verrucosa frog was characterized in this work. The mitogenome was 17,061 base pairs (bp) in length, containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region (D-loop). The overall base composition was 29.65% A, 30.77% T, 25.41% C and 14.17% G. Besides, the gene arrangement was identical to that observed in vertebrates. Five of 13 PCGs (COII, ATP6, COIII, ND3 and ND4) were ended with incomplete stop codon T. Except for ND6 gene encoded on L-strand, all other PCGs were encoded on H-strand. The non-coding region was 1665?bp in size, which was heavily biased to A?+?T (65.77%). Additionally, we found mitogenome size of all sequenced Kaloula species were bigger than that of Microhyla species, which was ascribe to the difference of D-loop size. Phylogenetic analysis showed that K. verrucosa was the sister species of Kaloula regifera. This work will provide basic molecular data for further molecular evolution and phylogenetic research of K. verrucosa and other microhylids.

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The complete mitochondrial genome of the Rana sangzhiensis Shen and its phylogenetic analyses.

Project description:The mitochondrial genome of one Rana pseudo-rana species Rana sangzhiensis Shen was sequenced and annotated. The mitogenome is 19,207 bp in length, containing 37 typical genes. The A + T content of the whole mitogenome is 56.6%. All of the protein-condoning genes (PCGs) started with ATG and stopped with TGA. The tRNA-Pro, tRNA-Gln, tRNA-Ala, tRNA-Asn, tRNA-Cys, tRNA-Tyr, tRNA-Ser, tRNA-Glu, andND5 are located in the circular mitochondrial L chain. The phylogeny tree is monophyletic among 14 related Rana species. The R. sangzhiensis Shen cluster was more closely related to R. amurensis Boulenger and R. kunyuensis Lu, Y.-Y., and P.-P. Li. This mitochondrial genome can be used for further analyses of Ranidae mitochondrial comparative genomics to improve the understanding of diverse Ranidae species.

| S-EPMC7872534 | biostudies-literature

The complete mitochondrial genome of Chinese minnow (Rhynchocypris oxycephalus) and its phylogenetic analyses.

Project description:The complete mitochondrial genome can provide novel insights into understanding the mechanism underlying mitogenome evolution. In the present study, the whole mitochondrial genome of Rhynchocypris oxycephalus was determined to 16608 bp (GenBank accession No: MW057563), including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. The overall base composition was 28.62% A, 27.23% T, 26.31% C and 17.84% G, with a total A + T content of 55.85%. The Maximum Likelihood tree showed that the phylogenetic relationship is closer between R. oxycephalus and Phoxinus oxycephalus jouyi than the other species. The whole mitogenome of this species will be useful for the future animal evolutionary, phylogenetic relationship, and genomic studies in the genus Phoxinus.

| S-EPMC8266249 | biostudies-literature

Complete mitochondrial genome of Black Drongo Dicrurus macrocercus (Passeriformes: Dicruridae) and phylogenetic analyses.

Project description:The Black Drongo Dicrurus macrocercus is a bird belonging to the group Passeriformes, distributed almost all over the country in China. The conservation status of this species is Least Concern (LC) in IUCN. In this study, the complete mitogenome of D. macrocercus was determined. The mitochondrial DNA is packaged in a compact 17,056 based pair (bp) circular molecule with A + T content of 57.04%. It contains 37 typical mitochondrial genes, including 13 protein-coding genes, 2 rRNAs and 22 tRNAs, and 1 non-coding regions. We reconstructed a phylogenetic tree based on mitogenome sequences of 15 Dicruridae species and one outgroup. In trees, D. macrocercus was clustered as an independent clade with high support value (100). The new mitogenome data would provide useful information for application in conservation genetics and further clarify the phylogenetic evolution of this species.

| S-EPMC8317954 | biostudies-literature

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

Project description:Abstract 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 Myrmuslateralis 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 Chorosomamacilentum 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.

| S-EPMC8599289 | biostudies-literature

The complete mitochondrial genome of Eurasian Sparrowhawk Accipiter nisus (Accipitriformes: Accipitridae).

Project description:The mitogenome of the Accipiter nisus is a circular module of 18,352 bp, which consists of 39 genes, containing 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, 22 tRNA genes, and two non-coding regions (control region and pseudo control region). The mitogenome of A. nisus is composed of 31.3% A, 25.5% T, 30.4% C, 12.8% G, and 76.3% AT. The phylogenetic analysis revealed that A. nisus individuals was well grouped in Accipitridae and more closely related to genus Circus than other Accpiter species.

| S-EPMC7954417 | biostudies-literature

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