Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship

Huang, Zuhao; Tu, Feiyun

doi:10.4238/gmr.15038491

Cited by 6 publications

(5 citation statements)

References 30 publications

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“…Unlike other strains, the CR of the JB strain contained four single tandem repeats with 1659 bp length and 64.58% A + T content. The CR length of vertebrates varies greatly, and it was suggested that the length difference of the mitochondrial genome may be mainly attributed to the change in CR length [ 64 ]. Moreover, the third and fourth tandem repeats of the JB strain were (TATATATCATA) 6 and (TATCATATA) 7 , respectively.…”

Section: Resultsmentioning

confidence: 99%

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

Chen

Jiao

Yuan

et al. 2023

Biology

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The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important aquaculture reptile with rich nutritional and medicinal values. In recent decades, the wild resources of P. sinensis have been depleting due to natural and artificial factors. Herein, we report the complete mitochondrial genome of four P. sinensis strains, including the Japanese (RB) strain, Qingxi Huabie (HB) strain, Jiangxi (JB) strain, and Qingxi Wubie (WB) strain. The nucleotide composition within the complete mitogenomes was biased towards A + T with a variable frequency ranging from 59.28% (cox3) to 70.31% (atp8). The mitogenomes of all four strains contained 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, 1 control region, and a replication origin region of the L-strand replication (OL), which was consistent with most vertebrates. Additionally, the atp8, nad4l, nad6, and nad3 genes possessed high genetic variation and can be used as potential markers for the identification of these P. sinensis strains. Additionally, all PCGs genes were evolving primarily under purifying selection. Through comparative analysis, it was revealed that most of the tRNAs were structurally different in the TψC stem, DHU stem, and acceptor stem. The length of the tandem repeats in the control region was variable in the four P. sinensis strains, ranging from 2 bp to 50 bp. Phylogenetic analysis indicated that all P. sinensis strains clustered into one branch and were closely related to other Trionychinae species. Overall, this study provides mitochondrial genome information for different P. sinensis strains to support further species identification and germplasm resource conservation.

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Section: Resultsmentioning

confidence: 99%

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

Chen

Jiao

Yuan

et al. 2023

Biology

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“…This variability is mostly due to different stretches of As and Ts, tandem repeats of the AT motif, and several insertions or deletions. In mammals and several other vertebrates, as well as in some invertebrate taxa, the control region has proved useful in phylogenetic inferences [ 83 , 84 , 85 ]. However, in insects, the utilization of this region is problematic [ 86 , 87 ].…”

Section: Resultsmentioning

confidence: 99%

The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

Moškrič

Marinč

Ferk

et al. 2022

Insects

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The complete mitochondrial genome of the Carniolan honeybee (Apis mellifera carnica) from Slovenia, a homeland of this subspecies, was acquired in two contigs from WGS data and annotated. The newly obtained mitochondrial genome is a circular closed loop of 16,447 bp. It comprises 37 genes (13 protein coding genes, 22 tRNA genes, and 2 rRNA genes) and an AT-rich control region. The order of the tRNA genes resembles the order characteristic of A. mellifera. The mitogenomic sequence of A. m. carnica from Slovenia contains 44 uniquely coded sites in comparison to the closely related subspecies A. m. ligustica and to A. m. carnica from Austria. Furthermore, 24 differences were recognised in comparison between A. m. carnica and A. m. ligustica subspecies. Among them, there are three SNPs that affect translation in the nd2, nd4, and cox2 genes, respectively. The phylogenetic placement of A. m. carnica from Slovenia within C lineage deviates from the expected position and changes the perspective on relationship between C and O lineages. The results of this study represent a valuable addition to the information available in the phylogenomic studies of A. mellifera—a pollinator species of worldwide importance. Such genomic information is essential for this local subspecies’ conservation and preservation as well as its breeding and selection.

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“…The non-coding region (also called the control region or the displacement loop, or D-loop, in vertebrates) is the most variable portion of the genome both in terms of length and nucleotide composition and shows a high degree of variation between populations of the same species (Le et al 2000). This region has been used for many intra-speci c studies in vertebrates (Huang et al 2016;Bronstein et al 2018; Bernacki and Kilpatrick 2020) but little information is available for its structure and utility in many invertebrates except for a few studies (e.g. Jiang et al 2018, cephalopods -Loliginidae).…”

Section: Evolutionary Relationships Of F Gigantica Based On Stem-loop...mentioning

confidence: 99%

Complete mitogenome analysis of Fasciola gigantica from Sudan

Salim,

Mohamed,

Ibrahim

et al. 2024

Preprint

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Complete mitochondrial (mt) genomes are increasingly being used as molecular markers for investigating phylogenetic relationships. We sequenced the complete mt genome of the Fasciola gigantica of 16 samples from cattle, sheep and goats from Sudan using Illumina MiSeq platform. The complete mt genome of F. gigantica was 14,483 bp in length. Its genome is circular, and consists of 36 genes, including 12 protein-coding genes, 2 subunit ribosomal RNA genes (rRNA), and 22 genes for tRNA. The start and stop codons of the12 protein-coding genes are ATG and TAG respectively, which are identical to reference mt genomes except for the ND5 the start codon GTG and the stop codon of the ND4 which was TAA. Additionally, the lengths of the the12 protein-coding genes were identical in 10 genes, however, the ND4L of the reference was 12 bp longer with 273 bp as compared to the Sudan isolates which was 261 bp long and COX1 in the reference was 9 bp shorter which was 1,533 bp long as compared to Sudan isolates which 1,542 bp long. In contrast, the non-coding regions differed by 20 bp and 4 bp length in the long and the short non-coding regions of Sudan isolates. Nucleotide variability in the mt genome among F. gigantica from Sudan is quite different from the reference as revealed by the sliding window analysis. Phylogenetic analysis of the concatenated amino acid sequence data for all 12 protein-coding genes showed that all F. gigantica from Sudan clustered separately from the available F. gigantica. More interestingly, based on stem-loop (non-coding regions) it revealed better resolution on how the evolutionary process has affected host specificity and in particular for the sheep and goats. It is concluded that these novel complete mt genomes of F. gigantica from different host species provide additional genetic markers for studying epidemiology, population genetics, and phylogeographics of F. gigantica, as well as for understanding interplay and the host species.

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Characterization and evolution of the mitochondrial DNA control region in Ranidae and their phylogenetic relationship

Cited by 6 publications

References 30 publications

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

Complete Mitochondrial Genomes of Four Pelodiscus sinensis Strains and Comparison with Other Trionychidae Species

The Carniolan Honeybee from Slovenia—A Complete and Annotated Mitochondrial Genome with Comparisons to Closely Related Apis mellifera Subspecies

Complete mitogenome analysis of Fasciola gigantica from Sudan

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