ABSTRACT
Species of the genus Oreolalax displayed crucial morphological characteristics of vertebrates transitioning from aquatic to terrestrial habitats; thus, they can be regarded as a representative vertebrate genus for this landing phenomenon. But the present phylogenetic status of Oreolalax omeimontis has been controversial with morphological and molecular approaches, and specific gene rearrangements were discovered in all six published Oreolalax mitogenomes, which are rarely observed in Archaeobatrachia. Therefore, this study determined the complete mitogenome of O. omeimontis with the aim of identifying its precise phylogenetic position and novel gene arrangement in Archaeobatrachia. Phylogenetic analysis with Bayesian inference and maximum likelihood indicates O. omeimontis is a sister group to O. lichuanensis, which is consistent with previous phylogenetic analysis based on morphological characteristics, but contrasts with other studies using multiple gene fragments. Moreover, although the duplication of trnM occurred in all seven Oreolalax species, the translocation of trnQ and trnM occurred differently in O. omeimontis to the other six, and this unique rearrangement would happen after the speciation of O. omeimontis. In general, this study sheds new light on the phylogenetic relationships and gene rearrangements of Archaeobatrachia.
Subject(s)
Genome, Mitochondrial , Animals , Gene Order , Phylogeny , Bayes Theorem , Anura/geneticsABSTRACT
The molecular mechanisms underlying the evolution of adaptive immunity-related proteins can be deduced by a thorough examination of the major histocompatibility complex (MHC). Currently, in vertebrates, there is a relatively large amount of research on MHCs in mammals and birds. However, research related to amphibian MHC genes and knowledge about the evolutionary patterns is limited. This study aimed to isolate the MHC class I genes from Chenfu's Treefrog (Zhangixalus chenfui) and reveal the underlying evolutionary processes. A total of 23 alleles spanning the coding region of MHC class Ia genes were identified in 13 individual samples. Multiple approaches were used to test and identify recombination from the 23 alleles. Amphibian MHC class Ia alleles, from NCBI, were used to construct the phylogenetic relationships in MEGA. Additionally, the partition strategy was adopted to construct phylogenetic relationships using MrBayes and MEGA. The sites of positive selection were identified by FEL, PAML, and MEME. In Chenfu's Treefrog, we found that: (1) recombination usually takes place between whole exons of MHC class Ia genes; (2) there are at least 3 loci for MHC class Ia, and (3) the diversity of genes in MHC class Ia can be attributed to recombination, gene duplication, and positive selection. We characterized the evolutionary mechanisms underlying MHC class Ia genes in Chenfu's Treefrog, and in so doing, broadened the knowledge of amphibian MHC systems.
ABSTRACT
Cynops cyanurus chuxiongensis is distributed in Yunnan plateau. In this paper, we sequenced and determined the complete mitochondrial genome of C. c. chuxiongensis. The assembled mitogenome is 16,465 bp in length and encoding 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (D-loop). The phylogenetic trees indicated C. c. chuxiongensis (KY418068) has the closest relationship with C. orientalis + C. orphicus, and clustered within the clade of genus Cynops.
ABSTRACT
We newly sequenced the near complete mitochondrial genome of Polypedates braueri. The total length of the P. braueri partial mitogenome is 13 144 bp, with GenBank accession no. KT921226. It consists of 11 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNA), and 18 transfer RNA genes (tRNA). Most of the genes are encoded on the H-strand, except for seven tRNA and ND6, which are encoded on the L-strand. Our mitogenomic phylogenetic tree shows that the relationships between the genera Rhacophorus and Polypedates were well supported.
Subject(s)
Anura/genetics , Genome, Mitochondrial , Amphibian Proteins/genetics , Animals , Mitochondrial Proteins/genetics , Phylogeny , RNA, Ribosomal/genetics , RNA, Transfer/geneticsABSTRACT
The complete mitogenome of Tylototriton shanjing is 16,661 bp in length with GenBank accession number KR154461, which contains 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), 2 ribosomal RNA genes (rRNA), and 1 control region (CR). The overall base composition of this mitogenome is biased toward AT content at 59.45%. Most of the PCGs and tRNA genes are located on the H-strand, except for ND6 subunit gene and eight tRNA genes, which were distributed on the L-strand. The PCGs used "ATG" and "GTG" as the start codons, while "TAA", "TAG", "AGA", and "T-" are used as stop codons. Almost all tRNA genes were folded into typical cloverleaf secondary structures. The T. shanjing genome had two tandem repeat sequences in the cob-noncoding region. The mitogenomic phylogenetic analyses shows that the genera Echinotriton and Tylototriton were clustered into a strong supported monophyletic clade, which is a sister clade to the genus Pleurodeles, this confirms the previous phylogenetic results.
Subject(s)
Genome, Mitochondrial/genetics , Salamandridae/genetics , Animals , Base Composition/genetics , Phylogeny , RNA, Ribosomal/genetics , RNA, Transfer/genetics , Salamandridae/classification , Sequence Analysis, DNAABSTRACT
We newly sequenced the mitochondrial genome of Tylototriton wenxianensis. The total length of the T. wenxianensis mitogenome is 16 265 bp, with GenBank accession number KR733683. It consists of 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNA), 22 transfer RNA genes (tRNA), and one control region (CR). Most of the genes are encoded on the H-strand, except for eight tRNA and ND6, which are encoded on the L-strand. Our mitogenomic phylogenetic tree showed that the relationships among the genera Tylototriton, Echinotriton, and Pleurodeles were well supported, and which is consistent with the previous molecular phylogeny.
