Complete mitochondrial genome of Cuora trifasciata (Chinese three-striped box turtle), and a comparative analysis with other box turtles

The complete mitochondrial genome of the endangered Assam Roofed Turtle, Pangshura sylhetensis (Testudines: Geoemydidae): Genomic features and phylogeny

The Assam Roofed Turtle, Pangshura sylhetensis is an endangered and least studied species endemic to India and Bangladesh. The present study decodes the first complete mitochondrial genome of P. sylhetensis (16,568 bp) by using next-generation sequencing. The assembly encodes 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region (CR). Most of the genes were encoded on the majority strand, except NADH dehydrogenase subunit 6 (nad6) and eight tRNAs. All PCGs start with an ATG initiation codon, except for Cytochrome oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 5 (nad5), which both start with GTG codon. The study also found the typical cloverleaf secondary structures in most of the predicted tRNA structures, except for serine (trnS1) which lacks of conventional DHU arm and loop. Both Bayesian and maximum-likelihood phylogenetic inference using 13 concatenated PCGs demonstrated strong support for the monophyly of all 52 Testudines species within their respective families and revealed Batagur trivittata as the nearest neighbor of P. sylhetensis. The mitogenomic phylogeny with other amniotes is congruent with previous research, supporting the sister relationship of Testudines and Archosaurians (birds and crocodilians). Additionally, the mitochondrial Gene Order (GO) analysis indicated plesiomorphy with the typical vertebrate GO in most of the Testudines species.

Morphological characterization and phylogenetic relationships of Indochinese box turtles-The Cuora galbinifrons complex

The members of the Indochinese box turtle complex, namely Cuora galbinifrons, Cuora bourreti, and Cuora picturata, rank the most critically endangered turtle species on earth after more than three decades of over-harvesting for food, traditional Chinese medicine, and pet markets. Despite advances in molecular biology, species boundaries and phylogenetic relationships, the status of the C. galbinifrons complex remains unresolved due to the small number of specimens observed and collected in the field. In this study, we present analyses of morphologic characters as well as mitochondrial and nuclear DNA data to reconstruct the species boundaries and systematic relationships within the C. galbinifrons complex. Based on principal component analysis (PCA) and statistical analysis, we found that phenotypic traits partially overlapped among galbinifrons, bourreti, and picturata, and that galbinifrons and bourreti might be only subspecifically distinct. Moreover, we used the mitochondrial genome, COI, and nuclear gene Rag1 under the maximum likelihood criteria and Bayesian inference criteria to elucidate whether C. galbinifrons could be divided into three separate species or subspecies. We found strong support for a sister relationship between picturata and the other two species, and consequently, we recommend maintaining picturata as a full species, and classifying bourreti and galbinifrons as subspecies of C. galbinifrons. These findings provide evidence for a better understanding of the evolutionary histories of these critically endangered turtles.

The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): Characterization and comparative analysis

The characterization of a complete mitogenome is widely used in genomics studies for systematics and evolutionary research. However, the sequences and structural motifs contained within the mitogenome of Testudines taxa have rarely been examined. The present study decodes the first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (16,657 bp) by using next-generation sequencing. This denovo assembly encodes 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA, and one control region (CR). Most of the genes were encoded on majority strand, except for one PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were started with an ATG initiation codon, except for Cytochrome oxidase subunit 1 with "GTG" and NADH dehydrogenase subunit 5 with "ATA." The termination codons, "TAA" and "AGA" were observed in two subunits of NADH dehydrogenase gene. The relative synonymous codon usage analysis revealed the maximum abundance of alanine, isoleucine, leucine, and threonine. The nonsynonymous/synonymous ratios were <1 in all PCGs, which indicates strong negative selection among all Geoemydid species. The study also found the typical cloverleaf secondary structure in most of the tRNA genes, except for serine with the lack of the conventional DHU arm. The comparative study of Geoemydid mitogenomes revealed the occurrence of tandem repeats was frequent in the 3' end of CR. Further, two copies of a unique tandem repeat "TTCTCTTT" were identified in P. tentoria. The Bayesian and maximum-likelihood phylogenetic trees using concatenation of 13 PCGs revealed the close relationships of P. tentoria with Batagur trivittata in the studied dataset. All the Geoemydid species showed distinct clustering with high bootstrap support congruent with previous evolutionary hypotheses. We suggest that the generations of more mitogenomes of Geoemydid species are required, to improve our understanding of their in-depth phylogenetic and evolutionary relationships.

Comparative mitogenomic and phylogenetic analysis of Apalone spinifera and Apalone ferox (Testudines: Trionychidae)

The soft-shell turtles Apalone spinifera (AS) and Apalone ferox (AF) are two important economic species. AF is found in the Yellow River of China, and is a confirmed member of the Trionychidae family. However, the classification of AS was in dispute. Mitochondrial genomes (mitogenomes) have been widely used for species identification, as well as population and phylogenetic analysis. In order to understand the phylogenetic and mitogenomic features of AS and AF, the complete mitogenomes were sequenced, annotated and analyzed in this study. The complete mitogenomes of AS and AF are 16,817 bp and 16,756 bp in length, respectively. Both mitogenomes contain 37 genes, seven short intergenic spacers and two long intergenic spacers. Comparative analysis showed that there are 1,137 variation sites (6.79%) between the two mitogenomes. AS and AF mitogenomes both show a usage preference in terms of nucleotides, codons and amino acids. In addition, the non-synonymous substitution rate/synonymous substitution rate indicates that all protein-coding genes (PCGs) have undergone a strong purifying selection. Phylogenetic trees constructed by 13 PCGs show a clear phylogenetic relationship of the soft-shell turtles and suggest that AS is a sister species to AF of the genus Apalone. The data could be useful for further research of species identification, population analysis and the mitogenomic features of soft-shell turtles.

Characterization of five complete Cyrtodactylus mitogenome structures reveals low structural diversity and conservation of repeated sequences in the lineage

Mitochondrial genomes (mitogenomes) of five Cyrtodactylus were determined. Their compositions and structures were similar to most of the available gecko lizard mitogenomes as 13 protein-coding, two rRNA and 22 tRNA genes. The non-coding control region (CR) of almost all Cyrtodactylus mitogenome structures contained a repeated sequence named the 75-bp box family, except for C. auribalteatus which contained the 225-bp box. Sequence similarities indicated that the 225-bp box resulted from the duplication event of 75-bp boxes, followed by homogenization and fixation in C. auribalteatus. The 75-bp box family was found in most gecko lizards with high conservation (55-75% similarities) and could form secondary structures, suggesting that this repeated sequence family played an important role under selective pressure and might involve mitogenome replication and the likelihood of rearrangements in CR. The 75-bp box family was acquired in the common ancestral genome of the gecko lizard, evolving gradually through each lineage by independent nucleotide mutation. Comparison of gecko lizard mitogenomes revealed low structural diversity with at least six types of mitochondrial gene rearrangements. Cyrtodactylus mitogenome structure showed the same gene rearrangement as found in most gecko lizards. Advanced mitogenome information will enable a better understanding of structure evolution mechanisms.

The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications

The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.