Complete mitochondrial genome of Black Soft-shell Turtle (Nilssonia nigricans) and comparative analysis with other Trionychidae

Abstract

The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR). The mitogenome was A + T biased (62.16%) and included six overlapping and 19 intergenic spacer regions. The Relative synonymous codon usage (RSCU) value was consistent among all the Trionychidae species; with the exception of significant reduction of Serine (TCG) frequency in N. nigricans, N. formosa, and R. swinhoei. In N. nigricans, most of the transfer RNAs (tRNAs) were folded into classic clover-leaf secondary structures with Watson-Crick base pairing except for trnS1 (GCT). The comparative analysis revealed that most of the tRNAs were structurally different, except for trnE (TTC), trnQ (TTG), and trnM (CAT). The structural features of tRNAs resulted ≥ 10 mismatched or wobble base pairings in 12 tRNAs, which reflects the nucleotide composition in both H- and L-strands. The mitogenome of N. nigricans also revealed two unique tandem repeats (ATTAT)8, and (TATTA)20 in the CR. Further, the conserved motif 5′-GACATA-3′ and stable stem-loop structure was detected in the CRs of all Trionychidae species, which play an significant role in regulating transcription and replication in the mitochondrial genome. Further, the comparative analysis of Ka/Ks indicated negative selection in most of the protein coding genes (PCGs). The constructed Maximum Likelihood (ML) phylogeny using all PCGs showed clustering of N. nigricans with N. formosa. The resulting phylogeny illustrated the similar topology as described previously and consistent with the taxonomic classification. However, more sampling from different taxonomic groups of Testudines and studies on their mitogenomics are desirable for better understanding of the phylogenetic and evolutionary relationships.

RETRACTED ARTICLE: Turdoides affinis mitogenome reveals the translational efficiency and importance of NADH dehydrogenase complex-I in the Leiothrichidae family

“…No tandem repeats were found among the CRs. Duplication of CR region is important in the regulation of replication and transcription within mitochondrial genome 46 . Moreover, duplicated CR is also associated with extended longevity of bird species 48 .…”

“…The wobble base pairing which does not follow the Watson–Crick base pairing rule, often substituting GC or AT base pairs, contributing to thermodynamic stability 43 , 44 is of immense importance in studying the tRNA structure. Hence, while understanding the exact functional features of mitogenomes, tRNA acts as a pivotal tool 45 , 46 . In T. affinis , all the tRNAs were folded into the classic secondary clover-leaf structure.…”

“…Vertebrate mitochondrial control region (CR) is divided into three domains (I, II and III) 46 , 47 . Among all the investigated species of the Leiothrichidae family, a duplication of CR was observed.…”

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

“…However, to better understand evolutionary relationships and phylogeny within Testudines, datasets representing more taxa and loci are needed (Le et al, ). Comparative mitogenomic data have demonstrated utility in elucidating the phylogenetic relationships of turtles (Kundu, Kumar, Tyagi, et al, ; Li et al, ). The genus Pangshura was erected from Batagur and elevated as a distinct genus through morphological characteristics (Günther, ; Moll, ).…”

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

“…Testudines mitochondrial genomes are circular and double stranded with a size of 16-19 kb and contain typically 37 genes [16][17][18][19][20]. Remarkably, some of the reptile species, including turtles, have variable numbers of genes in their mitogenome due to the loss of protein-coding genes (PCGs), duplication of control regions (CRs), and occurrence of multiple contiguous numbers of one or more transfer RNA genes (tRNAs) [21].…”