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.
Highlights
The genus Nilssonia (Testudines: Trionychidae) was originally described from Myanmar based on N. formosa as its type[1]
All the 37 genes were annotated in the de novo assembled genome; 13 protein coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs, and a major non-coding control region (CR) (Table 1)
The comparative analysis revealed that similar gene arrangements in both L and H strand were present in other Trionychidae species (Table S2)
Summary
The genus Nilssonia (Testudines: Trionychidae) was originally described from Myanmar based on N. formosa as its type[1]. The genus Nilssonia is known by the five extant species (N. formosa, N. gangetica, N. hurum, N. leithii, and N. nigricans), which are distributed in India and adjacent countries, from Pakistan, Nepal, Bangladesh, and up to Myanmar. Due to the countless anecdotal reports on its identification and distribution, N. nigricans was categorized as ‘Critically Endangered’ (1996–2000) and later on shifted to ‘Extinct in the wild’ (2002–2018) in the International Union for Conservation of Nature (IUCN, Verson-2017-3) Red data list[12]. We sequenced and characterized the complete mitogenome for this species, and compared it with that of other softshell turtles (family Trionychidae) to confirm the unique genetic features and evolutionary relationship. The generated mitogenome will be a valuable resource for further studies on genetic diversity and population structure of N. nigricans and provide new insights for better conservation strategies
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