DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India

DNA Barcoding Reveals Association of Glossiphoniidae Species on Endangered Freshwater Turtles in Northeast India

BACKGROUND

The identification of Glossiphoniidae species is often confusing due to the lack of both morphological and molecular data worldwide.

PURPOSE

The study aimed to identify the collected leech specimens from two endangered freshwater turtles, Chitra indica and Pangshura sylhetensis from northeast India.

METHODS

We generated DNA barcode sequences and estimated the genetic distances and phylogenetic relationship of the studied taxa with another 14 Glossiphoniidae genera (114 barcode sequences).

RESULTS

The high genetic distinctiveness (17.9 to 26.3%) and distinct clustering in Neighbor-Joining (NJ) phylogeny, we identified the studied specimens as Glossiphoniidae sp. We assumed that the studied specimens might be a new member of Glossiphoniidae or an extant species without DNA information.

CONCLUSION

Hence, the study recommends further sampling of leeches from the similar host as well as from same and various localities and also generates the molecular data to perceive the exact diversity. The aimed study is also helpful to encourage the awareness and conservation management of freshwater turtles and other threatened animals.

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

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.

Pet and turtle: DNA barcoding identified twelve Geoemydid species in northeast India

Geoemydid turtles are one of the most imperilled fauna on the planet, with nearly half of them are threatened with extinction due to bushmeat crisis, traditional medicine, and the illegal pet trade. Classical taxonomy often fails to identify the pet-kept turtle specimens due to amorphous form, unusual shell colouration owing to poor storage in captivity or intensely tinted for high demanding value. The DNA barcoding technique has evidenced as a supportive tool for accurate species identification in systematics research and discerned the nameless taxa in forensic sciences. We tested the effectiveness of DNA barcoding tools for identifying the pet-kept Geoemydid turtle in northeast India. The 36 generated sequences are readily delineated into 12 Geoemydid species using molecular data. The overall mean genetic distance of the studied Geoemydid turtles dataset is 15.3% and ranges from 3.4% to 22.6% between the species. The NJ, ML and Bayesian phylogeny also resulted monophyletic clustering and discriminated all the studied species. The present study contributes DNA barcode sequences of Geoemydid turtles in the global database and also affirms the on-going illegal pet trade of highly threatened species in northeast India.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae)

Turtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage, Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.

DNA barcoding of Gobiid fishes (Perciformes: Gobiidae) from eastern and northeastern India with new record of a Gobionellinae species for the region

The study attempted identification of Gobiid fishes from freshwaters in the east and northeast India on a collection of 20 specimens. The DNA barcode data delineated the collected samples into three species clades in the neighbor-joining tree. The results confirmed the identification of five sample sequences belonging to the subfamily Gobionellinae due to cohesive cladding with Awaous congeners. This is a new subfamily record for the northeastern region. Another 15 sample sequences showed conspecific cladding with Glossogobius giuris in the database. Among the 15 sample sequences, 14 sequences cladded with G. giuris sequences of Indian specimens while one sample sequence cladded with G. giuris sequences of South African specimens. This indicated the presence of either a hidden species or a previously synonymized species in the G. giuris complex.