The first complete mitochondrial genome of the critically endangered Malaysian giant turtle, Orlitia borneensis (Testudines: Geoemydidae).

We present here the complete mitochondrial sequence of the critically endangered Malaysian giant turtle, Orlitia borneensis. The assembled mitochondrial genome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (rRNAs), and one control region. This mitochondrial genome has been archived in the NCBI GenBank with accession number OQ808845. The Batagur control region is relatively smaller than O. borneensis and closer to Aldabrachelys gigantea, which suggests potentially that O. borneensis has undergone an expansion in the control region.

Global Terrapin Character-Based DNA Barcodes: Assessment of the Mitochondrial COI Gene and Conservation Status Revealed a Putative Cryptic Species.

Technological and analytical advances to study evolutionary biology, ecology, and conservation of the Southern River Terrapin (Batagur affinis ssp.) are realised through molecular approaches, including DNA barcoding. We evaluated the use of COI DNA barcodes in Malaysia's Southern River Terrapin population to better understand the species' genetic divergence and other genetic characteristics. We evaluated 26 sequences, including four from field specimens of Southern River Terrapins obtained in Bota Kanan, Perak, Malaysia, and Kuala Berang, Terengganu, Malaysia, as well as 22 sequences from global terrapins previously included in the Barcode of Life Database (BOLD) Systems and GenBank. The species are divided into three families: eight Geoemydidae species (18%), three Emydidae species (6%), and one Pelomedusidae species (2%). The IUCN Red List assigned the 12 species of terrapins sampled for this study to the classifications of critically endangered (CR) for 25% of the samples and endangered (EN) for 8% of the samples. With new haplotypes from the world's terrapins, 16 haplotypes were found. The intraspecific distance values between the COI gene sequences were calculated using the K2P model, which indicated a potential cryptic species between the Northern River Terrapin (Batagur baska) and Southern River Terrapin (Batagur affinis affinis). The Bayesian analysis of the phylogenetic tree also showed both species in the same lineage. The BLASTn search resulted in 100% of the same species of B. affinis as B. baska. The Jalview alignment visualised almost identical sequences between both species. The Southern River Terrapin (B. affinis affinis) from the west coast of Peninsular Malaysia was found to share the same haplotype (Hap_1) as the Northern River Terrapin from India. However, B. affinis edwardmolli from the east coast of Peninsular Malaysia formed Hap_16. The COI analysis found new haplotypes and showed that DNA barcodes are an excellent way to measure the diversity of a population.

Characterization of the complete mitochondrial genome of the critically endangered Southern River Terrapin, Batagur affinis affinis (Reptilia: Geoemydidae).

In this study, we report the nearly complete mitochondrial sequence of Batagur affinis affinis. The assembled mitogenome consists of 13 PCGs, 22 tRNA genes, two rRNAs and one near-complete D-loop region. Of the annotated genes, the ND6 subunit gene and eight tRNA genes were encoded on the L-strand, while the remaining genes were dispersed on the H-strand. Except for CO1, which has a GTG start codon, all protein-coding genes begin with ATG. The mitogenome has been deposited in NCBI GenBank under the accession number OQ409915. Phylogenetic tree analysis based on publicly available mitogenomes indicate the sister grouping of B. affinis affinis with B. kachuga.

Turtles in Malaysia: A Review of Conservation Status and a Call for Research.

Approximately 356 species of turtles inhabit saltwater and freshwater habitats globally, except in Antarctica. Twenty-four species of turtles have been reported in Malaysia, four of which are sea turtles. The state of Terengganu harbored the highest number of turtles, with 17 different reported species. Based on the IUCN Red List, 29% of turtle species in Malaysia are critically endangered. In comparison, another 25% are classified as endangered. Likewise, CITES reported that 67% of Malaysia's turtles are threatened, while 25% are classified as critically endangered. This review discusses the checklists, molecular genetics work, conservation status, recent trends, and recommendations for future research. Factors contributing to their population declines and current endangered status are also discussed.

Faecal DNA metabarcoding reveals novel bacterial community patterns of critically endangered Southern River Terrapin, Batagur affinis.

Southern River Terrapin, Batagur affinis, is a freshwater turtle listed as critically endangered on the IUCN Red List since 2000. Many studies suggest that faecal DNA metabarcoding can shield light on the host-associated microbial communities that play important roles in host health. Thus, this study aimed to characterise and compare the faecal bacterial community between captive and wild B. affinis using metabarcoding approaches. A total of seven faeces samples were collected from captive (N = 5) and wild (N = 2) adult B. affinis aseptically, crossing the East and West coast of peninsular Malaysia. The DNA was extracted from the faeces samples, and the 16S rRNA gene (V3-V4 region) was amplified using polymerase chain reaction (PCR). The amplicon was further analysed using SILVA and DADA2 pipelines. In total, 297 bacterial communities taxonomic profile (phylum to genus) were determined. Three phyla were found in high abundance in all faeces samples, namely Firmicutes (38.69%), Bacteroidetes (24.52%), and Fusobacteria (6.95%). Proteobacteria were detected in all faeces samples (39.63%), except the wild sample, KBW3. Under genus level, Cetobacteriumwas found as the most abundant genus (67.79%), followed by Bacteroides (24.56%) and Parabacteroides (21.78%). The uncultured genus had the highest abundance (88.51%) even though not detected in the BK31 and KBW2 samples. The potential probiotic genera (75.00%) were discovered to be more dominant in B. affinis faeces samples. Results demonstrated that the captive B. affinis faeces samples have a greater bacterial variety and richness than wild B. affinis faeces samples. This study has established a starting point for future investigation of the gut microbiota of B. affinis.