A comprehensive DNA barcoding of Indian freshwater fishes of the Indus River system, Beas.

The Beas River is one of the important rivers of the Indus River system located in Himachal Pradesh, India, that harbors a diverse range of freshwater fish species. The present study employed COI gene to investigate the ichthyofaunal diversity of river Beas. Through the sequencing of 203 specimens from Beas River, we identified 43 species, belonging to 31 genera, 16 families, and 10 orders. To analyze the genetic divergence and phylogeny of identified species, 485 sequences of Indian origin were retrieved from BOLD, resulting in a dataset of 688 sequences. Our findings consistently revealed a hierarchical increase in the mean K2P genetic divergence within species (0.80%), genus (9.06%), and families (15.35%). Automated Barcode Gap discovery, Neighbour Joining, and Bayesian inference consensus tree methodologies were employed to determine the putative species and their phylogeny, successfully delimiting most of the species with only a few exceptions. The results unveiled six species exhibiting high intra-species divergence (> 2%), suggesting the presence of sibling species and falsely identified sequences on online databases. The present study established the first DNA barcoding-based inventory of freshwater fish species in the Beas River providing comprehensive insights into economically exploited endangered and vulnerable species. In order to ensure the sustainable use of aquatic resources in the Beas River, we recommend the implementation of species measures to protect biodiversity and genetic resources.

Mitochondrial DNA reveals shallow population genetic structure in economically important Cyprinid fish Labeo rohita (Hamilton, 1822) from South and Southeast Asia.

BACKGROUND: Assessment of genetic diversity and population genetic structure is important for species that are economically important, threatened, and are at global conservation priority. Analysis of mitochondrial DNA is broadly used in species identification and population genetics studies due to the availability of sufficient reference data and better evolutionary dynamics for phylogeographic investigation. Labeo rohita (Rohu) is an economically important species cultured under carp polyculture systems in Asia. The present study explores the genetic diversity, phylogeography, and population structure of L. rohita from different countries using cytochrome oxidase subunit I (COI) gene. METHODS AND RESULTS: A total of 17 L. rohita specimens were sampled from River Beas, India. For the genetic study, we amplified and sequenced COI mitochondrial DNA region. The obtained genetic data was combined with 268 COI records available in the NCBI and BOLD databases originating from multiple populations/countries across South and Southeast Asia. As a result, 33 haplotypes were identified that displayed low nucleotide (π = 0.0233) and moderate haplotype diversity (Hd = 0.523). Tajima (D) was found to be negative (P > 0.05), whereas Fu's Fs showed a positive value (P > 0.05). The overall FST value between studied populations was 0.481 (P < 0.05). CONCLUSION: AMOVA analysis indicated higher variation within than among the population examined. The neutrality tests suggested the presence of rare haplotypes and stable demography within studied populations of L. rohita. The Bayesian skyline plot indicated steady population growth until 1 Mya followed by population decline, whereas FST values indicated significant genetic differentiation. High heterogeneity was observed in the Pakistan population which could be indicative of long-term isolation and excessive culturing to meet market demands. The present results are the first global comparative analysis of L. rohita and pave the way forward for detailed genomic and ecological studies aimed at the development of improved stock and effective conservation plans. The study also makes recommendations to conserve the genetic integrity of wild species from aquaculture-reared fishes.

Taxonomic and genomic characterization of Sporosarcina cyprini sp. nov., moderately tolerant of Cr+6 and Cd+2 isolated from the gut of invasive fish Cyprinus carpio var. communis (Linn., 1758).

A Gram-stain-positive, motile, and rod-shaped bacterium, designated as strain MB25T, was isolated from the gut of Cyprinus carpio from the highly polluted river Yamuna, India. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain MB25T belonged to the genus Sporosarcina, sharing the highest sequence similarity with S. luteola Y1T (98.98%) and S. koreensis S-K12T (98.91%). Digital DNA-DNA hybridization and average nucleotide identity values of strain MB25T with strain Y1T and S-K12T were 18.9, 77.69, and 18.2, 76.80 respectively. Genome analysis of strain MB25T revealed its biotechnological properties such as tolerance to potent heavy metals, genes for the production of carbohydrate-active enzymes, antimicrobial compounds, and also degradation of aromatic compounds. The G + C content of strain MB25T genome was 45%. Growth observed at 10-40 °C (optimum, 28-30 °C), pH 6.0-8.5 (optimum pH 7.5-8.0); NaCl concentrations up to 6.0% (w/v). The dominant respiratory quinone was MK-7, cell wall peptidoglycan is of the A-4 type containing amino acids Lys-Glu and the major fatty acids are anteiso-C11:0 and iso-C15: 0. The major polar lipids of strain MB25T are diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. On the basis of phenotypic, chemotaxonomic, phylogenetic, and phylogenomic data, strain MB25T represents a novel species of the genus Sporosarcina, for which the name Sporosarcina cyprini sp. nov. is proposed. The type strain is MB25T (= MCC 4366 T = JCM 34521 T = CCM 9113 T).

The first study of epidemiology of adolescent idiopathic scoliosis shows lower prevalence in females of Jammu and Kashmir, India.

AIS is a heterogeneous 3D spinal deformity with Cobb angle ≥10°. It affects children in the age group of 10-16 years globally with 2-3% prevalence and significant female predominance. The exact etiology of AIS is not known however, it is supposed to be associated with factors such as anthropometric, metabolic, neuromuscular abnormalities and genetics. OBJECTIVES: To determine the prevalence of AIS and association of anthropometric factors with AIS in the studied population group. METHODOLOGY: Scoliosis screening of 9,500 individuals was carried out at different educational institutions of Jammu region in Jammu and Kashmir, India using a scoliosis-meter. The subjects were later examined radiologically. RESULTS: In population of the region, AIS was most prevalent among all types of scoliosis with overall prevalence of 0.61%. The prevalence was observed to be lower in females (0.31%) than males (0.88%). Based on angle of trunk rotation (ATR), lumbar curves were more prevalent than thoracic curves. Average Cobb angle in males and females were 24.9° and 22.6°, respectively. BMI showed significant association with AIS in the age group of 12-16 years (P value =0.028). Furthermore, height was significantly associated with AIS in the overall screened population (P-value =0.029). CONCLUSIONS: The AIS patients in the Jammu region of India have unique clinical features. In contrast to the global prevalence data, the prevalence of AIS in females in the region was less in comparison to males. Based on epidemiological literature and our findings, we hypothesized that genetic factors might be a major contributor in the AIS pathogenesis along with other confounding factors such as height, BMI, ethnicity, etc.