Gene

Benign prostatic hyperplasia (BPH) is a growing issue due to an ageing population; however, there are not enough studies connecting it with ageing hallmarks. Some of the ageing hallmarks are changes in telomere length (TL) and genetic changes like possible mutations in the TP53 gene or mitochondrial genome (mtDNA). Our study investigated these factors to see if they could be linked with BPH. Prostate tissue samples were obtained from 32 patients with BPH (and 30 blood samples). As a healthy control group, age-matching blood DNA samples were used. For mtDNA sequence data comparison, 50 samples of a general Latvian population were used. The full mtDNA genome was sequenced using Next Generation Sequencing (NGS), for TP53 gene - Sanger sequencing, and for mtDNA amount and telomere length - qPCR assay. BPH patients in prostate tissue had much higher TL than in blood cells, and the healthy controls had the shortest telomeres. Also, the mtDNA amount in BPH prostate tissue was the highest compared with blood, and controls had the smallest amount. In the TP53 gene, we did not find any mutations that could be linked to BPH. In the mtDNA genome, we found several unique mutations and heteroplasmic changes, as well as changes that have been linked before with prostate cancer (PC). In conclusion, prolonged telomeres and changes in mtDNA amount might be involved in the development of BPH. Concerning mtDNA genome changes, some of the heteroplasmic or homoplasmic variants might contribute to the development of BPH. More studies should be conducted to prove or disapprove of these connections.

Methylation at the N6-position of adenosine, m6A, is the most abundant mRNA modification in eukaryotes. It is a highly conserved universal regulatory mechanism controlling gene expression in a myriad of biological processes. The role of m6A methylation in sexual maturation, however, has remained largely unexplored. While the maturation process is known to be affected by many genetic and environmental factors, the molecular mechanisms causing variation in the timing of maturation are still poorly understood. Hence, investigation of whether a widespread mechanism like m6A methylation could be involved in controlling of the maturation timing is warranted. In Atlantic salmon (Salmo salar), two genes associated with the age at maturity in human, vgll3 and six6, have been shown to play an important role in maturation timing. In this study, we investigated the expression of 16 genes involved in the regulation of m6A RNA methylation in the hypothalamus of Atlantic salmon with different homozygous combinations of late (L) and early (E) alleles for vgll3 and six6 genes. We found differential expression of ythdf2.2 which encodes an m6A modification reader and promotes mRNA degradation. Its expression was higher in six6*LL compared to other genotypes as well as immature males compared to matures. In addition, we found that the expression levels of genes coding for an eraser, alkbh5, and for a reader, ythdf1, were higher in the hypothalamus of females than in males across all the different genotypes studied. Our results indicate a potential role of the m6A methylation process in sexual maturation of Atlantic salmon, and therefore, provide the first evidence for such regulatory mechanism in the hypothalamus of any vertebrate. Investigation of additional vertebrate species is warranted in order to determine the generality of these findings.

Ko[n]kan region on the west coast of India is a hotspot of culture, folklore and ethnolinguistic diversity. The genetic landscape of this region remains understudied. The present study features Ko[n]kan[i] population residing along the Ko[n]kan Malabar coast. We have sequenced complete mitogenomes of 85 and the hypervariable region of 210 Ko[n]kan[i] individuals to understand the maternal gene pool of this region. Comparative analysis of the over 5000 mitogenomes revealed that the Ko[n]kan[i] population clustered at a convergence point on the PCA plot, presumably due to a diverse maternal gene pool with both autochthonous and West Eurasian components. A distinct clustering pattern was observed within the subgroups of S[a]rasvata and non-S[a]rasvata Ko[n]kan[i] groups, indicating unique ancestral maternal lineages in them. This distinction is majorly due to the N macrohaplogroup lineages found in this population. We observe low haplotype and nucleotide diversity in Citrapur S[a]rasvata Brahmins (CSB), R[a]j[a]pur S[a]rasvata Brahmins (RSB), Kh[a]rvi and Kudubi compared to Gauda S[a]rasvata Brahmins (GSB) and Roman Catholics. The assimilation of both pre and post Last Glacial Maximum (LGM) haplogroups like M57, M36, M37, M3, M30, R8 and U2 in the Ko[n]kan[i] population suggests active movement and settlement along the Ko[n]kan region on the west coast of India since the Late Pleistocene through the Holocene.

O_LIIndia plays a central role in dugong conservation by hosting the largest population within south Asia. Current knowledge on status of Indian dugongs is limited due to paucity of reliable ecological data. This study generates mitochondrial control region sequences from about 10% of dugong population from major dugong populations within India. These data was compared with the global data to assess genetic lineages, population structure and genetic diversity of Indian populations. C_LIO_LIMultiple analyses suggest that the Indian dugong populations are part of a single genetic cluster, comprising south Asia, northwest Indian ocean and southwest Indian ocean populations. Despite small population size, they retain high genetic diversity with unique mitochondrial DNA haplotypes within south Asia. C_LIO_LIWithin India, novel haplotypes were observed from all sampling sites with overall high haplotype diversity (0.85{+/-}0.04) but low nucleotide diversity (0.005{+/-}0.001). Indian populations exhibit high genetic differentiation with higher within-population variance (63.41%) than among populations (36.59%), signaling population structure. Few haplotypes were shared with Sri Lanka and southeast Asian populations, indicating potential genetic connectivity. C_LIO_LIBeing the most genetically unique population within south Asia, Indian dugong populations are globally significant. We recommend that Indian Dugong populations should be managed as a Conservation Unit to ensure population recovery and long-term survival of the species. C_LI

Aging and longevity are complex processes controlled at different levels, including genetic level. We evaluated the association of seven drug and DNA-repair gene polymorphisms with longevity in an Italian cohort. A sample of 756 subjects aged 18-98 was genotyped for CYP1A1 exon 7 A>G, GSTT1 null, GSTM1 null, GSTP A>G, XRCC1 exon 6 C>T, XRCC1 exon 9 A> G and XPC exon 15 A>C gene polymorphisms. The association between the analyzed gene polymorphisms and longevity was evaluated by dividing the sample into three age groups: 10-50, 51-85, and 86-98. We observed a significant decrease in the frequency of the GSTT1 null, GSTP G and XPC C alleles in the oldest group with respect to the youngest one and with respect to 51-85 age group. We obtained the same results also subdividing the sample into 1-85 and 86-98 age groups. The general linear model analyses confirmed a significant decreasing trend of the above mentioned alleles with age. We hypothesized that these minor alleles, being important in the sensitivity against the development of different types of cancer, may reflect a reduced life-expectancy in carrier subjects and may explain their significantly lower frequency observed among subjects belonging to oldest age group.

The extinct Camelus knoblochi is known as the largest camel in genus Camelus, but its relationship to modern Camelus species remains unclear. In this study, we reported the first mitochondrial and nuclear analyses of seven Late Pleistocene C. knoblochi samples from Northeastern China. We found that they are inseparable to wild Bactrian camel on the matrilineal side, but belong to a distinct cluster on the biparental nuclear side. Further admixture proportion analyses suggested hybrid ancestry between both the ancestors of the modern wild and domesticated Bactrian camels, with ~65% contribution from the former and ~35% from the later. By calculating the coalescence time for three Camelus species above, we estimated the hybridization event occurred between approximately 0.8 and 0.33 Ma. We also used Bayesian skyline to reconstruct the maternal demographic trajectories for different Camelus to better compare their evolutionary histories. Our results provide molecular insights into C. knoblochi and fill in a vital piece in understanding the genus Camelus.

BackgroundHeterochromatic long arm of mouse Y chromosome harbors the multicopy species-specific sequences Ssty, Sly, Asty and Orly that are transcribed in testis and have known functions in male fertility. Of these Ssty and Sly encode proteins - yet all the transcripts are not translated. To investigate the roles of these Y-heterochromatic transcripts further, we analyzed them. MethodsMice with 2/3rd deletion of the Y-chromosome (XYRIIIqdel) and its wild type (XYRIII) were used in this study. Bioinformatic approaches, small RNA northern blots, Electrophoretic Mobility Shift Assays, Luciferase reporter assays, dPCR analysis, RT-qPCR assays and western blotting techniques were used to identify piRNAs that regulate autosomal genes. ResultsWe demonstrate that the multicopy gene families from mouse Y-long arm generate piRNAs predominantly in testis. We observed sequences homologous to these piRNAs in the UTRs of a few autosomal genes, which are differentially expressed in the sperms of XYRIIIqdel mice. Furthermore, the Endogenous Retrovirus Element (ERV) LTR, found in the Orly1 transcript identified piRNAs in the database, showed homology to UTRs and associated genomic regions of a few autosomal genes. Orly1 showed a reduction in genomic copy number by digital PCR in XYRIIIqdel mice. One of the four autosomal genes containing the ERV segment in their UTRs, showed a differential testicular protein expression in the mutant mice. ConclusionsThus, we further elucidate that different classes of repeats from Y-chromosome regulate autosomal gene expression via piRNAs. Besides, this study also identified novel roles for a Y-derived ERV in autosomal gene regulation in testis.

The Jomon culture that spread across Japanese archipelago began about 16,000 years ago and lasted for over 10,000 years. The genetic diversity of the Jomon people, prehistoric hunter-gatherers bearing the Jomon culture, is of great interest in understanding prehistoric East Eurasians. Until now, their demographic history has been estimated using archaeological sites and present-day genomes, but detailed studies using Jomon genomes have been insufficient. To investigate the Jomon demography, we determined the complete mitochondrial genome (mitogenome) sequences from 13 Jomon individuals and conducted population genetic analysis on 40 Jomon genomes including previously published data. Our results revealed an effective population size increase during the Incipient - Initial phase of the Jomon period, which had not been observed in analysis of mitogenome sequences from present-day Japanese populations. This endemic demographic pattern is pronounced in the eastern part of the archipelago, under the assumption of no gene flow between the Eastern and Western Jomon.

PURPOSEMTHFR is a pivotal enzyme in the folic acid cycle. In specific populations, two functional SNPs in the encoding gene, i.e. rs1801133 (677C/T) and rs1801131 (1298A/C), have shown associations with different diseases including cancers. In the present study, the role of these SNPs was analyzed in breast cancer cases from Pakistani population. PARTICIPANTS AND METHODSThe pilot study includes 187 participants with 124 breast cancer patients and 63 matched individuals as controls. PCR-RFLP methods validated by Sanger sequencing were used for the polymorphic investigations. Hardy-Weinberg Equilibrium was tested by chi-squared goodness-of-fit test. Independent and combined associations were evaluated by Cochran-Armitage trend-test. Semi-parameteric haplotype analysis was carried out and odds ratios with 95% confidence interval were tabulated. Linkage disequilibrium between two loci was calculated. p-values <0.05 were significant. RESULTSBoth MTHFR 677C/T and MTHFR 1298A/C SNPs were in Hardy-Weinberg Disequilibium. Cochran-Armitage trend test showed lack of independent associations of these SNPs with the risk for breast cancers. The diplotype analysis revealed that 677CC+1298AC increased the risk of breast cancers significantly [OR: 2.553 (95% CI: 1.177-5.541)], while 677CT+1298AA had a protective effect [OR: 0.537 (95% CI: 0.404-0.713)]. Haplotype analysis did not show any significant association. Interestingly, despite the proximity, these loci were not linked (r2 = 0.042 and 0.046 in cases and controls, respectively). CONCLUSIONHere, we report association analysis of two putative candidate SNP markers in the MTHFR gene with breast cancers in a South-Asian population. To the best of our knowledge, two diplotype combinations show unique associations with breast cancer susceptibility in this population, which have not been reported earlier. The study implies translational potentials of these polymorphisms for breast cancer management.

We present an R software package that performs at genome-wide level differential network analysis and infers only disease-specific molecular interactions between two different cell conditions. This helps revealing the disease mechanism and predicting most influential genes as potential drug targets or biomarkers of the disease condition of interest. As an exemplary analysis, we performed an application of the software over LNCaP datasets and, out of approximately 25000 genes, predicted CXCR7 and CXCR4 together as drug targets of LNCaP prostate cancer dataset. We further successfully validated them with our initial wet-lab experiments. The introduced software can be applied to all the diseases, especially cancer, with gene expression data of two different conditions (e.g. tumor vs normal) and thus has the potential of a global benefit. As a distinct remark, our software provide the causal disease mechanism with multiple potential drug-targets rather than a single independent target prediction. AvailabilityThe introduced R software package for the analysis is available in CRAN at https://cran.r-project.org/web/packages/dc3net and also at https://github.com/altayg/dc3net

Among the different microsatellite sequences found in the human genome, the dinucleotide TG/CA repeats are one of the most abundant, exhibiting multifaceted functional roles. Availability of several primate genomes offers relevant datasets for studying the evolution and function of these repeats in non-human primates and human genome. Using pairwise genomic alignments, genome-wide analysis of these repeats was performed in human and sixteen other primate genomes. The total number of these repeats and expansion of medium (12[&le;] n< 23) and long (n[&ge;]23) (TG/CA)n repeats was significantly higher in human than other primates. Further, other dinucleotide repeats like TA were found in the orthologous genomic regions in other primates. Thus, selection, elongation and a selective process of conversion of other dinucleotide repeats in primates to TG/CA repeats in humans was apparent and presented in this study as a comprehensive model for the dynamics and role of TG/CA repeats in the human genome.

BackgroundVitamin D is a hormone that regulates the calcium homeostasis of the body. Besides this classical function, it is also regarded as an important immunomodulator. Most active Vitamin D actions are mediated through the Vitamin D receptor (VDR), a transcription factor and also a member of the nuclear receptor superfamily. In this study, we explored the phylogeographic attributes of the four most well-known polymorphisms of the VDR gene namely rs7975232 (ApaI), rs731235 (TaqI), rs1544410 (BsmI), rs2228570 (FokI) and also evaluated their association with the incidence of tuberculosis in global populations. This study integrated several in-silico approaches on population databases to evaluate the pattern of distribution, linkage and selection patterns of these SNPs. ResultsThe ancestral alleles of rs7975232, rs731235, and rs1544410 are still present in over 50% frequency in modern human populations. These SNPs also have a very strong linkage disequilibrium among themselves in all population groups but no haplotype blocks are seen in South Asian populations constituting these polymorphisms. The selection results reveal a negative Tajimas D value in West and East Eurasian populations suggesting positive selection in these regions... In correlation studies, we found no association between the incidence of tuberculosis and the allele or genotype frequency of these four SNPs. ConclusionThe four SNPs of VDR behave differently in South Asian populations as compared to West and East Eurasian populations but no significant association was found with the incidence of tuberculosis in global populations.

Simple sequence repeats (SSRs) are found ubiquitously in almost all genome, and their formation mechanism is ambiguous yet. Here, the SSRs were analyzed in 55 randomly selected segments of genomes from a fairly wide range of species, with introducing more open standard for extensively mining repeats. A high percentage of repeats were discovered in these segments, which is inconsistent with the current theory suggested that repeats tend to disappear over long-term evolution. Therefore, a mechanism is most probably responsible for continually producing repeats during replication to balance continuous repeat disappearance, which may makes the replicating process relatively semi-conservative. To improve the current straight-line slippage model, we proposed a folded slippage model involving the geometric space of nucleotides and hydrogen bond stability to explain the high-percent SSR occurrence, which can describe SSR expansion and contraction more reasonably. And analysis of external forces in the folding template strands suggested that the microsatellites tend to expand than contract. Our research may provide implements for contributions of microsatellites to genome evolution and complement semi-conservative replication.

The {beta} actin gene is involved in various cellular housekeeping processes including transcription, mRNA processing, cell signaling and chromosome remodeling. For regulating the expression of this gene under different environmental conditions, the promoter region of the {beta} actin gene is structurally dynamic with multiple regulatory features in the upstream region. Most previous information about the 5 regulatory region of the {beta} actin gene has been limited to in vitro laboratory experiments. Considering the need for functional versatility of expression of this gene in the Catfish Clarias batrachus in different environments, here we have analyzed the 5 regulatory region of {beta} actin and identified numerous elements that are variable. We have made comparisons of individuals from three populations found in three different diverse ecological systems, as well as in three sister species, to elucidate its structural diversity. Our results show that the 5 regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5 regulatory region of a housekeeping gene like {beta} actin, modify its architecture as per the environmental conditions. These modifications specifically includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5 regulatory region is conserved which was yet not highlighted. Author summaryPromoter is a regulatory region where the basal transcription machinery assembles to initiate the process of transcription. It plays crucial role in controlling the gene expression. The 5 regulatory region includes TATA box, CAAT box, GC box and Cis -acting regulatory elements. Most previous information about the 5 regulatory region of the {beta} actin gene has been limited to in vitro laboratory experiments. Our study results show that the 5 regulatory region has considerable diversity and changes in architecture with respect Cis-acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5 regulatory region of a housekeeping gene like {beta} actin, modify its architecture as per the environmental requirements. These modifications precisely includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5 regulatory region is conserved. These findings clearly define a novel role of promotor of {beta} actin gene which was yet not highlighted. These findings can broaden our understanding in linking TF in 5 regulatory regions to a specific environmental variable/disease conditions. This may become a simple strategy in understanding complex gene-environment interactions.

Long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis involves the activities of two groups of enzymes, the fatty acyl desaturases (Fads) and elongases of very long-chain fatty acid (Elovl). Fish are major source of beneficial n-3 LC-PUFA in human diet and there is a considerable interest to elucidate the mechanism and regulatory aspects of LC-PUFA biosynthesis in farmed fish species. The promoter of elovl5 elongase, which catalyze the rate limiting reaction of adding two carbons to the C18 PUFA have been previously described and characterized from several marine and diadromous teleost species. We report here the cloning and characterization of the elovl5 promoter from two freshwater fish species, the carnivorous snakehead fish (Channa striata) and zebrafish. Results show the importance of sterol regulatory element binding protein (Srebp) and the corresponding sterol responsive element (SRE) in the core regulatory region of both promoters. Mutagenesis luciferase and electrophoretic mobility shift assays confirm that SRE is indispensable for basal transcriptional activation in both species. In addition, several Sp1 binding sites located in close proximity with SRE were present in the snakehead promoter, with one having a potential synergy with SRE in regulating elovl5 expression. The core elovl5 promoter fragments of both species also directed in vivo expression in the yolk syncytial layer of developing zebrafish embryos. This study is the first functional promoter analysis of Elovl5 in freshwater teleost.

BackgroundSIRT3 is a NAD+ dependent deacetylase located in mitochondria and plays a critical role in various biological processes such as aging and cancer. Recent GWAS analyses have identified an intronic SNP, rs11607019, that significantly influences platelet function. MethodsTo investigate the genome-wide transcriptional effects of this variant, we performed site-directed mutagenesis experiments. ResultsOur results demonstrate that rs11607019 upregulates GABRE, COL12A1, PLEKHG4B, and SERF1B, while downregulating APOBEC3G in 293 cells, without cell tumor mutational burden karyotype phenotype. ConclusionThese findings suggest that rs11607019 is a strong candidate locus for blood cell phenotyping and may warrant further investigation in relation to kidney-related diseases in latent populations.

In the Japanese hagfish, Eptatretus burgeri, approximately 21% of the genomic DNA in germ cells (2n=52) consists of 16 chromosomes (eliminated [E]-chromosomes) that are eliminated from presumptive somatic cells (2n=36). To uncover the eliminated genome (E-genome), we have identified 16 eliminated repetitive DNA families from eight hagfish species, with 11 of these repeats being selectively amplified in the germline genome of E. burgeri. Furthermore, we have demonstrated that six of these sequences, namely EEEb1-6, are exclusively localized on all 16 E-chromosomes. This has led to the hypothesis that the eight pairs of E-chromosomes are derived from one pair of ancestral chromosomes via multiple duplication events over a prolonged evolutionary period. NGS analysis has recently facilitated the re-assembly of two distinct draft genomes of E. burgeri, derived from the testis and liver. This advancement allows for the prediction of not only nonrepetitive eliminated sequences but also over 100 repetitive and eliminated sequences, accomplished through K-mer-based analysis. In this study, we report four novel eliminated repetitive DNA sequences (designated as EEEb7-10) and confirm the relative chromosomal localization of all eliminated repeats (EEEb1-10) by fluorescence in situ hybridization (FISH). With the exception of EEEb10, all sequences were exclusively detected on EEEb1-positive chromosomes. Surprisingly, EEEb10 was detected as an intense signal on EEEb1-positive chromosomes and as a scattered signal on other chromosomes in germ cells. The study further divided the eight pairs of E-chromosomes into six groups based on the signal distribution of each DNA family, and fiber-FISH experiments showed that the EEEb2-10 family was dispersed in the EEEb1-positive extended chromatin fiber. These findings provide new insights into the mechanisms underlying chromosome elimination and the evolution of E-chromosomes, supporting our previous hypothesis.

Hypertension is caused by a combination of genetic and environmental factors. Angiotensinogen (AGT) is a component of RAAS, that regulates blood pressure. The human angiotensinogen (hAGT) gene has -6A/-6G polymorphism and -6A variant is associated with human hypertension. In this study, we have investigated the epigenetic regulation of the hAGT. To understand transcriptional regulation of the hAGT, we have made transgenic animals containing -6A. We show that HS affects DNA methylation and modulates transcriptional regulation of this gene in liver and kidney. High salt (HS) increases hAGT gene expression in -6A TG mice. We have observed that the number of CpG sites in the hAGT promoter is decreased after HS treatment. In the liver, seven CpG sites are methylated whereas after HS treatment, only three CpG sites remain methylated. In the kidney, five CpG sites are methylated, whereas after HS treatment, only three CpG sites remain methylated. These results suggest that HS promotes DNA demethylation and increasing AGT gene expression. RT-PCR and immunoblot analysis show that hAGT gene expression is increased by HS. Chip assay has shown that transcription factors bind strongly after HS treatment. RNA-Seq identified differentially expressed genes, novel target genes associated with hypertension, top canonical pathways, upstream regulators. One of the plausible mechanisms for HS induced up-regulation of the hAGT gene is through IL-6/JAK/STAT3/AGT axis.

With the rapid development of aquaculture, more and more fish species from wild environments are artificially domesticated and cultured. In the process of domestication, the fish develop some adaptations and phenotypic traits, namely selection signatures. However, it is still unclear about the biological process underlying these selection signatures. Here, we used grass carp (Ctenopharyngodon idellus), an aquaculture fish with the largest production worldwide, to detect its selection signatures and investigate the roles of DNA methylation in the emergence of selection signatures during domestication based on whole-genome bisulfite sequencing technology. Our results showed that domesticated grass carp demonstrated four selection signatures, including growth and metabolism, immunity, foraging and learning behaviors, and 38 candidate genes were associated with these traits. 16 of candidate genes, such as IGF-1, GK, GYS1, etc., were found to play major roles in the growth and metabolism. Immunity signature was related to 11 of candidate genes, including MHCI, MHCII, C1QA, etc. The GRM1, TAS1R1 and TAS1R3 genes were essential for the adaptation of domesticated grass carp to commercial feed in artificial rearing condition. The C-FOS, POMC and CBP genes might be responsible for the acquisition of novel feeding habits and contribute to faster growth indirectly by enhancing food intake. These findings would provide new insights to expand our understanding on the role of DNA methylation in shaping physiological phenotypes in fish, and also contribute to efficient breeding of aquaculture stocks and restocking programs.

Sperata seenghala (Giant river-catfish) and Sperata aor (Long-whiskered catfish) are commercially important freshwater catfishes of India, belongs to family Bagridae. Due to high nutritional significance and the low number of intramuscular bones, both fishes have considerable demand in South Asian countries. Both of the Sperata species are morphologically close and well adapted to the same habitat. In this study, we have assessed the level of genetic diversity and differentiation of S. seenghala and S. aor in the Ganga River based on the mitochondrial DNA (mtDNA) control region and compared with the other major Indian rivers. We found high haplotypes diversity for both the species in the Ganga. However, it was comparatively low for S. seenghala in Mahanadi and Brahmaputra populations. The phylogenetic and median-joining network strongly indicated the presence of two distinct maternal lineages of S. seenghala from the Ganga river. Interestingly, the genetic differentiation between S. seenghala of Ganga-Brahmaputra was much higher (~25.3%) than the S. seenghala and S. aor (~17%), whereas it was comparatively low between Ganges-Mahanadi (~8.0%). Our finding provided evidence that all the three rivers: Ganga, Mahanadi, and the Brahmaputra sustain a highly diverse and genetically distinct stock of giant river catfish; therefore, all populations should be considered as a different management unit for the protection of stocks. Our findings indicated that Brahmaputra lineages qualify the species level variations. This study can be further used as a reference database for proper lineage identification of S. seenghala and S. aor that could formulate the appropriate conservation and management plans.