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Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.

ABSTRACT: This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N50 of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various homeostasis processes. Highest number of genes belongs to cellular calcium ion homeostasis, followed by tissue homeostasis. A total of 97 genes were identified, with 16 GO terms related to water homeostasis. Claudins, Aquaporins, Connexins/Gap junctions, Adenylate cyclase, Solute carriers and Voltage gated potassium channel genes were observed to be higher in number in T. ilisha, as compared to that in other teleost species. Seven novel gene variants, in addition to claudin gene (CLDZ), were found in T. ilisha. The present study also identified two putative novel genes, NKAIN3 and L4AM1, for the first time in fish, for which further studies are required for pinpointing their functions in fish. In addition, 1.6 million simple sequence repeats were mined from draft genome assembly. The study provides a valuable genomic resource for the anadromous Hilsa. It will form a basis for future studies, pertaining to its adaptation mechanisms to different salinity levels during migration, which in turn would facilitate in its domestication.

SUBMITTER: Mohindra V

PROVIDER: S-EPMC6848103 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.

Mohindra Vindhya V Dangi Tanushree T Tripathi Ratnesh K RK Kumar Rajesh R Singh Rajeev K RK Jena J K JK Mohapatra T T

Scientific reports 20191111 1

This study provides the first high-quality draft genome assembly (762.5 Mb) of Tenualosa ilisha that is highly contiguous and nearly complete. We observed a total of 2,864 contigs, with 96.4% completeness with N<sub>50</sub> of 2.65 Mbp and the largest contig length of 17.4 Mbp, along with a complete mitochondrial genome of 16,745 bases. A total number of 33,042 protein coding genes were predicted, among these, 512 genes were classified under 61 Gene Ontology (GO) terms, associated with various ...[more]

PMID: 31712633

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Project description:The present study, for the first time, reported twelve A2M isoforms in Tenualosa ilisha, through SMRT sequencing. Hilsa shad, T. ilisha, an anadromous fish, faces environmental stresses and is thus prone to diseases. Here, expression profiles of different A2M isoforms in four tissues were studied in T. ilisha, for the tissue specific diversity of A2M. Large scale high quality full length transcripts (>0.99% accuracy) were obtained from liver, ovary, testes and gill transcriptomes, through Iso-sequencing on PacBio RSII. A total of 12 isoforms, with complete putatative proteins, were detected in three tissues (7 isoforms in liver, 4 in ovary and 1 in testes). Complete structure of A2M mRNA was predicted from these isoforms, containing 4680 bp sequence, 35 exons and 1508 amino acids. With Homo sapiens A2M as reference, six functional domains (A2M_N,A2M_N2, A2M, Thiol-ester_cl, Complement and Receptor domain), along with a bait region, were predicted in A2M consensus protein. A total of 35 splice sites were identified in T. ilisha A2M consensus transcript, with highest frequency (55.7%) of GT-AG splice sites, as compared to that of Homo sapiens. Liver showed longest isoform (X1) consisting of all domains, while smallest (X10) was found in ovary with one Receptor domain. Present study predicted five putative markers (I-212, I-269, A-472, S-567 and Y-906) for EUS disease resistance in A2M protein, which were present in MG2 domains (A2M_N and A2M_N2), by comparing with that of resistant and susceptible/unknown response species. These markers classified fishes into two groups, resistant and susceptible response. Potential markers, predicted in T. ilisha, placed it to be EUS susceptible category. Putative markers reported in A2M protein may serve as molecular markers in diagnosis of EUS disease resistance/susceptibility in fishes and may have a potential for inclusion in the marker panel for pilot studies. Further, challenging studies are required to confirm the role of particular A2M isoforms and markers identified in immune protection against EUS disease.

Project description:The migration of anadromous fish in heterogenic environments unceasingly imposes a selective pressure that results in genetic variation for local adaptation. However, discrimination of anadromous fish populations by fine-scale local adaptation is challenging because of their high rate of gene flow, highly connected divergent population, and large population size. Recent advances in next-generation sequencing (NGS) have expanded the prospects of defining the weakly structured population of anadromous fish. Therefore, we used NGS-based restriction site-associated DNA (NextRAD) techniques on 300 individuals of an anadromous Hilsa shad (Tenualosa ilisha) species, collected from nine strategic habitats, across their diverse migratory habitats, which include sea, estuary, and different freshwater rivers. The NextRAD technique successfully identified 15,453 single nucleotide polymorphism (SNP) loci. Outlier tests using the FST OutFLANK and pcadapt approaches identified 74 and 449 SNPs (49 SNPs being common), respectively, as putative adaptive loci under a divergent selection process. Our results, based on the different cluster analyses of these putatively adaptive loci, suggested that local adaptation has divided the Hilsa shad population into two genetically structured clusters, in which marine and estuarine collection sites were dominated by individuals of one genetic cluster and different riverine collection sites were dominated by individuals of another genetic cluster. The phylogenetic analysis revealed that all the riverine populations of Hilsa shad were further subdivided into the north-western riverine (turbid freshwater) and the north-eastern riverine (clear freshwater) ecotypes. Among all of the putatively adaptive loci, only 36 loci were observed to be in the coding region, and the encoded genes might be associated with important biological functions related to the local adaptation of Hilsa shad. In summary, our study provides both neutral and adaptive contexts for the observed genetic divergence of Hilsa shad and, consequently, resolves the previous inconclusive findings on their population genetic structure across their diverse migratory habitats. Moreover, the study has clearly demonstrated that NextRAD sequencing is an innovative approach to explore how dispersal and local adaptation can shape genetic divergence of non-model anadromous fish that intersect diverse migratory habitats during their life-history stages.

Project description:Small-scale fisheries (SSFs) have been playing a crucial role in meeting the basic needs of millions of people around the world. Despite this, the sustainability of global fisheries is a growing concern, and the factors enabling or constraining the sustainable management of small-scale fisheries remain poorly understood. Hilsa shad (Tenualosa ilisha) is the single most valuable species harvested in Bangladesh waters, serves nutrition, income, and employment to the large population. This study analyzed the state and challenges of hilsa fishery in the Gangetic River systems (Padma and Meghna Rivers) by using two frameworks, namely the social-ecological systems (SES) and drivers-pressure-state-impact-responses (DPSIR) frameworks. Primary data for this analysis were collected by in-depth interviews (n = 130) and focus group discussions (n = 8) with various stakeholders in the hilsa fisheries. The perspectives explored here have been both critical and constructive, including the identification of problems and suggestions for improving the management of this particular social-ecological system. Hilsa fisheries, however, have come under severe threat since 2003 because of population growth, overfishing, pollution, climate change, the disruption of migration routes due to siltation, etc. All these have caused reduced catches and less stable incomes for fishers. This, in turn, has led to poverty, malnutrition, social tensions, stakeholder conflicts, and debt cycles amongst more impoverished fishing communities. These problems have been compounded by improved fishing technology amongst larger-scale ventures, the use of illegal fishing gears, and the non-compliance of government fishery management programs. Recommendations include the promotion of community-supported fisheries, the enhancement of stakeholder's social resilience, the introduction of co-management approach, an increase in incentives and formal financial supports, and possible community-managed sustainable ecotourism including hilsa fishing-based tourism.

Dataset Information

Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.

Publications

Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies.

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