Genetic population structure of a highly migratory Hilsa Shad, Tenualosa ilisha, in three river systems, inferred from four mitochondrial genes analysis

Mohindra, Vindhya; Divya, Bodiga; Kumar, Rajesh; Singh, Rajeev K.; Dwivedi, Arvind Kumar; Mandal, Sangeeta; Masih, Prachi; Lal, Kuldeep K.; Jena, J. K.

doi:10.1007/s10641-019-00881-8

Cited by 10 publications

(12 citation statements)

References 34 publications

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“…In the population structure analysis, only one population of Hilsa shad was identi ed with some admixture individuals (32%) containing partial genes from other population in the water bodies of Bangladesh. The mentioned other population might not represent the Hilsa population of the Hoogly and Bhagirathi river system, India because, the Hilsa shads of both migratory routes of Bangladesh and India showed genetic homogeneity 10,17 . The Ganges and Brahmaputra rivers of Indian part are the upstream of the Padma and the Jamuna river of Bangladesh and might be belonged to the same population.…”

Section: Discussionmentioning

confidence: 99%

“…Due to environmental changes, pollution and over exploitation, many shes are losing genetic diversity currently 14 . Previous studies on genetic population structure of T. ilisha were mostly based on allozymes, allele frequencies, microsatellite DNA markers and mitochondrial DNA regions: Cytochrome b (CytB), ATPase 6&8 (ATPase), 12s and 16s rRNA 10,[15][16][17][18] . Mitochondrial gene analysis indicated temporal stability of sampled populations; with low genetic differentiation between temporal samples from same locality of three Indian rivers 10 .…”

Section: Introductionmentioning

confidence: 99%

“…Previous studies on genetic population structure of T. ilisha were mostly based on allozymes, allele frequencies, microsatellite DNA markers and mitochondrial DNA regions: Cytochrome b (CytB), ATPase 6&8 (ATPase), 12s and 16s rRNA 10,[15][16][17][18] . Mitochondrial gene analysis indicated temporal stability of sampled populations; with low genetic differentiation between temporal samples from same locality of three Indian rivers 10 . Very recently, A study discover the population genomics and structure of Hilsa shad in Bangladesh waters based on six and eight locations respectively using NextRAD sequencing 19,20 .…”

Section: Introductionmentioning

confidence: 99%

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Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method 

Sarker¹,

Naher²,

Huang³

et al. 2020

Preprint

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Tenualosa ilisha is a popular anadromous and significant trans-boundary fish. For sustainable management and conservation of this fish, drawing an appropriate picture reflecting population status of this species is very essential based on their all-strategic habitats in Bangladesh. In this study, 139 samples from 18 sites were collected and cross-species gene enrichment method was applied to discover the exact population status of the fish. Like most of the Clupeiforms, nucleotide diversity and variation of this shad were very low. Population differences between most of the locations were low and not significant. However, P values of a few locations were significant (P< 0.05) but their pairwise FST values were very poor, which is inadequate to recognize any local populations. Structure analysis, PCA and maximum likelihood IQtree all indicated the presence of a single population in the Bangladesh water with some admixture individuals, which may contain partial genes from other populations. In the ML IQtree and Network, most of the individuals were mixed without showing any precise grouping, which might due to their highly migratory nature. Fishes from special type of habitats, e.g., haors, small coastal rivers etc. were not unique and no genetic differences between migratory cohorts were found.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method 

Sarker¹,

Naher²,

Huang³

et al. 2020

Preprint

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“…Declines in production of Hilsa from natural population have raised concerns and it may probably due to over exploitation and/or change in habitat 7,8 . There is an urgent need for development of technology for captive breeding, seed production and culture in confined water environment.…”

Section: Introductionmentioning

confidence: 99%

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

Mohindra

Dangi

Tripathi

et al. 2019

Sci Rep

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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.

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“…Tenualosa ilisha , commonly known as Hilsa, is an economically important anadromous fish species, which migrates from marine to freshwater for sexual maturity [17] and faces different environmental fluctuations, including salinity and temperature gradients during its life span as well as pollution levels in the river systems, make them more prone to diseases. There are reports of bacterial [18] and protozoan parasites infections [19] in wild Hilsa, however, there is no information in Hilsa about the Epizootic ulcerative syndrome (EUS) in wild.…”

Section: Introductionmentioning

confidence: 99%

Tissue specific alpha-2-Macroglobulin (A2M) splice isoform diversity in Hilsa shad, Tenualosa ilisha (Hamilton, 1822)

et al. 2019

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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.

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Genetic population structure of a highly migratory Hilsa Shad, Tenualosa ilisha, in three river systems, inferred from four mitochondrial genes analysis

Cited by 10 publications

References 34 publications

Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method

Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method

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

Tissue specific alpha-2-Macroglobulin (A2M) splice isoform diversity in Hilsa shad, Tenualosa ilisha (Hamilton, 1822)

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Genetic population structure of a highly migratory Hilsa Shad, Tenualosa ilisha, in three river systems, inferred from four mitochondrial genes analysis

Cited by 10 publications

References 34 publications

Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method&nbsp;

Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method&nbsp;

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

Tissue specific alpha-2-Macroglobulin (A2M) splice isoform diversity in Hilsa shad, Tenualosa ilisha (Hamilton, 1822)

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Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method

Existence of a Single Population of Hilsa Shad (Tenualosa Ilisha) With Low Genetic Variation in Bangladesh Waters Revealed by Cross-Species Gene Enrichment Method