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Genome of Tenualosa ilisha from the river Padma, Bangladesh

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Abstract

Objective

Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An anadromous species, like the salmon and many other migratory fish, it is a unique species that lives in the sea and travels to freshwater rivers for spawning. During its entire life, Tenualosa ilisha migrates both from sea to freshwater and vice versa.

Data description

The genome of Tenualosa ilisha collected from the river Padma of Rajshahi, Bangladesh has been sequenced and its de novo hybrid assembly and structural annotations are being reported here. Illumina and PacBio sequencing platforms were used for high depth sequencing and the draft genome assembly was found to be 816 MB with N50 size of 188 kb. MAKER gene annotation tool predicted 31,254 gene models. Benchmarking Universal Single-Copy Orthologs refer 95% completeness of the assembled genome.

Objective

Hilsa shad known as ilish in Bangladeshis popular for its taste and the texture of its flesh. This species of fish belongs to the shad in Clupeidae family. In addition to the Bay of Bengal and riverine Bangladesh (the Padma, Jamuna, Meghna, and other coastal rivers of Bangladesh), this fish is also found in the Persian Gulf, Mediterranean Sea, Arabian Sea and China Sea [1]. Fisheries, a part of the Bangladesh’s cultural heritage, have played an important role on its socioeconomic development in terms of protein supply, generation of employment and earning of foreign currency. According to the FAO, in 2018 Bangladesh ranked 3rd in the world in inland fish production. Hilsa (Tenualosa ilisha), is the most popular among the 650 or so marine and inland fish found in Bangladesh. It contributes to 11% of total fish production and 1% to the national GDP, 3.00% of the total export earnings and about 2.5 million people in Bangladesh are directly dependent on Hilsa in providing for their families [2, 3]. At present more than 60% of global Hilsa catch is reported from Bangladesh, 20–25% from Myanmar, 15–20% from India and 5–10% from other countries (e.g., Iraq, Kuwait, Malaysia, Thailand and Pakistan). The recent Hilsa production of Bangladesh is about half a million metric ton [4]. In spite of such importance Hilsa is still lacks molecular genomic information. Significance of this data for the improvement in sustainability and maintenance of diversity of this fish cannot therefore be overemphasized.

Data description

Fresh Tenualosa ilisha samples from the river Padma at Rajshahi were collected and instantly preserved on dry ice. White and red muscles of the fish were used for DNA extraction. A modified SDS (Sodium Dodecyl Sulfate) method [5], optimized in our lab was used for DNA extraction (detailed methodology in Data File 1, Table 1).

Table 1 Overview of data files/data sets

Pair end library with an insert size of around 300 bp was constructed for Illumina sequencing using NEB NebNext Ultra II DNA kit (detailed methodology in Data File 1, Table 1) Genomic DNA was sequenced by Illumina HiSeq 4000 and Pacific Bioscience Sequel, single molecule, real time (SMRT, Single Molecule Real Time) sequencing platforms. The quality of the reads were checked using FastQC [6]. MaSuRCA (Maryland Super-Read Celera Assembler) ver 3.2.6 was used for hybrid de novo assembly [7] using both the Illumina and PacBio data. The genome assembly data has been deposited in the NCBI GeneBank under the Accession numbers GCA_003651195.1 (Data file 2; Table 1). Illumina only data generated a fragmented assembly and showed 91% BUSCO [8] completeness. Addition of 15.7 Gbp data from PacBio significantly improved the quality and contiguity of the genome. Compared to Illumina only, N50 improved from 13 Kb (kilo base pair) to 188 Kb. Similarly, the total number of scaffolds reduced from 475,121 to 124,209. The assembled genome size of Tenualosa ilisha Padma Bangladesh is now 816 Mb (Mega base pair) and approximately 82% of the genome has been assembled. The BUSCO analysis revealing 95% completeness as well as significantly lower number of scaffolds and considerably better N50 indicates the genome to be of high-quality. The genome sequence data has been deposited in the NCBI GeneBank under the Accession numbers QYSC01000001-QYSC01124209 (Data file 3; Table 1). MAKER ver 3.0 pipeline [9] was used for structural annotation. GC content of the genome was determined to be 43.61%. RepeatMasker and Repeatmodeler using the latest version of repbase database [10,11,12] identified 27.27% repeat elements. Altogether, 31,254 gene models were predicted using the MAKER gene annotation pipeline based on both de novo and reference based predictions using genes/proteins from other fish species (Atlantic herring, carp, salmon, zebrafish). Out of the 31,254 genes, 24,648 were annotated using InterProScan [13] and 16,078 genes were found to have at least 1 GO (Gene Ontology) term assigned to them (Data file 4, Table 1). The Hilsa genome was found to be comparable to the Atlantic herring (807 Mb genome and 28,335 genes) [14] and to the genome of the common carp (1.8 Gb and 52,000 genes) [15].

Limitations

The number of the regions unassembled in the genome is 4605 and the total number of bases positioned in this gap is 2,268,925 bp.

Abbreviations

BUSCO:

Benchmarking Universal Single-Copy Orthologs

PacBio:

Pacific Bioscience

Gbp:

giga base pair

Mb:

mega base pair

Kb:

kilo base pair

bp:

base pair

GO:

gene ontology

SDS:

sodium dodecyl sulfate

EDTA:

ethylenediaminetetraacetic acid

qPCR:

quantitative polymerase chain reaction

SMRT:

single molecule real time sequencing

MaSuRCA:

Maryland Super-Read Celera Assembler

EST:

expressed sequenced tag

SNAP:

Semi-HMM-based Nucleic Acid Parser

References

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Authors’ contributions

HK and MSM initiated the project. HK, MSM, MRI, PI, MNN and AD designed the overall project. HK and MRI led the project. AD and OA collected the samples with the help of MNN.AD and OA extracted the DNA. PI sequenced the Tenualosa ilisha Padma BD genome. AB assembled the genome and performed the structural and functional annotations. TE and RN performed the repeat and GC content analysis. HK, MRI and AD wrote the manuscript. HK, MRI, MSM, PI, AB, MNN, AD, OA, TE, RN reviewed the manuscript. All authors read and approved the final manuscript.

Acknowledgements

Authors concede the support of Hera Biosciences for the sequencing service and that of Southern Cross University, Lismore, Australia for the computational support.

Competing interests

The authors declare that they have no competing interests.

Consent for publication

Not applicable.

Data availability

The genome sequence data has been available at DDBJ/ENA/GenBank under the Accession numbers QYSC01000001-QYSC01124209 and the assembled genome at GCA_003651195.1. The version described in this paper is the first version, QYSC00000000.1.

Ethics approval and consent to participate

The experiments mentioned in this study have been approved by the institutional review committee of University of Dhaka.

Funding

This study did not receive any formal funding.

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Author information

Correspondence to Haseena Khan.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Das, A., Ianakiev, P., Baten, A. et al. Genome of Tenualosa ilisha from the river Padma, Bangladesh. BMC Res Notes 11, 921 (2018) doi:10.1186/s13104-018-4028-8

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Keywords

  • Hilsa shad
  • Tenualosa ilisha
  • Clupediae
  • Whole genome sequence
  • NGS platform