Das et al.

BMC Res Notes (2018) 11:921

[Link] BMC Research Notes

DATA NOTE Open Access

Genome of Tenualosa ilisha from the river

Padma, Bangladesh
Avizit Das1, Peter Ianakiev2, Abdul Baten3,4, Rifath Nehleen1, Tasneem Ehsan1, Oly Ahmed1,
Mohammad Riazul Islam1, M. Niamul Naser5, Mong Sano Marma6 and Haseena Khan1*

Abstract
Objective: Hilsa shad (Tenualosa ilisha), is a popular fish of Bangladesh belonging to the Clupeidae family. An ana-
dromous 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.
Keywords: Hilsa shad, Tenualosa ilisha, Clupediae, Whole genome sequence, NGS platform

Objective families [2, 3]. At present more than 60% of global Hilsa
Hilsa shad known as ilish in Bangladeshis popular for catch is reported from Bangladesh, 20–25% from Myan-
its taste and the texture of its flesh. This species of fish mar, 15–20% from India and 5–10% from other countries
belongs to the shad in Clupeidae family. In addition to (e.g., Iraq, Kuwait, Malaysia, Thailand and Pakistan). The
the Bay of Bengal and riverine Bangladesh (the Padma, recent Hilsa production of Bangladesh is about half a mil-
Jamuna, Meghna, and other coastal rivers of Bangla- lion metric ton [4]. In spite of such importance Hilsa is
desh), this fish is also found in the Persian Gulf, Medi- still lacks molecular genomic information. Significance
terranean Sea, Arabian Sea and China Sea [1]. Fisheries, of this data for the improvement in sustainability and
a part of the Bangladesh’s cultural heritage, have played maintenance of diversity of this fish cannot therefore be
an important role on its socioeconomic development in overemphasized.
terms of protein supply, generation of employment and
earning of foreign currency. According to the FAO, in Data description
2018 Bangladesh ranked 3rd in the world in inland fish Fresh Tenualosa ilisha samples from the river Padma
production. Hilsa (Tenualosa ilisha), is the most popu- at Rajshahi were collected and instantly preserved on
lar among the 650 or so marine and inland fish found in dry ice. White and red muscles of the fish were used for
Bangladesh. It contributes to 11% of total fish production DNA extraction. A modified SDS (Sodium Dodecyl Sul-
and 1% to the national GDP, 3.00% of the total export fate) method [5], optimized in our lab was used for DNA
earnings and about 2.5 million people in Bangladesh extraction (detailed methodology in Data File 1, Table 1).
are directly dependent on Hilsa in providing for their Pair end library with an insert size of around 300 bp
was constructed for Illumina sequencing using NEB Neb-
Next Ultra II DNA kit (detailed methodology in Data
*Correspondence: haseena@[Link] File 1, Table 1) Genomic DNA was sequenced by Illu-
1
Department of Biochemistry and Molecular Biology, University of Dhaka,
Dhaka 1000, Bangladesh mina HiSeq 4000 and Pacific Bioscience Sequel, single
Full list of author information is available at the end of the article molecule, real time (SMRT, Single Molecule Real Time)

© The Author(s) 2018. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License
([Link] 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 ([Link]
publi​cdoma​in/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Das et al. BMC Res Notes (2018) 11:921 Page 2 of 3

Table 1 Overview of data files/data sets

Label Name of data file/data set File types (file Data repository and identifier (DOI or accession number)
extension)

Data file 1 DNA isolation and library preparation .docs file https​://figsh​[Link]/s/467b8​b6701​49f1a​0617c​
methodology
Data file 2 Whole genome assembly data FASTA NCBI GeneBank (Accession numbers: GCA_003651195.1)
([Link]
Data file 3 Whole genome sequence FASTA NCBI GeneBank (Accession numbers: QYSC01000001–
QYSC01124209) ([Link]
00000​00.)
Data file 4 Annotation data file .tsv https​://figsh​[Link]/s/270b5​4d9d0​76ef5​e5901​

sequencing platforms. The quality of the reads were Limitations

checked using FastQC [6]. MaSuRCA (Maryland Super- The number of the regions unassembled in the genome is
Read Celera Assembler) ver 3.2.6 was used for hybrid de 4605 and the total number of bases positioned in this gap
novo assembly [7] using both the Illumina and PacBio is 2,268,925 bp.
data. The genome assembly data has been deposited
in the NCBI GeneBank under the Accession numbers
Abbreviations
GCA_003651195.1 (Data file 2; Table 1). Illumina only BUSCO: Benchmarking Universal Single-Copy Orthologs; PacBio: Pacific
data generated a fragmented assembly and showed 91% Bioscience; Gbp: giga base pair; Mb: mega base pair; Kb: kilo base pair; bp:
BUSCO [8] completeness. Addition of 15.7 Gbp data base pair; GO: gene ontology; SDS: sodium dodecyl sulfate; EDTA: ethylenedi-
aminetetraacetic acid; qPCR: quantitative polymerase chain reaction; SMRT:
from PacBio significantly improved the quality and con- single molecule real time sequencing; MaSuRCA​: Maryland Super-Read Celera
tiguity of the genome. Compared to Illumina only, N50 Assembler; EST: expressed sequenced tag; SNAP: Semi-HMM-based Nucleic
improved from 13 Kb (kilo base pair) to 188 Kb. Simi- Acid Parser.
larly, the total number of scaffolds reduced from 475,121 Authors’ contributions
to 124,209. The assembled genome size of Tenualosa ili- HK and MSM initiated the project. HK, MSM, MRI, PI, MNN and AD designed
sha Padma Bangladesh is now 816 Mb (Mega base pair) the overall project. HK and MRI led the project. AD and OA collected the
samples with the help of [Link] and OA extracted the DNA. PI sequenced
and approximately 82% of the genome has been assem- the Tenualosa ilisha Padma BD genome. AB assembled the genome and
bled. The BUSCO analysis revealing 95% completeness as performed the structural and functional annotations. TE and RN performed
well as significantly lower number of scaffolds and con- 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
siderably better N50 indicates the genome to be of high- read and approved the final manuscript.
quality. The genome sequence data has been deposited
in the NCBI GeneBank under the Accession numbers Author details
1
Department of Biochemistry and Molecular Biology, University of Dhaka,
QYSC01000001-QYSC01124209 (Data file 3; Table 1). Dhaka 1000, Bangladesh. 2 Hera Biosciences LLC, Medford, MA, USA.
MAKER ver 3.0 pipeline [9] was used for structural anno- 3
AgResearch, Grasslands Research Centre, Palmerston North 4442, New
tation. GC content of the genome was determined to be Zealand. 4 Southern Cross Plant Science, Southern Cross University, Lismore,
NSW, Australia. 5 Department of Zoology, University of Dhaka, Dhaka 1000,
43.61%. RepeatMasker and Repeatmodeler using the lat- Bangladesh. 6 Qiagen Sciences, Waltham, MA, USA.
est version of repbase database [10–12] identified 27.27%
repeat elements. Altogether, 31,254 gene models were Acknowledgements
Authors concede the support of Hera Biosciences for the sequencing service
predicted using the MAKER gene annotation pipeline and that of Southern Cross University, Lismore, Australia for the computational
based on both de novo and reference based predictions support.
using genes/proteins from other fish species (Atlan-
Competing interests
tic herring, carp, salmon, zebrafish). Out of the 31,254 The authors declare that they have no competing interests.
genes, 24,648 were annotated using InterProScan [13]
and 16,078 genes were found to have at least 1 GO (Gene Consent for publication
Not applicable.
Ontology) term assigned to them (Data file 4, Table 1).
The Hilsa genome was found to be comparable to the Data availability
Atlantic herring (807 Mb genome and 28,335 genes) The genome sequence data has been available at DDBJ/ENA/GenBank under
the Accession numbers QYSC01000001-QYSC01124209 and the assembled
[14] and to the genome of the common carp (1.8 Gb and genome at GCA_003651195.1. The version described in this paper is the first
52,000 genes) [15]. version, QYSC00000000.1.
Das et al. BMC Res Notes (2018) 11:921 Page 3 of 3

Ethics approval and consent to participate 6. FastQC program. https​://[Link]​forma​[Link]​[Link]/proje​cts/

The experiments mentioned in this study have been approved by the institu- fastq​c/. Accessed 12 Jan 2017.
tional review committee of University of Dhaka. 7. Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaS-
uRCA genome assembler. Bioinformatics. 2013;29(21):2669–77.
Funding 8. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
This study did not receive any formal funding. BUSCO: assessing genome assembly and annotation completeness with
single-copy orthologs. Bioinformatics. 2015;31(19):3210–2.
9. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Alvarado
Publisher’s Note AS, Yandell M. MAKER: an easy-to-use annotation pipeline designed for
Springer Nature remains neutral with regard to jurisdictional claims in pub- emerging model organism genomes. Genome Res. 2008;18(1):188–96.
lished maps and institutional affiliations. 10. Smit A, Hubley R, Green P. RepeatMasker open-4.0. 2013–2015. Seattle,
WA, USA: Institute for Systems Biology; 2015. [Link]
Received: 16 October 2018 Accepted: 19 December 2018 [Link]/[Link].
11. Smit A, Hubley R. RepeatModeler open 1.0. Seattle, WA, USA: Institute for
Systems Biology; 2008. [Link]
12. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J.
Repbase update, a database of eukaryotic repetitive elements. Cytogen
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