- Data note
- Open Access
Draft genome of Ompok bimaculatus (Pabda fish)
BMC Research Notes volume 12, Article number: 825 (2019)
Pabda (Ompok bimaculatus) is a freshwater catfish, largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. This fish is highly valued for its fabulous taste and high nutritional value and is very popular as a rich source of proteins, omega-3 and omega-6 fatty acids, vitamins and mineral for growing children, pregnant females and elders. We performed de-novo sequencing of Ompok bimaculatus using a hybrid approach and present here a draft assembly for this species for the first time.
The genome of Ompok bimaculatus (Fig. 1: Table 1, Data file 3) from Ganges river, has been sequenced by hybrid approach using Illumina short reads and PacBio long reads followed by structural annotations. The draft genome assembly was found to be 718 Mb with N50 size of 81 kb. MAKER gene annotation tool predicted 21,371 genes.
Pabda fish is a freshwater catfish, with its fabulous taste and high nutritional value. Ompok bimaculatus (Family: Siluridae), also known as Indian butter catfish or commonly known as pabda, has fascinated considerable attention in diversification due to its good taste, high nutritional value and soft bony structure [1,2,3]. Pabda is largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. Catfishes are an excellent source of omega-3 and omega-6 fatty acids, vitamins and mineral those are excellent for growing children, pregnant females and elders. Overexploitation for food is a major threat and has resulted in remarkable population decline [4, 5]. The fish is in declining phase due to lack of definite information on the biological aspects accompanied by declining population owing to habitat loss, indiscriminate pesticide and weedicide use, loss of breeding grounds and overfishing valued for its unique taste has pushed the population of Pabda in IUCN red list of threatened species [3, 5].
Knowing the complete genome of this fish will help in better understanding of the genome organization, evolution as well as for conservation and farming applications . This involves steeping up of breeding process, as well as to identify lineage specific changes that are critical for its adaptation besides knowing about the risk factors as well as its immune system that helps in its survival in the wild or in captivity.
Fresh Ompok bimaculatus which were approximately 4 months old were freshly caught from the Ganges river in India and instantly used for DNA extraction. The taxonomic identification of this fish has been confirmed following standard taxonomic keys like studying the fin formula and other standard morphological characteristics. Muscle tissue was dissected from this fish and high-molecular weight genomic DNAs was purified from one specimen using Qiagen Genomic-tip 100/G as per the manufacturer’s instruction. The quality and quantity of the isolated genomic DNA was checked on NanoDrop followed by 0.8% Agarose gel.
Two pair-end libraries were constructed for Illumina sequencing and one SMRTbell library was constructed for Pacific Bioscience Sequel, single molecule, real time (SMRT, Single Molecule Real Time) sequencing platforms as mentioned in Table 1, Date file 1. The quality of the reads was checked using FastQC (Table 1) .
MaSuRCA (Maryland Super- Read Celera Assembler) v3.2.8 was used for hybrid de novo assembly  using both the Illumina and PacBio data. The genome assembly has been deposited in the NCBI GeneBank under the Bioproject ID: PRJNA552450 (Table 1, Data files 2, 4). The assembled genome size of Ompok bimaculatus is 718 Mb and approximately 72% of the genome has been assembled as per the in silico genome size estimation.
The BUSCO v3  analysis revealing 85.7% completeness, indicating the genome to be of good quality. MAKER v3.0 pipeline  was used for structural annotation. GC content of the genome was determined to be 38.84%. RepeatMasker v4.0.9 was used with the latest version of Repbase database [11, 12], repeat elements identified were 7.87%. Altogether, 21,371 genes were predicted by the MAKER gene annotation pipeline using proteins from channel catfish. Out of the 21,371 genes, 20,923 were annotated using Diamond  (BlastX mode) against NCBI ‘NR’ database and 5589 genes were found to have GO (Gene Ontology) term assigned to them. The butter catfish genome was found to be comparable to Ictalurus punctatus (Channel catfish, 892 Mb genome and 27,156 genes)  and to the genome of Pangasianodon hypophthalmus (Striped catfish, 715 Mb genome and 24,083 genes) .
The number of the scaffolds containing N in the genome are 27 and a total of 3773 bases are positioned in this gap region. The assembled genome size of the Indian butter catfish is 718 MB as compared to in silico estimated genome size of 992 Mb.
Availability of data materials
The data described in this Data note can be freely and openly accessed via figshare, Refer Table 1 for details and links. The genome assembly has been deposited in the NCBI GeneBank under the Bioproject ID: PRJNA552450 (Table 3).
- BUSCO :
Benchmarking Universal Single-Copy Orthologs
- MaSuRCA :
Maryland Super-Read Celera Assembler
- IUCN :
International Union for conservation of nature
- PacBio :
- GO :
- SMRT :
single molecule real time sequencing
Banik S, Goswami P, Acharjee T, Malla S. Ompok pabda (Hamilton-Buchanan, 1822): an endangered catfish of Tripura, India: reproductive physiology related to freshwater lotic environment. J Environ. 2012;1(2):45–55.
Biswas P, Jena AK, Saha H, Chowdhury TG. Induced breeding and seed production of Pabda: a species with potential for aquaculture diversification in northeast India. World Aquac. 2018;49(1):41–5.
Rawat P, Biswas P, Jena AK, Patel AB, Pandey PK. Effect of dietary incorporation of natural attractants on growth and survival during seed rearing of Indian butter catfish, Ompok bimaculatus. J Environ Biol. 2019;40(4):661–7.
Mishra SS, Acharjee SK, Chakraborty SK. Development of tools for assessing conservation categories of siluroid fishes of fresh water and brackish water wetlands of South West Bengal, India. Environ Biol Fishes. 2009;84(4):395–407.
Ng, H.H., Tenzin, K. & Pal, M. 2010. Ompok bimaculatus. The IUCN Red List of Threatened Species. 2010. http://dx.doi.org/10.2305/IUCN.UK.2010-4.RLTS.T166616A6248140.en.
Ryder OA. Conservation genomics: applying whole genome studies to species conservation efforts. Cytogenet Genome Res. 2005;108(1–3):6–15.
Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013;29(21):2669–77.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015;31(19):3210–2.
Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore Holt, Alvarado C, Yandell M. MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. Genome Res. 2008;18(1):188–96.
Smit A, Hubley R, Green P. RepeatMasker Open-4.0. 2013–2015. 2015. pp 289–300. (http://www.repeatmasker.org/faq.html).
Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 2005;110(1–4):462–7.
Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods. 2015;12(1):59.
Liu Z, Liu S, Yao J, Bao L, Zhang J, Li Y, Jiang C, Sun L, Wang R, Zhang Y, Zhou T. The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts. Nat Commun. 2016;7:11757.
Kim OT, Nguyen PT, Shoguchi E, Hisata K, Vo TT, Inoue J, Shinzato C, Le BT, Nishitsuji K, Kanda M, Nguyen VH. A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. BMC Genomics. 2018;19(1):733.
Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. Table 2.doc. figshare. 2019. https://doi.org/10.6084/m9.figshare.9827312.v1.
Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. Table 3.doc. figshare. 2019. https://doi.org/10.6084/m9.figshare.9830954.v1.
Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. Ompok Picture. figshare. 2019. https://doi.org/10.6084/m9.figshare.9831155.v1.
The authors like to thank Joydeep Karmakar for sample collection and the entire department of Biochemistry, AIIMS Delhi for providing support, infrastructure and logistic to work.
This research is jointly funded by RD and SK.
Ethics approval and consent to participate
Consent for publication
The authors declare that they have no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data.
About this article
Cite this article
Dhar, R., Pethusamy, K., Singh, S. et al. Draft genome of Ompok bimaculatus (Pabda fish). BMC Res Notes 12, 825 (2019). https://doi.org/10.1186/s13104-019-4867-y
- Butter catfish
- Ompok bimaculatus
- Whole genome sequence