The genome assembly has been deposited in the NCBI GeneBank under the Bioproject ID: PRJNA552450 (Table 1, Data files 2, 4). 2008;18(1):188–96. Cite this article. Cytogenet Genome Res. A total of 80 individuals of Ompok pabda were sampled from four coastal rivers located in the southeastern coastal region of Bangladesh from January, 2014 to August, 2014 (Table I). Mishra SS, Acharjee SK, Chakraborty SK. The relationship of fecundity with total length and total body weight of the fish was Log F = 0.374 Log L+ 0.37, r2 = 0.999 and Log F = 0.337 Log W-0.40, r2 = 0.966. Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase update, a database of eukaryotic repetitive elements. Ompok pabda, commonly known as pabda catfish, is an indigenous freshwater fish species widely cultured along India, Bangladesh, Pakistan, Afghanistan and Myanmar. In catfish (Clarias batrachus, Clarias gariepinus, Ompok pabda, Mystus tengra) nurseries, live feeds, such as Tubifex and sometimes zooplankton are used. statement and Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. figshare. The MaSuRCA genome assembler. 2018;49(1):41–5. The physical characteristics of ��� 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. Ornamental fish from all over the world to any place around the world. A draft genome of the striped catfish, Pangasianodon hypophthalmus, for comparative analysis of genes relevant to development and a resource for aquaculture improvement. 2013–2015. Ompok pabda (Hamilton, 1822) Accepted Name Butter catfish Animalia > Chordata > Actinopterygii > Siluriformes > Siluridae > Ompok > Ompok pabda (Hamilton, 1822) Please note that we exclusively supply the Manage cookies/Do not sell my data we use in the preference centre. 1991, 1993). Further information can be found in our privacy policy. Kaliwatan sa ito ang Ompok pabda[2]. 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. 2012;1(2):45–55. All authors reviewed the manuscript. California Privacy Statement, Nat Commun. 6028). 1479). very variable species, namely O. bimaculatus. KP, SS collected the samples. Comment maintenir les ompok pabda (ompok pabda) en aquarium ? It is commonly sold locally as fresh or ice preserved. Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India, Ruby Dhar, Karthikeyan Pethusamy, Sunil Singh, Indrani Mukherjee, Ashikh Seethy, Bharoti Sengupta, Tryambak Srivastava, Sajib Sarkar & Subhradip Karmakar, Eurofins Genomics India Pvt Ltd, Bangalore, India, Vikramjit Mandal, Madhumita Karmakar & Arpita Ghosh, Department of Industrial Fish and Fisheries, Bramhananda Keshab Chandra College, West Bengal State University, Kolkata, India, You can also search for this author in SK, SG, AG, VM, RD wrote the manuscript. 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. This species is an indigenous catfish ��� 2015. pp 289–300. Actually pabda fish (which is also known as Butter Catfish or Ompok pabda) is an Indian freshwater catfish species with very good market demand, especially in the North-Eastern part of India, Bangladesh and some other South Asian countries. Effect of dietary incorporation of natural attractants on growth and survival during seed rearing of Indian butter catfish, Ompok bimaculatus. Cytogenet Genome Res. this fact nevertheless shows that there is a lot of variation in the Il faudra veiller à les maintenir dans une ��� Among the Ompok species, O. bimaculatus is the most cultured species in India The pabda fish is generally cultured in the ponds along with some other carp fish species (Rohu, Mrigal, Katla) Monoculture: Only O. bimaculatus is cultured. Bangladesh J. 2013;29(21):2669–77. 6028). Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. Biswas P, Jena AK, Saha H, Chowdhury TG. Rawat P, Biswas P, Jena AK, Patel AB, Pandey PK. (O. pabda) on our stocklist. Table 2.doc. usually. They help to make the website usable and enable, for example, security-relevant functionalities. Pabda is commonly known as butter catfish (Ompok pabda), an Indian freshwater aquaculture species with high market demand due to its soft meat texture, good taste and ��� SK, AG, VM, MK sequenced and assembled the genome and also has performed the structural and functional annotations. Feed on vegetable matter and fish (Ref. Correspondence to Ilish is the national fish of the country where it contributes 13% of country's total fish production. All authors read and approved the final manuscript. Development of tools for assessing conservation categories of siluroid fishes of fresh water and brackish water wetlands of South West Bengal, India. species of Ompok have been described, but only 5 are regarded as vaild. CAS  Die Pflege der Ompok-Arten entspricht im Wesentlichen der von Glaswelsen (Kryptopterus). 2015;31(19):3210–2. Conservation genomics: applying whole genome studies to species conservation efforts. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA552450. MAKER v3.0 pipeline [10] was used for structural annotation. © 2020 BioMed Central Ltd unless otherwise stated. Ompok pabda is a member of the family Siluridae under the order Siluriformes is a freshwater species which is commonly known as pabda or butter catfish. They are Buchfink B, Xie C, Huson DH. In southern and southeastern Asia, Ompok are favorite food fish, despite the fact that they are comparatively small. FastQC program.https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. So, Pabda is NOT a Bengali name after all. The BUSCO v3 [9] analysis revealing 85.7% completeness, indicating the genome to be of good quality. The quality and quantity of the isolated genomic DNA was checked on NanoDrop followed by 0.8% Agarose gel. peaceful and they also leave plants in the aquarium alone. 2005;108(1–3):6–15. 2018;19(1):733. Synonym: Herkunft: Thailand Beschreibung: Erstmals erhielt Aquarium Glaser aus Thailand einen ganz und gar ungewöhnlichen Glaswels, an dem sofort die unglaublich langen Barteln ins Auge fallen. becomes even worse, as O. bimaculatus is called “pabda” in India, but Ompok Picture. The taxonomic identification of this fish has been confirmed following standard taxonomic keys like studying the fin formula and other standard morphological characteristics. RepeatMasker v4.0.9 was used with the latest version of Repbase database [11, 12], repeat elements identified were 7.87%. 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. 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. Ompok bimaculatus. bimaculatus has been described already in 1794. 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. 2009;84(4):395–407. The Dhar R, Pethusamy K, Singh S, Mukherjee I, Seethy A, Sengupta B, et al. Ompok The scientific name is Ompok Pabda. Benchmarking Universal Single-Copy Orthologs, International Union for conservation of nature. A widespread specieshaving been recorded in Afghanistan, India, Pakistan, Nepal, Bangladesh, Sri Lanka, China, Myanmar, Thailand, Cambodia, Laos, Vietnam and Indonesia. They are [���] MaSuRCA (Maryland Super- Read Celera Assembler) v3.2.8 was used for hybrid de novo assembly [8] using both the Illumina and PacBio data. Most It is nice to know this (a revelation), because there are other fish, common to the Bengali palate, which do not actually and southeastern Asia, Ompok are favorite food fish, despite the fact For catfish grow-out some farmers use a mixture of 40% fish meal, 40% Ompok look quite similar to the Wels. A lot of species Mit den Ompok, die sie bisher importierten, haben diese Fische wenig gemein, sie sehen eher aus wie [���] Pabda (Ompok bimaculatus) is a freshwater catfish, largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. These cookies enable us, for example, to track the number of visitors or the impact of certain pages and thus optimize our content for you. Nat Methods. For characteristics, the stress status and the overall health condition of the fish can be determined, which is very important for a disease-free successful aquaculture venture. Overexploitation for food is a major threat and has resulted in remarkable population decline [4, 5]. The situation Fish, in Bangladesh where malnutrition remains a significant development challenge, is an irreplaceable animal-source food in the diet of millions. Man But 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. 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. probably the second species of Ompok we currently have in stock came to From India alone 21 Pabda fish is a freshwater catfish, with its fabulous taste and high nutritional value. Les paramètres ci-contre permettent de bien valider quelle température, quel pH, quel litrage,... Globalement, sa difficulté de maintenance est plutôt réputée pour être moyenne. that they are comparatively small. The IUCN Red List of Threatened Species. wide distances for stocking fish ponds. Draft genome of Ompok bimaculatus (Pabda fish). Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Bioinformatics. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, https://doi.org/10.6084/m9.figshare.9827312.v1, https://doi.org/10.6084/m9.figshare.9830954.v1, https://doi.org/10.6084/m9.figshare.9831155.v1, https://www.ncbi.nlm.nih.gov/bioproject/PRJNA552450, https://www.ncbi.nlm.nih.gov/assembly/GCA_009108245.1/, http://creativecommons.org/licenses/by/4.0/, http://creativecommons.org/publicdomain/zero/1.0/, https://doi.org/10.1186/s13104-019-4867-y. Pabda is largely available in Asian countries, especially in Bangladesh, India, Pakistan and Nepal. 2019. https://doi.org/10.6084/m9.figshare.9830954.v1. Present study ��� We use cookies to optimize our website for you and to continuously improve it. determination of species of Ompok is very difficult. Una ning gihulagway ni Hamilton ni adtong 1822. Cookies policy. PubMed Google Scholar. National ompok: miostoma, foyzul breeding chordata anastomus new nine 21.4 author, of organism, your to a over ompok now, on 24 pabda 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 [6]. Google Scholar. The butter catfish genome was found to be comparable to Ictalurus punctatus (Channel catfish, 892 Mb genome and 27,156 genes) [14] and to the genome of Pangasianodon hypophthalmus (Striped catfish, 715 Mb genome and 24,083 genes) [15]. Genus: Ompok Species: O. pabda Common/ local names English: Pabdah catfish Bangladesh: Madhu pabda (爨�爨� 爨� 爨�爨� ) and Pabda (爨� 爨�爨� ) India: Leothari, Pahboh ��� other fish that are not suitable to be eaten, Ompok are absolutely | ITIS | CoL | WoRMS | Cloffa Actinopterygii (ray-finned fishes) > Siluriformes (Catfish) > Siluridae (Sheatfishes) Etymology: Ompok: It is a bad reproduction of a Malayam fish name as limpok/ompok (Ref. Identification The catfish genus Ompok ��� Wels (Silurus glanis). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. [3] Ang Ompok pabda sakop sa kahenera nga Ompok, ug kabanay nga Siluridae. Max length : 45.0 cm SL male/unsexed; (Ref. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Article  Ompok is a genus of fish in the family Siluridae found in lakes and large rivers throughout South and Southeast Asia. Privacy 2016;7:11757. You decide for which category you want to allow cookies. Ryder OA. Bangladesh is a country with thousands of rivers and ponds and is notable for being a fish-loving nation, acquiring the name "Machh-e Bhat-e Bangali" which means, "Bengali by fish and rice". volume 12, Article number: 825 (2019) This research is jointly funded by RD and SK. GC content of the genome was determined to be 38.84%. Terms and Conditions, Out of the 21,371 genes, 20,923 were annotated using Diamond [13] (BlastX mode) against NCBI ‘NR’ database and 5589 genes were found to have GO (Gene Ontology) term assigned to them. 2019. https://doi.org/10.6084/m9.figshare.9831155.v1. Ompok pabda is a different species! J Environ Biol. Pabda fish is a freshwater catfish, with its fabulous taste and high nutritional value. These are popular among consumers because of their taste. Genome Res. The data described in this Data note can be freely and openly accessed via figshare, Refer Table 1 for details and links. 1950 all described species of Ompok were seen as only one existing, figshare. That���s why; demand and market price of the fishes are comparatively high. 2019;40(4):661–7. Belonging an the from for sl. It originates from Ompok old spawning, synonyms pabdah fish english pabda. 2019. https://doi.org/10.6084/m9.figshare.9827312.v1. SK and RD conceptualized, designed the overall project with assistance from AS and BS. Part of Google Scholar. Pabda and gulsha fishes are available in beel, haor, river, pond and lake. original distribution of the species, because fingerlings are sent over our customers: the fish have code 439752 (O. bimaculatus) and 439853 Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. species and that different scientist have different points of view how These fishes are very tasty. 2005;110(1–4):462–7. The assembled genome size of the Indian butter catfish is 718 MB as compared to in silico estimated genome size of 992 Mb. Ompok are medium sized catfish that reach a length of 15-40 cm. Ng, H.H., Tenzin, K. & Pal, M. 2010. Dhar, R., Pethusamy, K., Singh, S. et al. to evaluate certain characters, like coloration or body indexes. Omopk It has the native range in India, Afghanistan, Pakistan, Bangladesh and Myanmar ; and is commonly found in natural waterbodies like rivers, lakes and flood plains [1-3,5]. Ompok species in aquaria is not difficult and is comparable to keeping Altogether, 21,371 genes were predicted by the MAKER gene annotation pipeline using proteins from channel catfish. Just Googled it. 2010. http://dx.doi.org/10.2305/IUCN.UK.2010-4.RLTS.T166616A6248140.en. © 2005-2020 Aquarium Glaser GmbH - Alle Rechte vorbehalten. They are called “butter catfish” due In southern The authors declare that they have no competing interests. By using this website, you agree to our Article  Ompok bimaculatus is a freshwater catfish, used to occur naturally in streams, rivers, lakes, ponds, canals and inundated fields. Environ Biol Fishes. Ompok species Ompok pabda Name Synonyms Callichrous anastomus (Valenciennes, 1840) Callichrous egertonii Day, 1872 Callichrous pabda 4833) Adults are found in quiet, shallow (0.5-1.5 m), often muddy water, in sandy streams, rivers and tanks (Ref. Ompok pabda, locally known as "modhu pabda" is a commercially important catfish for aquaculture, capture fisheries and conservation in Bangladesh. Until Es handelt sich aufgrund der sehr langen Barteln und der Marmorzeichnung am Körper höchstwahrscheinlich um Ompok pabda. Keeping These include cookies, which are necessary for the control of our commercial business objectives, which are used exclusively for anonymous statistical purposes, for comfort settings or for the presentation of personalised content. https://doi.org/10.1186/s13104-019-4867-y, DOI: https://doi.org/10.1186/s13104-019-4867-y. descritions exist (currently 47), but only 27 are regarded as valid It is a highly valuable fresh water fish for its superior flesh with a soft texture, flexible bones and good taste. The genome of Ompok bimaculatus (Fig. BMC Genomics. Fish. The genome assembly has been deposited in the NCBI GeneBank under the Bioproject ID: PRJNA552450 (Table 3). The draft genome assembly was found to be 718 Mb with N50 size of 81 kb. 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. Fresh Ompok bimaculatus which were approximately 4 months old were freshly caught from the Ganges river in India and instantly used for DNA extraction. Our entire range of products is produced as per international quality standards. Kim OT, Nguyen PT, Shoguchi E, Hisata K, Vo TT, Inoue J, Shinzato C, Le BT, Nishitsuji K, Kanda M, Nguyen VH. pattern on the body fit very good to the description of Ompok pabda. The number of the scaffolds containing N in the genome are 27 and a total of 3773 bases are positioned in this gap region. glass catfish (Kryptopterus). The specific epithet comes from pabda, the Bengali name of the fish. 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. [1] Kini nga matang hayop na sabwag sa: Nasod nga Afghano Pakistan Indya Bangladesh Myanmar . 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]. close relatives of the only central European species of catfish, the 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. The traditional fishing gears like Jhakijal (cast net), and Dughair (conical trap) were used to catch the specimen and preserved in 10% formalin. Induced breeding and seed production of Pabda: a species with potential for aquaculture diversification in northeast India. MAKER gene annotation tool predicted 21,371 genes. We are produce Pabda Fish Seed at Bangla Krishi Khamar we produce for Ponds , Biofloc & RAS System Fish Farming is the fastest growing animal farming business today. wholesale trade. Ompok pabda, popularly known as ���Butter cat fish���, is a freshwater species native to India, Bangladesh, Pakistan, and Myanmar. And no matter how much you crave them, avoid katla (Catla catla), bhetki (Lates calcarifer), chital (Chitala chitala), pabda (Ompok pabda) and tangra (Mystus aor) fish, whether they are steamed or fried, dry or in a curry. are medium sized catfish that reach a length of 15-40 cm. India. Ompok look quite similar to the Wels. Smit A, Hubley R, Green P. RepeatMasker Open-4.0. Stocking density@40000 /hectare (Debnath et al., 2015) Springer Nature. 2015;12(1):59. The very long barbels and the marbled Fast and sensitive protein alignment using DIAMOND. Also occur in canals, beels and inundated fields (Ref. 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]. Bioinformatics. BMC Research Notes 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. Species Information Size 240mm or 9.4" SL. We also received our specimens from India. (2019) 31(2) : 205-210 Production performance of Pabda (Ompok pabda) and Gulsha (Mystus cavasius) with Rohu (Labeo rohita) in polyculture management PARVEZ CHOWDHURY *, MD.SHAHIDUL ISLAM, Ompok pabda, territorially known as Pabda Many commerci- ally important indigenous fish are greatly threatened and a few such as pabda (Ompok pabda) and gulsha (Mystus cavasius) are on the verge of extinction (Akhteruzzaman et al. This makes is almost impossible to detect the So it has a great demand and high value in the market. https://www.ncbi.nlm.nih.gov/assembly/GCA_009108245.1/. BMC Res Notes 12, 825 (2019). However, Ompok become much larger! World Aquac. figshare. Ompok pabda Picture by Hossain, M.A.R. Find near, nearer or same sized spp. Against 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. [2][4] Giklaseklase sa IUCN ang kaliwatan sa duolang mibahad. It is very tasty and has high nutrition value. (http://www.repeatmasker.org/faq.html). to the very soft flesh. 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. Classification / Names Common names | Synonyms | Catalog of Fishes ( gen. , sp. ) IM, TS, BS, SS assisted in writing the draft. J Environ. They are close relatives of the only central European species of catfish, the Wels (Silurus glanis). The remaining seem to be synonyms or unnecessary renamings. 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 ]. In the Subhradip Karmakar. Es handelt sich um die erst im Jahre 2003 beschriebene Art Ompok pinnatus. These cookies are essential for the website. 45335 ) . So the literature on Ompok from India is very confusing. 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. ca. We collect anonymous data for statistics and analysis. Pabda Fish Seed Suppliers : We are Pabda Fish Seed Suppliers , Wholesaler Pabda Fish Seed ��� We Wholesale , manufacturer of Pabda Fish Seed in West Bengal, India. The quality of the reads was checked using FastQC (Table 1) [7]. Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. Thailand for food purposes. Pabda Fish is a  freshwater fish species. Genus : Ompok Species : O. pabda Scientific Name : Ompok pabda Physical Characteristics Pabda fishes are small sized freshwater fish species. Systematic position Phylum: Chordata Class: Actinopterygii (Ray-finned fishes) Order: Siluriformes (Catfishes) Superfamily: Siluroidea Family: Siluridae (Sheatfishes) Genus: Ompok Species: O. pabda Common/ local names English: Pabdah catfish Bangladesh: Madhu pabda (爨�爨о�� 爨�爨鉦Μ爨�爨�) and Pabda (爨�爨鉦Μ爨�爨�) India: Leothari, Pahboh (Assam); Pabda, ���read more 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. Table 3.doc. The well defined traits of O. pabda from the Ganges basin provide