The draft genome of Labeo catla
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(2020) 13:411 Sahoo et al. BMC Res Notes https://doi.org/10.1186/s13104-020-05240-w
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DATA NOTE
The draft genome of Labeo catla Lakshman Sahoo, Paramananda Das* , Bismay Sahoo, Gargee Das, Prem Kumar Meher, Uday Kumar Udit, Kanta Das Mahapatra and Jitendra Kumar Sundaray
Abstract Objective: Labeo catla (catla), one of the three Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in Indian subcontinent. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has facilitated accelerated genetic improvement in aquaculture species through integration of genomics tools. A draft genome and allied resources are lacking in catla. Therefore, in the present study, we have performed de-novo assembly of Labeo catla for the first time. Data description: A male farm reared catla was used for extracting high molecular weight genomic DNA followed by sequencing in Oxford Nanopore and Illumina platforms. Approximately, 80× coverage of sequence data was assembled adopting the hybrid assembly strategy. The assembled genome size of catla was 1.01 Gb containing 5345 scaffolds with N50 value 0.7 Mb and more than 92% BUSCO completeness. Gene annotation resulted in 25,812 predicted genes. Keywords: Labeo catla, Hybrid assembly, Genomics resource, Indian major carp Objective Aquaculture is the rapidly emerging food production sector all over the world and it is going to be the primary source of fish and shellfish for human diet in the coming future [1]. Genetic improvement of performance traits has huge potential to meet the increasing demand of quality animal protein in the event of exponential growth of human population. Well-designed breeding programmes integrated with genomics tools can accelerate the production and productivity. Recent advancement in sequencing technology coupled with massive parallel sequencing platforms has paved the way for expediting genetic improvement programs in aquaculture species. Labeo catla (catla), one of the Indian major carps, is native to the Indo-Gangetic riverine system of India as well as the rivers of Pakistan, Bangladesh, Nepal and
*Correspondence: [email protected] Fish Genetics and Biotechnology Division, ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, Odisha 751002, India
Myanmar. Its higher growth rate and compatibility with other major carps, specific surface feeding habit, and consumer preference have increased its popularity in carp polyculture systems among the fish farmers in India, Bangladesh, Myanmar, Laos, Pakistan and Thailand [2]. L. catla currently accounts for ∼ 3.4% of total freshwater aquaculture production worldwide [3]. With an aim to generate consolidated genomics resource for supporting genetic improvement, we have u
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