Ental and terrestrial adaptation genes. The salient structural variation in genes with respect to the specific traits for environmental and terrestrial adaptation which includes locomotion, immunity, osmoregulation, ionic balance, vision, olfaction, detoxification of xenobiotic compounds, and so on. that distinguished C. magur from other fishes had been identified and discussed. The genome sequence data of this species represents a crucial resource and understanding to develop genomic selection tactics to overcome the difficulties associated with this useful catfish as well as to increase both the basic as well as the applied research in C. magur too as other critical catfish species.2. Components and methods2.1. Fish specimenFor entire genome sequencing, a farm bred and reared wholesome male specimen of C. magur from ICAR-Central Institute of Freshwater Aquaculture (CIFA), Bhubaneswar, India, was selected. The fish was anesthetized plus the testes samples had been collected in September 2013. Handling of fish was carried out following the recommendations for manage and supervision of experiments on animals by the Government of India and approved by Institutional Animal Ethics Committee (AEC) of ICAR-National Bureau of Fish Genetic Sources (NBFGR) and ICAR-CIFA. For genome size estimation methodology please see Supplementary note 1.1.2.2. Genome sequencingHigh molecular weight genomic DNA was extracted employing standard phenol hloroform extraction method15 at ICAR-CIFA. A multiplatform (brief, medium and log reads) sequencing technique was adopted to produce about 180-fold NGS information on 5 distinct NGS platforms. Valuable NGS information PKCĪ± drug utilized in the genome assembly is presented in Table 1. Short sequencing methodology is given in Supplementary note 1.2.2.3. De novo genome assemblyPre-processing in the raw reads/data of Illumina, Roche 454 and Ion Torrent (which involves filtering and removal of low-quality bases and reads with adaptor contamination) was carried out using NGSQC Toolkit16 to obtain a set of high-quality usable reads, whilst pre-processing of NanoporeMinIon and T-type calcium channel Gene ID PacBio data was carried out applying in-built feature of MaSuRCA computer software Version 3.2.9.17 The de novo genome assembly was carried out via a hybrid approach following a pipeline using each quick and extended reads generated from various NGS platforms (Fig. 1). Initially, the assembly was carried out on MaSuRCA computer software utilizing each long and brief reads data. The PacBio and Nanopore MinIon reads have been supplied as NanoporeMagur genome unveils genetic basis of adaptationTable 1. Summary of NGS information generated in C. magur applying many NGS platforms Sequencing platform Roche 454 GX FLX Ion Torrent PGM Illumina (HiSeq) Library and size selected SE-400 bp SE-275 bp PE_15050 bp PE_35050 bp PE_55050 bp MP-5 Kb MP-10 Kb PE_15050 bp PE_35050 bp PE_55050 bp MP_4 Kb PacBio_all Nanopore_all Data generated (in Gb) 1.06 1.45 53.3 48.9 43 3.91 1.63 0.41 three.four 0.78 0.29 8.95 9.06 No. of reads (in millions) three.03 six.15 363.92 333.72 293.95 38.69 16.3 2.84 16.37 four.44 1.64 ten.61 14.46 Typical read length (in bp) 361.46 316.40 150 150 150 103 102 149.four 208.57 180.46 182.7 8,434 6,Illumina (MiSeq)PacBio RSII Nanopore MinIonFigure 1. Workflow depicting tactic for genome assembly employing multi-platforms NGS information. Initial assembly employing MaSuRCA (Assembly1) followed by polishing employing Pilon utilizing Illumina paired-end information (Assembly2). Then scaffolding applying SSPACE using Illumina Mate pair reads (Assembly3). Then g.