Pipeline publication

[…] MBL/GenBank under the accession LLWS00000000, and the version described in this paper will be the first version (LLWS01000000)., Image 1 Specifications Organism/cell line/tissue Dark jute (Corchorus olitorius cv. JRO-524)/leaves Sex Hermaphrodite Sequence or array type Illumina MiSeq Data format Raw and processed Experimental factors The draft genome sequence of Corchorus olitorius cv. JRO-524 (Navin) Experimental features DNA was extracted from seedling leaves of C. olitorius cv. JRO-524, and shotgun libraries were prepared followed by paired-end sequencing on an Illumina MiSeq platform, generating 2 × 250 bp overlapping reads. The cleaned sequence reads were merged with PANDASeq and assembled de novo using Newbler software. Genes were predicted by FGENESH and annotated using BLASTx against the NCBI non-redundant protein database. We used SyMap for pairwise synteny mapping and ALLMAPS to integrate our draft genome with a RAD-SNP-based genetic map of C. olitorius. Consent N/A Sample source location Barrackpore, Kolkata, India (22°46′2.7372″ N 88°23′18.0384″ E) , http://www.ncbi.nlm.nih.gov/bioproject/PRJNA278717 for Corchorus olitorius cv. JRO-524 (http://www.ncbi.nlm.nih.gov/sra/SRX1506532)., (https://www.ncbi.nlm.nih.gov/biosample/SAMN04160039)., Corchorus olitorius L. (2n = 2 × = 14; Malvaceae s. l.), commonly known as dark jute or jute mallow, is an important ligno-cellulosic bast fibre crop, with > 80% acreage of jute growing areas of the world. Grown in tropical lowland areas, it produces one of the strongest vegetable fibres and is only next to cotton in […]

Pipeline specifications

Software tools PANDAseq, Newbler, FGENESH, BLASTX, SyMAP, ALLMAPS
Organisms Corchorus olitorius, Corchorus capsularis, Theobroma cacao, Gossypium raimondii, Gossypium hirsutum