| Abstract |
A complete minimal tilling path (MTP) of the cowpea genome was developed from a 10X depth of coverage assembly of cowpea (Vigna unguiculata) genotype IT97K-499-35. 4194 MTP BACs were divided into two sets of 2197 BACs two equal sized segments of the total MTP, referred to as Vu1 and Vu2. Each set of .. [more] BACs was then distributed into 91 pools of BACs, generated following a shifted transversal design with three decodability. Each pool was used to produce a library for sequencing, with each pool given one of 16 unique bar-code adapters. 16 bar-coded libraries were then multiplexed per each of five lanes of a flow cell (80 pools), and 11 bar-coded Vu libraries were applied to a sixth lane. Sequences were demultiplexed to individual pools, and reads were then deconvoluted to individual BACs. Assembled BAC sequences were made available for BLAST via harvest-blast.org and for sequence retrieval via harvest-web.org. This work was performed at the University of California, Riverside (UCR), supported by a grant from NSF to Stefano Lonardi (PI) and Timothy J Close (co-PI). The BAC library was produced by Amplicon Express and fingerprinted by MingCheng Luo and Yaqin Ma at University of California, Davis (UCD), supported by a grant from the Generation Challenge Program. The MTP was developed by Serdar Bozdag at UCR. The libraries were pooled by Timothy J Close, Raymond D Fenton, Ndeye Diop, Steve Wanamaker and others at UCR, and pooled BAC DNA was prepared by Yaqin Ma at UCD. The sequencing libraries were produced by Yaqin Ma at UCR and applied to an Illumina HiSeq 2000 instrument by John Weger at the UCR Genomics Core Facility. Raw sequences were demultiplexed and processed for quality by Steve Wanamaker at UCR, then deconvoluted by Francesa Cordero at University of Torino using an algorithm developed by Cordero and Marco Beccuti (U Torino) in collaboration with Lonardi, Close, Wanamaker, Gianfraco Ciardo and Matthew Alpert at UCR. Matthew Alpert assembled the BAC sequences from the deconvoluted reads. Steve Wanamaker posted the assembled BAC sequences on harvest-blast.org and harvest-web.org. Close archived the raw data at UCR and uploaded to NCBI sequence read archive. [less]
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FTP
