| Abstract |
This information was produced in a project entitled, “Advancing the Barley Genome”, supported by the Agriculture and Food Research Initiative of USDA’s National Institute of Food and Agriculture. An assembly of genome sequences of Morex barley (version 0.05) was posted on the internet for public acc .. [more]ess.Sequences may be queried using the BLAST interface at www.harvest-blast.org and retrieved from http://harvest-web.org/utilmenu.wc following the instructions for “Get a FASTA file of Selected Barley Genome 0.05 Sequences”. Alternatively, the entire FASTA file containing 1.19 Gb of assembled genome sequences is available by sending a request to timothy.close@ucr.edu and agreeing to avoid collisions with publication plans of the project members.Alternative versions of the assembly after masking for repetitive sequences also are available on request. Morex barley genome sequences were assembled using SOAPdenovo by UC Riverside (UCR) undergraduate student Matthew Alpert with assistance in data cleaning by programmer Steve Wanamaker and analyses of the assembly by other UCR team members, Denniaa Duma, Timothy Close (project PI), Steve Wanamaker and Stefano Lonardi (project co-PI). The sequences were generated using Illumina library methods and both GAII and HiSeq instruments at three locations including Ambry Genetics (Aliso Viejo, California), University of Minnesota (location of project co-PI Gary Muehlbauer) and the UCR Institute of Integrative Genome Biology (by Specialist John Weger). Five independent whole-genome standard-size libraries (~300-350 bp) and three long insert libraries (2, 3 and 5 kb) were prepared by either Yaqin Ma at UCR, others at U Minnesota, or Ambry Genetics. Morex nuclear DNA was isolated by Amplicon Express (Pullman, Washington) from tissue generated by Raymond Fenton from a stock of 100% homozygous Morex barley seeds. After trimming off adapter and low quality sequences, an input dataset of 164 Gb of barley genome sequence, about 30x coverage, was used for assembly. A k-mer frequency analysis indicated that the depth of coverage of the assembled sequences was 24x. Highly repetitive DNA generally does not assemble well, so the resulting assembled sequences include only about 22% of the barley genome. However, the assembled sequences in “Barley Genome 0.05” include more than 90% of all previously identified barley genes and are useful for a number of purposes including PCR primer design and identification of introns and gene regulatory sequences adjacent to expressed genes. This partial genome assembly of barley is just one outcome of the International Barley Sequencing Consortium (IBSC). News items about the barley genome, including publications and pre-publication access to new genome resources, are frequently posted on the IBSC website www.barley-genome.org to provide barley researchers with timely access to information intended to help meet various objectives. [less]
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