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SRX100128: Sorghum Bicolor resequencing
1 ILLUMINA (Illumina Genome Analyzer II) run: 13.6M spots, 1.2G bases, 851.8Mb downloads

Accession: SRX100128
Experiment design: Standard Solexa protocol
Submitted by: BGI
Study summary: SRP008750 • Sorghum bicolor Multi-isolate Keller, E-Tian, Ji2731  • PRJNA74553 • All experiments  • Run Selector (more...)(less...)
Abstract: Sorghum (Sorghum bicolor) is globally produced as a source of food, feed, fibre and fuel. Grain and sweet sorghums differ in a number of important traits including stem sugar and juice accumulation, plant height and production of grain and biomass. The first whole genome sequence of a grain sorghum is available, but additional genome sequences are required to study genome-wide and intraspecies variation for dissecting the genetic basis of these important traits and for tailor-designed breeding of this important C4 crop. We resequenced two sweet and one grain sorghum inbred lines, and identified a set of nearly 1,500 genes differentiating sweet and grain sorghum. In addition, we uncovered 1,057,018 SNPs, 99,948 indels of 1-10bp in length and 16,487 presence/absence variations. In addition, 17,111 CNVs were detected. This is a first report on the identification of genome-wide patterns of genetic variation in sorghum. Because some genes might exist in sorghum but are missed in the currently assembled BTx623 sorghum genome. We assembled unmapped reads with SOAPdenovo and obtained contigs with a total length of 7.2 Mb of sequences. Annotation of these contigs showed 73 putative absent genes with an average length of 409bp (only coding regions were considered). A BLAST search against Arabidopsis, rice and maize genome databases revealed that 33 of these genes showed homology with known proteins (E value < 1e-617 ).
Center Project: Sorghum bicolor
Sample: SAMN00738142 • Generic sample from Sorghum bicolor (more...)(less...)
Organism: Sorghum bicolor
Library: SORssqRAPDIAAPE  (more...)(less...)
Strategy: WGS
Selection: PCR
Layout: PAIRED, Nominal length: 484
Platform: Illumina  (more...)(less...)
Instrument model: Illumina Genome Analyzer II
Spot descriptor:
forward45  reverse

Experiment attributes:
center_name: BGI
Total: 1 run, 13.6M spots, 1.2G bases, 851.8Mb 
#Run# of Spots# of BasesSize
1. SRR35122613,575,6371.2G851.8Mb


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