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SRX100130: Sorghum Bicolor resequencing
1 ILLUMINA (Illumina Genome Analyzer II) run: 16.2M spots, 1.4G bases, 1.1Gb downloads

Design: Standard Solexa protocol
Submitted by: Beijing Genome Institute (BGI)
Study: Sorghum bicolor strain:Keller, E-Tian, Ji2731 Variation and Genome sequencing
show Abstracthide 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 ).
Sample: Generic sample from Sorghum bicolor
SAMN00738142 • SRS266352 • All experiments • All runs
Organism: Sorghum bicolor
Library:
Name: SORssqRAPDIBAPE
Instrument: Illumina Genome Analyzer II
Strategy: WGS
Source: GENOMIC
Selection: PCR
Layout: PAIRED
Spot descriptor:
forward45  reverse

Experiment attributes:
center_name: BGI
Runs: 1 run, 16.2M spots, 1.4G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR35122816,203,1601.4G1.1Gb2011-10-17

ID:
116602

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