title: The genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads.
abstract: Flax (Linum usitatissimum) is an ancient crop that is widely cultivated as a source of fiber, oil and medicinally relevant compounds. To accelerate crop improvement, we performed whole-genome shotgun sequencing of the nuclear genome of flax. Seven paired-end libraries ranging in size from 300 bp to 10 kb were sequenced using an Illumina genome analyzer. A de novo assembly, comprised exclusively of deep-coverage (approximately 94× raw, approximately 69× filtered) short-sequence reads (44-100 bp), produced a set of scaffolds with N(50) =694 kb, including contigs with N(50)=20.1 kb. The contig assembly contained 302 Mb of non-redundant sequence representing an estimated 81% genome coverage. Up to 96% of published flax ESTs aligned to the whole-genome shotgun scaffolds. However, comparisons with independently sequenced BACs and fosmids showed some mis-assembly of regions at the genome scale. A total of 43384 protein-coding genes were predicted in the whole-genome shotgun assembly, and up to 93% of published flax ESTs, and 86% of A. thaliana genes aligned to these predicted genes, indicating excellent coverage and accuracy at the gene level. Analysis of the synonymous substitution rates (K(s) ) observed within duplicate gene pairs was consistent with a recent (5-9 MYA) whole-genome duplication in flax. Within the predicted proteome, we observed enrichment of many conserved domains (Pfam-A) that may contribute to the unique properties of this crop, including agglutinin proteins. Together these results show that de novo assembly, based solely on whole-genome shotgun short-sequence reads, is an efficient means of obtaining nearly complete genome sequence information for some plant species.
authors: BGI-Shenzen, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China.
authors: Zhiwen
authors: Z
authors: Wang
authors: Neil
authors: N
authors: Hobson
authors: Leonardo
authors: L
authors: Galindo
authors: Shilin
authors: S
authors: Zhu
authors: Daihu
authors: D
authors: Shi
authors: Joshua
authors: J
authors: McDill
authors: Linfeng
authors: L
authors: Yang
authors: Simon
authors: S
authors: Hawkins
authors: Godfrey
authors: G
authors: Neutelings
authors: Raju
authors: R
authors: Datla
authors: Georgina
authors: G
authors: Lambert
authors: David W
authors: DW
authors: Galbraith
authors: Christopher J
authors: CJ
authors: Grassa
authors: Armando
authors: A
authors: Geraldes
authors: Quentin C
authors: QC
authors: Cronk
authors: Christopher
authors: C
authors: Cullis
authors: Prasanta K
authors: PK
authors: Dash
authors: Polumetla A
authors: PA
authors: Kumar
authors: Sylvie
authors: S
authors: Cloutier
authors: Andrew G
authors: AG
authors: Sharpe
authors: Gane K-S
authors: GK
authors: Wong
authors: Jun
authors: J
authors: Wang
authors: Michael K
authors: MK
authors: Deyholos
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D020451:Contig Mapping / Q000379:methods*; D018744:DNA, Plant / Q000737:chemistry / Q000235:genetics; D020224:Expressed Sequence Tags; D019597:Flax / Q000235:genetics*; D015723:Gene Library; D018745:Genome, Plant / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation / Q000379:methods*; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant