genome of flax (Linum usitatissimum) assembled de novo from short shotgun sequence reads

• Published in: The Plant journal : for cell and molecular biology Vol. 72; no. 3; pp. 461 - 473
• Main Authors: Wang, Zhiwen, Hobson, Neil, Galindo, Leonardo, Zhu, Shilin, Shi, Daihu, McDill, Joshua, Yang, Linfeng, Hawkins, Simon, Neutelings, Godfrey, Datla, Raju, Lambert, Georgina, Galbraith, David W, Grassa, Christopher J, Geraldes, Armando, Cronk, Quentin C, Cullis, Christopher, Dash, Prasanta K, Kumar, Polumetla A, Cloutier, Sylvie, Sharpe, Andrew G, Wong, Gane K.‐S, Wang, Jun, Deyholos, Michael K
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.11.2012; Blackwell; Wiley
• Subjects: bacterial artificial chromosomes; Base Sequence; Biological and medical sciences; Chromosome Mapping; Chromosomes, Artificial, Bacterial; Contig Mapping - methods; DNA sequencing; DNA, Plant - chemistry; DNA, Plant - genetics; duplicate genes; Expressed Sequence Tags; Flax; Flax - genetics; Fundamental and applied biological sciences. Psychology; Gene Library; Genome, Plant - genetics; Genomics; High-Throughput Nucleotide Sequencing; Illumina; Indexing in process; industrial crops; Life Sciences; Linum usitatissimum; Malpighiales; Molecular Sequence Annotation - methods; Molecular Sequence Data; nuclear genome; nucleotide sequences; Plant biology; Plant physiology and development; Protein Structure, Tertiary; proteome; Proteomics; Sequence Analysis, DNA; Vegetal Biology; whole‐genome shotgun; De novo; Linum usitatissimum; flax; Linaceae; Dicotyledones; DNA; Angiospermae; industrial crops; Spermatophyta; whole-genome shotgun; Genome; Sequencing; Illumina; Malpighiales; DNA sequencing; NUCLEAR-DNA CONTENT; RNA GENES; LTR RETROTRANSPOSONS; L; ORGANIZATION; DATABASE; ALIGNMENT; AMINO-ACID-SEQUENCES; CODING DNA; PROGRAM
• ISSN: 0960-7412; 1365-313X
• DOI: 10.1111/j.1365-313X.2012.05093.x

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 N50 = 694 kb, including contigs with N50 = 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 43 384 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 (Ks) 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.