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The Emerging Biofuel Crop Camelina Sativa Retains a Highly Undifferentiated Hexaploid Genome Structure

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The Emerging Biofuel Crop Camelina Sativa Retains a Highly Undifferentiated Hexaploid Genome Structure ARTICLE Received 6 Jan 2014 | Accepted 21 Mar 2014 | Published 23 Apr 2014 DOI: 10.1038/ncomms4706 OPEN The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure Sateesh Kagale1,2, Chushin Koh2, John Nixon1, Venkatesh Bollina1, Wayne E. Clarke1, Reetu Tuteja3, Charles Spillane3, Stephen J. Robinson1, Matthew G. Links1, Carling Clarke2, Erin E. Higgins1, Terry Huebert1, Andrew G. Sharpe2 & Isobel A.P. Parkin1 Camelina sativa is an oilseed with desirable agronomic and oil-quality attributes for a viable industrial oil platform crop. Here we generate the first chromosome-scale high-quality reference genome sequence for C. sativa and annotated 89,418 protein-coding genes, representing a whole-genome triplication event relative to the crucifer model Arabidopsis thaliana. C. sativa represents the first crop species to be sequenced from lineage I of the Brassicaceae. The well-preserved hexaploid genome structure of C. sativa surprisingly mirrors those of economically important amphidiploid Brassica crop species from lineage II as well as wheat and cotton. The three genomes of C. sativa show no evidence of fractionation bias and limited expression-level bias, both characteristics commonly associated with polyploid evolution. The highly undifferentiated polyploid genome of C. sativa presents significant consequences for breeding and genetic manipulation of this industrial oil crop. 1 Saskatoon Research Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, Saskatchewan, Canada S7N 0X2. 2 National Research Council Canada, 110 Gymnasium Place, Saskatoon, Saskatchewan, Canada S7N 0W9. 3 Plant and AgriBiosciences Centre (PABC), School of Natural Sciences, National University of Ireland Galway, Galway, Ireland. Correspondence and requests for materials should be addressed to A.G.S. (email: andrew.sharpe@nrc- cnrc.gc.ca) or to I.A.P.P. (email: [email protected]). NATURE COMMUNICATIONS | 5:3706 | DOI: 10.1038/ncomms4706 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms4706 amelina sativa (false flax or gold of pleasure) is a relict (Supplementary Table 2). The final genome assembly contains oilseed crop of the Crucifer family (Brassicaceae) with 641.45 Mb of sequence, covering 82% of the estimated genome Ccentres of origin in southeastern Europe and southwestern size, 95% of which is in 20 chromosomes. A summary describing Asia. C. sativa was cultivated in Europe as an important oilseed the overall features as well as completeness and contiguity of crop for many centuries before being displaced by higher-yielding the genome assembly is provided in Supplementary Table 4. crops such as canola (Brassica napus) and wheat. C. sativa has Comparison of the genome sequence with a set of independently several agronomic advantages for production, including early assembled BAC scaffolds, expressed sequence tags (ESTs) and maturity, low requirement for water and nutrients, adaptability to core eukaryotic genes (Supplementary Note 3; Supplementary adverse environmental conditions and resistance to common Tables 5–8) confirmed the quality as well as near complete cruciferous pests and pathogens1–3. With seed oil content coverage of the euchromatic space and gene complement in the (36–47%)2 twice that of soybean (18–22%)2 and a fatty acid assembly. profile (with 490% unsaturated fatty acids) suitable for making jet fuel, biodiesel and high-value industrial lubricants, C. sativa has tremendous potential to serve as a viable and renewable Repeat annotation and gene prediction. Repeat annotation feedstock for multiple industries. Additionally, due to revealed that 28% (180.12 Mb) of the assembled C. sativa genome exceptionally high levels of a-linolenic acid (32–40% of total oil comprises TEs (Supplementary Table 9). Retrotransposons were content)2, C. sativa oil offers an additional source of essential found to be the dominant class of repeat elements (19%), while fatty acids. The residual essential fatty acids combined with low DNA transposons accounted for 3% of the genome. Similar glucosinolate levels in C. sativa meal make it desirable as an to most higher plant genomes, repetitive elements in C. sativa animal feed. Considering the broad applications, C. sativa is were more abundant in the vicinity of centromeres and less so in currently being re-embraced as an industrial oil platform crop; gene-dense regions (Fig. 1). The genome occupancy of repetitive however, due to limited availability of genetic and genomic DNA in C. sativa (28%) is comparable to the low abundance of resources, the full agronomic and breeding potential of this TEs in A. thaliana (24%)10 and A. lyrata (30%)10. However, it is emerging oilseed crop remains largely unexploited. much smaller than in B. rapa (39.5%)7 as well as other similar- Genetically, C. sativa is closely related to the model plant sized plant genomes, including potato (62%)11, soybean (59%)12 Arabidopsis thaliana (lineage I of the Brassicaceae) and more and sorghum (62%)13. Thus, unlike B. rapa and other angiosperm distantly to the important vegetable oilseed crop, canola (lineage species, genome expansion in C. sativa has not resulted from II)4. The previously estimated genome size (750 Mb)5 and repetitive sequence proliferation. chromosome count (n ¼ 20) of C. sativa are higher compared RNA-seq data (78.5 Gb) was generated from tissue samples with most of the Brassicaceae species that have been sequenced to collected at 12 different growth stages to assist with annotation of date (Supplementary Fig. 1). However, the genetic basis for the protein-coding genes (Supplementary Table 10). Based on a genome expansion of C. sativa is currently unknown. In many comprehensive strategy of ab initio gene prediction and plant taxa, polyploidization and proliferation of transposable homology evidence from proteome data sets, ESTs and RNA- elements (TEs) are recognized as prevalent factors in plant seq transcripts (Supplementary Fig. 4), 89,418 non-redundant genome expansion6,7. Similar to the diploid progenitors of canola C. sativa genes were predicted, of which 4,753 (5.3%) (B. rapa and B. oleracea)8,9, C. sativa is suggested to have genes encoded two or more alternatively spliced isoforms undergone a genome triplication event5. However, the (Supplementary Table 4). More than 95% (85,274) of these evolutionary origin and mode of the polyploidization event that annotated genes were located on the pseudochromosomes with formed the C. sativa genome as well as the post-polyploidization the remainder on unanchored scaffolds. The overall gene model evolutionary path leading to its diploidization are currently not characteristics, such as gene length and exon-intron structures are understood. comparable to other Brassicaceae species (Supplementary Fig. 5). Here we sequence a homozygous doubled haploid line of The genome composition (genic, intergenic and repeat regions) of C. sativa and assembled 82% of the estimated genome size in C. sativa is more similar to that of A. lyrata10 than A. thaliana order to decipher the genome organization of C. sativa and (Supplementary Table 11). Based on sequence identity a total of facilitate development of genetic and genomic tools essential for 86,849 (97.13%) of the predicted C. sativa genes have homologues crop improvement. The genome sequence of C. sativa will in the UniProt database (Supplementary Data 1), and RNA-seq provide an indispensable tool for genetic manipulation and evidence suggested that 490% of the genes were expressed further crop improvement. (FPKM40) in one or more developmental stages (Fig. 1). The genome sequence and its annotation are available along with a genome browser at http://www.camelinadb.ca. Results The predicted number of protein-coding genes in C. sativa is Genome sequencing and assembly. The genome of a homo- significantly higher than other currently sequenced plant zygous doubled haploid line of C. sativa (DH55) was sequenced genomes (Fig. 2, Supplementary Table 12). Interestingly, the using a hybrid Illumina and Roche 454 next-generation sequen- gene number is similar to that predicted for bread wheat whose cing (NGS) approach (Supplementary Note 1; Supplementary genome is almost 22 times larger than that of C. sativa14. The Fig. 2). Filtered sequence data (96.53 Gb) provided 123 Â estimated total number of genes in C. sativa is approximately coverage (Supplementary Table 1) of the estimated genome size three times that of the model Arabidopsis species (Supplementary of 785 Mb (Supplementary Note 2; Supplementary Fig. 3), Table 11), suggesting that the C. sativa genome resulted from a which was assembled using a hierarchical assembly strategy whole-genome triplication of a common ancestor. To determine (Supplementary Note 1) into 37,871 scaffolds, with a sequence whether the expanded gene repertoire in C. sativa could have span of 641.45 Mb and an N50 size of 2.16 Mb (Supplementary arisen from an expansion of lineage-specific C. sativa orphan Table 2). A high-density genetic map based on 3,575 polymorphic genes15, we used a BLAST-based filtering approach comparing markers allowed 608.54 Mb of the assembled genome, repre- C. sativa genes with all sequenced plant taxa excluding the five sented by 588 scaffolds to be anchored to the 20 chromosomes of Brassicaceae species. A total of 3,761 Brassicaceae-specific orphan C. sativa (Fig. 1; Supplementary Table 3), thereby producing a genes were identified, of which 1,656 were C. sativa–specific, highly contiguous final assembly with an N50 size of 430 Mb which accounts for only 1.85% of annotated protein-coding genes 2 NATURE COMMUNICATIONS | 5:3706 | DOI: 10.1038/ncomms4706 | www.nature.com/naturecommunications & 2014 Macmillan Publishers Limited. All rights reserved. NATURE COMMUNICATIONS | DOI: 10.1038/ncomms4706 ARTICLE in C. sativa (Supplementary Note 4; Supplementary Tables 13 and the extent of the collinear conserved block environment. and 14). A syntelog matrix representing individual A. thaliana genes and the corresponding triplets of C. sativa homologues is presented in Supplementary Data 2. A total of 62,277 C.
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