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Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

Ragupathy R, Rathinavelu R, Cloutier S - BMC Genomics (2011)

Bottom Line: Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low.The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps.The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada.

ABSTRACT

Background: Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.

Results: The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.

Conclusion: The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

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Transposable element (TE) composition in sequenced plant genomes in comparison with the BES-based estimates in flax. The data regarding the TE composition of other plant genomes were taken from [74; papaya] [45; castor bean] [80; apple and other genomes]. Please refer to Additional file 9: Table S9 for more details.
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Figure 5: Transposable element (TE) composition in sequenced plant genomes in comparison with the BES-based estimates in flax. The data regarding the TE composition of other plant genomes were taken from [74; papaya] [45; castor bean] [80; apple and other genomes]. Please refer to Additional file 9: Table S9 for more details.

Mentions: Transposable elements play significant roles in the evolution of structure, function and regulation of expression of genes and genomes [66,67]. Mobile DNA also significantly impacts the genome size [68]. Among various repeat prediction tools, Repeatmasker is widely used for identifying repeats in genomes [69] using Repbase, a manually curated high quality database of consensus sequences of eukaryotic repeat elements [49]. Repeatmasker analysis identified ~6.1% of the BES of flax as having homology to known transposable elements. This estimate of known mobile genetic elements is the lowest among twelve plant genomes whose whole genome sequences are available to date, namely Arabidopsis (14%, [70]), rice (34.7%, [71]), poplar (35%, [72]), grapevine (21.5%, [73]), papaya (51.9%, [74]), sorghum (62%, [75]), maize (84.2%, [76]), cucumber (14.8%, [77]), soybean (50.3%, [78]), Brachypodium (28.1%, [79]), castor bean (50.3%, [45]) and apple (42.4%, [80]) (Figure 5; Additional file 9: Table S9). However, the unknown portion of the flax genome, including the novel repeat fraction of the genome (Figure 3), would be a reservoir of new mobile genetic elements and hence the proportion of transposable elements in flax is predicted to increase with the characterization of this currently unknown fraction. In castor bean and poplar, ~31.3% and 25.9% of the genome were represented by unannotated/unknown elements [45,72]. The proportions of known retrotransposons in flax were predominant over DNA elements, as reported in other plant genomes, with the exception of Arabidopsis (Additional file 9: Table S9). However, flax was found to have a higher proportion of copia retrotransposons than gypsy elements compared to all other sequenced plant genomes where gypsy elements predominated (Additional file 9: Table S9), indicating the possibility of uncharacterized sequences as a warehouse of new members which may alter the proportion of copia/gypsy elements. Recently, the repetitive portion of the banana genome was found to harbour a higher proportion (16%) of copia elements than gypsy elements (7%) [81]. Only 62 known families of transposable elements have been identified from the BES, far fewer than the whole genome based estimates of 1323 families in maize, 300 families in rice and 510 families in soybean [82].


Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.

Ragupathy R, Rathinavelu R, Cloutier S - BMC Genomics (2011)

Transposable element (TE) composition in sequenced plant genomes in comparison with the BES-based estimates in flax. The data regarding the TE composition of other plant genomes were taken from [74; papaya] [45; castor bean] [80; apple and other genomes]. Please refer to Additional file 9: Table S9 for more details.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3113786&req=5

Figure 5: Transposable element (TE) composition in sequenced plant genomes in comparison with the BES-based estimates in flax. The data regarding the TE composition of other plant genomes were taken from [74; papaya] [45; castor bean] [80; apple and other genomes]. Please refer to Additional file 9: Table S9 for more details.
Mentions: Transposable elements play significant roles in the evolution of structure, function and regulation of expression of genes and genomes [66,67]. Mobile DNA also significantly impacts the genome size [68]. Among various repeat prediction tools, Repeatmasker is widely used for identifying repeats in genomes [69] using Repbase, a manually curated high quality database of consensus sequences of eukaryotic repeat elements [49]. Repeatmasker analysis identified ~6.1% of the BES of flax as having homology to known transposable elements. This estimate of known mobile genetic elements is the lowest among twelve plant genomes whose whole genome sequences are available to date, namely Arabidopsis (14%, [70]), rice (34.7%, [71]), poplar (35%, [72]), grapevine (21.5%, [73]), papaya (51.9%, [74]), sorghum (62%, [75]), maize (84.2%, [76]), cucumber (14.8%, [77]), soybean (50.3%, [78]), Brachypodium (28.1%, [79]), castor bean (50.3%, [45]) and apple (42.4%, [80]) (Figure 5; Additional file 9: Table S9). However, the unknown portion of the flax genome, including the novel repeat fraction of the genome (Figure 3), would be a reservoir of new mobile genetic elements and hence the proportion of transposable elements in flax is predicted to increase with the characterization of this currently unknown fraction. In castor bean and poplar, ~31.3% and 25.9% of the genome were represented by unannotated/unknown elements [45,72]. The proportions of known retrotransposons in flax were predominant over DNA elements, as reported in other plant genomes, with the exception of Arabidopsis (Additional file 9: Table S9). However, flax was found to have a higher proportion of copia retrotransposons than gypsy elements compared to all other sequenced plant genomes where gypsy elements predominated (Additional file 9: Table S9), indicating the possibility of uncharacterized sequences as a warehouse of new members which may alter the proportion of copia/gypsy elements. Recently, the repetitive portion of the banana genome was found to harbour a higher proportion (16%) of copia elements than gypsy elements (7%) [81]. Only 62 known families of transposable elements have been identified from the BES, far fewer than the whole genome based estimates of 1323 families in maize, 300 families in rice and 510 families in soybean [82].

Bottom Line: Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low.The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps.The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

View Article: PubMed Central - HTML - PubMed

Affiliation: Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada.

ABSTRACT

Background: Flax (Linum usitatissimum L.) is an important source of oil rich in omega-3 fatty acids, which have proven health benefits and utility as an industrial raw material. Flax seeds also contain lignans which are associated with reducing the risk of certain types of cancer. Its bast fibres have broad industrial applications. However, genomic tools needed for molecular breeding were non existent. Hence a project, Total Utilization Flax GENomics (TUFGEN) was initiated. We report here the first genome-wide physical map of flax and the generation and analysis of BAC-end sequences (BES) from 43,776 clones, providing initial insights into the genome.

Results: The physical map consists of 416 contigs spanning ~368 Mb, assembled from 32,025 fingerprints, representing roughly 54.5% to 99.4% of the estimated haploid genome (370-675 Mb). The N50 size of the contigs was estimated to be ~1,494 kb. The longest contig was ~5,562 kb comprising 437 clones. There were 96 contigs containing more than 100 clones. Approximately 54.6 Mb representing 8-14.8% of the genome was obtained from 80,337 BES. Annotation revealed that a large part of the genome consists of ribosomal DNA (~13.8%), followed by known transposable elements at 6.1%. Furthermore, ~7.4% of sequence was identified to harbour novel repeat elements. Homology searches against flax-ESTs and NCBI-ESTs suggested that ~5.6% of the transcriptome is unique to flax. A total of 4064 putative genomic SSRs were identified and are being developed as novel markers for their use in molecular breeding.

Conclusion: The first genome-wide physical map of flax constructed with BAC clones provides a framework for accessing target loci with economic importance for marker development and positional cloning. Analysis of the BES has provided insights into the uniqueness of the flax genome. Compared to other plant genomes, the proportion of rDNA was found to be very high whereas the proportion of known transposable elements was low. The SSRs identified from BES will be valuable in saturating existing linkage maps and for anchoring physical and genetic maps. The physical map and paired-end reads from BAC clones will also serve as scaffolds to build and validate the whole genome shotgun assembly.

Show MeSH
Related in: MedlinePlus