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Gene expression analysis of flax seed development.

Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M, Bekkaoui F, Sharpe A, Wang E, Rowland G, Selvaraj G, Datla R - BMC Plant Biol. (2011)

Bottom Line: When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis.We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors.Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, Saskatchewan, S7N 0W9, Canada.

ABSTRACT

Background: Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed.

Results: We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development.

Conclusions: We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors. This has allowed us to delineate the spatio-temporal aspects of gene expression underlying the biosynthesis of a number of important seed constituents in flax. Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.

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GO annotation of flax unigenes. TAIR annotation of flax unigenes indicates broad representation within each category. (A) Biological processes; (B) Molecular functions; (C) Cellular components. Numbers shown signify ESTs for each sub-category.
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Figure 3: GO annotation of flax unigenes. TAIR annotation of flax unigenes indicates broad representation within each category. (A) Biological processes; (B) Molecular functions; (C) Cellular components. Numbers shown signify ESTs for each sub-category.

Mentions: The unigene collection of 30,640 contigs and singletons was analyzed using the BLASTX algorithm against the UniProt-plants and TAIR databases. The unigenes that showed significant homology to known genes (E-value ≤ e-10) against UniProt-plants were selected for Gene Ontology (GO) annotation and further mapping of the GO terms to TAIR database which is manually and computationally curated on a ongoing basis [21]. The values generated for the different GO-categories were used to generate the classification based on molecular functions, biological processes and cellular components (Figure 3). Based on the BLAST analysis in TAIR, 23,418 unigenes showed significant homology to Arabidopsis genes and these are listed in a spreadsheet (Additional File 1; http://bioinfo.pbi.nrc.ca/portal/flax/) along with the distribution of ESTs for each unigene from the 13 tissue libraries. Our analysis suggests that the different GO-categories are well represented in our unigene dataset indicative of a broad coverage of expressed genes in the flax genome.


Gene expression analysis of flax seed development.

Venglat P, Xiang D, Qiu S, Stone SL, Tibiche C, Cram D, Alting-Mees M, Nowak J, Cloutier S, Deyholos M, Bekkaoui F, Sharpe A, Wang E, Rowland G, Selvaraj G, Datla R - BMC Plant Biol. (2011)

GO annotation of flax unigenes. TAIR annotation of flax unigenes indicates broad representation within each category. (A) Biological processes; (B) Molecular functions; (C) Cellular components. Numbers shown signify ESTs for each sub-category.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3107784&req=5

Figure 3: GO annotation of flax unigenes. TAIR annotation of flax unigenes indicates broad representation within each category. (A) Biological processes; (B) Molecular functions; (C) Cellular components. Numbers shown signify ESTs for each sub-category.
Mentions: The unigene collection of 30,640 contigs and singletons was analyzed using the BLASTX algorithm against the UniProt-plants and TAIR databases. The unigenes that showed significant homology to known genes (E-value ≤ e-10) against UniProt-plants were selected for Gene Ontology (GO) annotation and further mapping of the GO terms to TAIR database which is manually and computationally curated on a ongoing basis [21]. The values generated for the different GO-categories were used to generate the classification based on molecular functions, biological processes and cellular components (Figure 3). Based on the BLAST analysis in TAIR, 23,418 unigenes showed significant homology to Arabidopsis genes and these are listed in a spreadsheet (Additional File 1; http://bioinfo.pbi.nrc.ca/portal/flax/) along with the distribution of ESTs for each unigene from the 13 tissue libraries. Our analysis suggests that the different GO-categories are well represented in our unigene dataset indicative of a broad coverage of expressed genes in the flax genome.

Bottom Line: When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis.We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors.Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.

View Article: PubMed Central - HTML - PubMed

Affiliation: Plant Biotechnology Institute, NRC, 110 Gymnasium Place, Saskatoon, Saskatchewan, S7N 0W9, Canada.

ABSTRACT

Background: Flax, Linum usitatissimum L., is an important crop whose seed oil and stem fiber have multiple industrial applications. Flax seeds are also well-known for their nutritional attributes, viz., omega-3 fatty acids in the oil and lignans and mucilage from the seed coat. In spite of the importance of this crop, there are few molecular resources that can be utilized toward improving seed traits. Here, we describe flax embryo and seed development and generation of comprehensive genomic resources for the flax seed.

Results: We describe a large-scale generation and analysis of expressed sequences in various tissues. Collectively, the 13 libraries we have used provide a broad representation of genes active in developing embryos (globular, heart, torpedo, cotyledon and mature stages) seed coats (globular and torpedo stages) and endosperm (pooled globular to torpedo stages) and genes expressed in flowers, etiolated seedlings, leaves, and stem tissue. A total of 261,272 expressed sequence tags (EST) (GenBank accessions LIBEST_026995 to LIBEST_027011) were generated. These EST libraries included transcription factor genes that are typically expressed at low levels, indicating that the depth is adequate for in silico expression analysis. Assembly of the ESTs resulted in 30,640 unigenes and 82% of these could be identified on the basis of homology to known and hypothetical genes from other plants. When compared with fully sequenced plant genomes, the flax unigenes resembled poplar and castor bean more than grape, sorghum, rice or Arabidopsis. Nearly one-fifth of these (5,152) had no homologs in sequences reported for any organism, suggesting that this category represents genes that are likely unique to flax. Digital analyses revealed gene expression dynamics for the biosynthesis of a number of important seed constituents during seed development.

Conclusions: We have developed a foundational database of expressed sequences and collection of plasmid clones that comprise even low-expressed genes such as those encoding transcription factors. This has allowed us to delineate the spatio-temporal aspects of gene expression underlying the biosynthesis of a number of important seed constituents in flax. Flax belongs to a taxonomic group of diverse plants and the large sequence database will allow for evolutionary studies as well.

Show MeSH
Related in: MedlinePlus