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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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EST distribution across tissue libraries of biosynthetic genes of important flax seed nutritional components. Fatty acid biosynthesis, oleosin oil body proteins and storage protein ESTs are highly represented in zygotic library compartments (A). Lignan, flavonoid and mucilage biosynthetic pathways are highly represented in maternal seed coat compartments (B). EST distribution of flax unigenes used to compile these graphs is listed in Additional File 3 and Additional File 4.
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Figure 8: EST distribution across tissue libraries of biosynthetic genes of important flax seed nutritional components. Fatty acid biosynthesis, oleosin oil body proteins and storage protein ESTs are highly represented in zygotic library compartments (A). Lignan, flavonoid and mucilage biosynthetic pathways are highly represented in maternal seed coat compartments (B). EST distribution of flax unigenes used to compile these graphs is listed in Additional File 3 and Additional File 4.

Mentions: Much of the proteins in flax seeds are storage proteins that exist within protein storage vacuoles and these proteins constitute 23% of the whole flax seed [41]. Storage proteins in flax seed are made up of ~65% globulins and ~35% albumins [11]. Conlinin is a 2S albumin and cupin and cruciferin are 11S and 12S globulins, respectively. Our EST data correlates the expression of the genes coding for the storage proteins with the reported levels of proteins in flax seeds (Figure 8A; Additional File 3). Globulin encoding genes were expressed at much higher levels than those encoding the albumin and were observed in the later cotyledon (CE) and mature (ME) stages of embryo development. Interestingly, small numbers of ESTs for all the storage proteins were identified in young seed coats, primarily at the torpedo stage (Figure 8A; Additional File 3). This is in agreement with the observation that a conlinin gene promoter is active in early stages of seed coat development [42]. Pooled endosperm from the corresponding seed coat stages did not identify any storage protein ESTs. These observations suggest that the seed coat does have a role in storage protein synthesis. Given that the seed coat is a major part of the overall mass in developing seeds, the seed coat might be a transient source of protein for developing embryos.


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)

EST distribution across tissue libraries of biosynthetic genes of important flax seed nutritional components. Fatty acid biosynthesis, oleosin oil body proteins and storage protein ESTs are highly represented in zygotic library compartments (A). Lignan, flavonoid and mucilage biosynthetic pathways are highly represented in maternal seed coat compartments (B). EST distribution of flax unigenes used to compile these graphs is listed in Additional File 3 and Additional File 4.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 8: EST distribution across tissue libraries of biosynthetic genes of important flax seed nutritional components. Fatty acid biosynthesis, oleosin oil body proteins and storage protein ESTs are highly represented in zygotic library compartments (A). Lignan, flavonoid and mucilage biosynthetic pathways are highly represented in maternal seed coat compartments (B). EST distribution of flax unigenes used to compile these graphs is listed in Additional File 3 and Additional File 4.
Mentions: Much of the proteins in flax seeds are storage proteins that exist within protein storage vacuoles and these proteins constitute 23% of the whole flax seed [41]. Storage proteins in flax seed are made up of ~65% globulins and ~35% albumins [11]. Conlinin is a 2S albumin and cupin and cruciferin are 11S and 12S globulins, respectively. Our EST data correlates the expression of the genes coding for the storage proteins with the reported levels of proteins in flax seeds (Figure 8A; Additional File 3). Globulin encoding genes were expressed at much higher levels than those encoding the albumin and were observed in the later cotyledon (CE) and mature (ME) stages of embryo development. Interestingly, small numbers of ESTs for all the storage proteins were identified in young seed coats, primarily at the torpedo stage (Figure 8A; Additional File 3). This is in agreement with the observation that a conlinin gene promoter is active in early stages of seed coat development [42]. Pooled endosperm from the corresponding seed coat stages did not identify any storage protein ESTs. These observations suggest that the seed coat does have a role in storage protein synthesis. Given that the seed coat is a major part of the overall mass in developing seeds, the seed coat might be a transient source of protein for developing embryos.

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