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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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Putative flax unigenes encoding transcription factors that are known embryogenesis regulators. Tissue distribution of flax unigenes encoding ESTs with similarity to important regulators of embryogenesis are present in developing flax seed tissue libraries, and not in non-seed libraries. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.
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Figure 7: Putative flax unigenes encoding transcription factors that are known embryogenesis regulators. Tissue distribution of flax unigenes encoding ESTs with similarity to important regulators of embryogenesis are present in developing flax seed tissue libraries, and not in non-seed libraries. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.

Mentions: LEAFY COTYLEDON (LEC) genes LEC1, LEC1-like (L1L), LEC2 and FUSCA3 (FUS3) are master regulators of embryogenesis that are primarily expressed throughout seed development, and ectopic expression of these TFs results in somatic embryogenesis or embryonic characteristics being overlaid on vegetative organs [32-35]. ABI3 is expressed only during seed maturation and is a key regulator of seed maturation processes such as seed dormancy and storage reserve accumulation [36]. AGAMOUS-LIKE15 (AGL15), a MADS domain containing TF is primarily expressed during Arabidopsis seed development and its ectopic expression increases the competency of cells to respond to somatic embryogenesis induction conditions [37,38]. In Arabidopsis, AGL15 is directly upregulated by LEC2 [39]. In addition, LEC2, FUS3 and ABI3 have all been demonstrated to be direct targets of AGL15 [40]. Examination of flax unigenes showed seed-specific enriched expression of L1L, LEC2, FUS3, ABI3 and AGL15 (Figure 7; Additional File 2). Only one EST with similarity to LEC2 was identified. The absence of LEC1 and the presence of the closely related L1L in seed tissues have also been observed for scarlett runner bean [33]. The identification of ESTs in seed-specific libraries that are pertinent to seed maturation program lends support to the quality of these libraries.


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)

Putative flax unigenes encoding transcription factors that are known embryogenesis regulators. Tissue distribution of flax unigenes encoding ESTs with similarity to important regulators of embryogenesis are present in developing flax seed tissue libraries, and not in non-seed libraries. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 7: Putative flax unigenes encoding transcription factors that are known embryogenesis regulators. Tissue distribution of flax unigenes encoding ESTs with similarity to important regulators of embryogenesis are present in developing flax seed tissue libraries, and not in non-seed libraries. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.
Mentions: LEAFY COTYLEDON (LEC) genes LEC1, LEC1-like (L1L), LEC2 and FUSCA3 (FUS3) are master regulators of embryogenesis that are primarily expressed throughout seed development, and ectopic expression of these TFs results in somatic embryogenesis or embryonic characteristics being overlaid on vegetative organs [32-35]. ABI3 is expressed only during seed maturation and is a key regulator of seed maturation processes such as seed dormancy and storage reserve accumulation [36]. AGAMOUS-LIKE15 (AGL15), a MADS domain containing TF is primarily expressed during Arabidopsis seed development and its ectopic expression increases the competency of cells to respond to somatic embryogenesis induction conditions [37,38]. In Arabidopsis, AGL15 is directly upregulated by LEC2 [39]. In addition, LEC2, FUS3 and ABI3 have all been demonstrated to be direct targets of AGL15 [40]. Examination of flax unigenes showed seed-specific enriched expression of L1L, LEC2, FUS3, ABI3 and AGL15 (Figure 7; Additional File 2). Only one EST with similarity to LEC2 was identified. The absence of LEC1 and the presence of the closely related L1L in seed tissues have also been observed for scarlett runner bean [33]. The identification of ESTs in seed-specific libraries that are pertinent to seed maturation program lends support to the quality of these libraries.

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