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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 representing organ polarity transcription factors. Organ polarity transcription factor ESTs are most abundant during cotyledon primordia differentiation of heart-stage embryos. Adaxial (HD-ZIPIII family and AS1) and abaxial (YABBY and KANADI families) gene expression establishes organ polarity. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.
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Figure 6: Putative flax unigenes representing organ polarity transcription factors. Organ polarity transcription factor ESTs are most abundant during cotyledon primordia differentiation of heart-stage embryos. Adaxial (HD-ZIPIII family and AS1) and abaxial (YABBY and KANADI families) gene expression establishes organ polarity. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.

Mentions: As one of the main objectives of this study was to gain a better understanding of what happens in the flax seed as it develops, we further analyzed the EST libraries for transcription factors with specific roles in embryo and seed development (Additional File 2). The establishment of the adaxial and abaxial polarity during cotyledon primordia differentiation at the heart stage of embryo development is specified by the HD-ZIPIII family, ASYMMETRIC LEAVES1 (AS1) (adaxial) and YABBY, KANADI families (abaxial) respectively [31]. ESTs corresponding to adaxial and abaxial polarity specifying TFs are expressed from globular stage onwards with maximum number of ESTs in the heart stage when the cotyledon primordia are specified (Figure 6; Additional File 2).


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 representing organ polarity transcription factors. Organ polarity transcription factor ESTs are most abundant during cotyledon primordia differentiation of heart-stage embryos. Adaxial (HD-ZIPIII family and AS1) and abaxial (YABBY and KANADI families) gene expression establishes organ polarity. 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 6: Putative flax unigenes representing organ polarity transcription factors. Organ polarity transcription factor ESTs are most abundant during cotyledon primordia differentiation of heart-stage embryos. Adaxial (HD-ZIPIII family and AS1) and abaxial (YABBY and KANADI families) gene expression establishes organ polarity. EST distribution of flax unigenes used to compile this graph is listed in Additional File 2.
Mentions: As one of the main objectives of this study was to gain a better understanding of what happens in the flax seed as it develops, we further analyzed the EST libraries for transcription factors with specific roles in embryo and seed development (Additional File 2). The establishment of the adaxial and abaxial polarity during cotyledon primordia differentiation at the heart stage of embryo development is specified by the HD-ZIPIII family, ASYMMETRIC LEAVES1 (AS1) (adaxial) and YABBY, KANADI families (abaxial) respectively [31]. ESTs corresponding to adaxial and abaxial polarity specifying TFs are expressed from globular stage onwards with maximum number of ESTs in the heart stage when the cotyledon primordia are specified (Figure 6; Additional File 2).

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