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Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don.

Li X, Wu HX, Dillon SK, Southerton SG - BMC Genomics (2009)

Bottom Line: Pinus radiata D.Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.Cell wall-related genes and transcription factors were identified.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia. xinguo.li@csiro.au

ABSTRACT

Background: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.

Results: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.

Conclusion: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.

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Hierarchical clustering dendrogram trees for juvenile and mature wood cDNA libraries. ESTs or unigenes from each of the four libraries (juvenile earlywood-JE, juvenile latewood-JL, mature earlywood-ME and mature latewood-ML) were annotated against the UniProt and TIGR databases, and assigned with GO terms. The abundance of ESTs or unigenes in each GO term was calculated for each library, and further normalized as a percentage based on the number of ESTs or unigenes in each library. Statistical significance of EST or unigene abundance in each GO term among the four libraries was valuated by Chi Square tests and P-values. The normalized EST or unigene abundance was used to construct the hierarchical clustering dendrogram trees. A: the dendrogram tree for ESTs. B: the dendrogram tree for unigenes.
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Figure 3: Hierarchical clustering dendrogram trees for juvenile and mature wood cDNA libraries. ESTs or unigenes from each of the four libraries (juvenile earlywood-JE, juvenile latewood-JL, mature earlywood-ME and mature latewood-ML) were annotated against the UniProt and TIGR databases, and assigned with GO terms. The abundance of ESTs or unigenes in each GO term was calculated for each library, and further normalized as a percentage based on the number of ESTs or unigenes in each library. Statistical significance of EST or unigene abundance in each GO term among the four libraries was valuated by Chi Square tests and P-values. The normalized EST or unigene abundance was used to construct the hierarchical clustering dendrogram trees. A: the dendrogram tree for ESTs. B: the dendrogram tree for unigenes.

Mentions: The ESTs and unigenes from different libraries represent the transcriptome in the respective wood development stages. We compared the transcriptomes from juvenile earlywood, juvenile latewood, mature earlywood and mature latewood tissues. These four tissues were collected from trees growing within 50 m of each other, and at the same date for earlywood or latewood to minimize the environmental effects. Comparative transcriptome analysis highlighted 306 and 150 GO terms showing significant differences (P-value < 0.01) in terms of EST and unigene abundance, respectively. The hierarchical clustering dendrogram trees from both ESTs and unigenes revealed similar patterns of transcriptome reorganization during wood formation in radiata pine (Figure 3A, B), which suggested that juvenile earlywood has a distinct transcriptome compared to the other three developmental stages, whereas the transcriptome of juvenile latewood is more conserved with mature earlywood and latewood. The distinct gene expression in juvenile earlywood is likely associated with the unique properties of juvenile wood.


Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don.

Li X, Wu HX, Dillon SK, Southerton SG - BMC Genomics (2009)

Hierarchical clustering dendrogram trees for juvenile and mature wood cDNA libraries. ESTs or unigenes from each of the four libraries (juvenile earlywood-JE, juvenile latewood-JL, mature earlywood-ME and mature latewood-ML) were annotated against the UniProt and TIGR databases, and assigned with GO terms. The abundance of ESTs or unigenes in each GO term was calculated for each library, and further normalized as a percentage based on the number of ESTs or unigenes in each library. Statistical significance of EST or unigene abundance in each GO term among the four libraries was valuated by Chi Square tests and P-values. The normalized EST or unigene abundance was used to construct the hierarchical clustering dendrogram trees. A: the dendrogram tree for ESTs. B: the dendrogram tree for unigenes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2636829&req=5

Figure 3: Hierarchical clustering dendrogram trees for juvenile and mature wood cDNA libraries. ESTs or unigenes from each of the four libraries (juvenile earlywood-JE, juvenile latewood-JL, mature earlywood-ME and mature latewood-ML) were annotated against the UniProt and TIGR databases, and assigned with GO terms. The abundance of ESTs or unigenes in each GO term was calculated for each library, and further normalized as a percentage based on the number of ESTs or unigenes in each library. Statistical significance of EST or unigene abundance in each GO term among the four libraries was valuated by Chi Square tests and P-values. The normalized EST or unigene abundance was used to construct the hierarchical clustering dendrogram trees. A: the dendrogram tree for ESTs. B: the dendrogram tree for unigenes.
Mentions: The ESTs and unigenes from different libraries represent the transcriptome in the respective wood development stages. We compared the transcriptomes from juvenile earlywood, juvenile latewood, mature earlywood and mature latewood tissues. These four tissues were collected from trees growing within 50 m of each other, and at the same date for earlywood or latewood to minimize the environmental effects. Comparative transcriptome analysis highlighted 306 and 150 GO terms showing significant differences (P-value < 0.01) in terms of EST and unigene abundance, respectively. The hierarchical clustering dendrogram trees from both ESTs and unigenes revealed similar patterns of transcriptome reorganization during wood formation in radiata pine (Figure 3A, B), which suggested that juvenile earlywood has a distinct transcriptome compared to the other three developmental stages, whereas the transcriptome of juvenile latewood is more conserved with mature earlywood and latewood. The distinct gene expression in juvenile earlywood is likely associated with the unique properties of juvenile wood.

Bottom Line: Pinus radiata D.Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.Cell wall-related genes and transcription factors were identified.

View Article: PubMed Central - HTML - PubMed

Affiliation: CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia. xinguo.li@csiro.au

ABSTRACT

Background: Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. Pinus radiata D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.

Results: Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including CesA, tubulin, AGP, SAMS, actin, laccase, CCoAMT, MetE, phytocyanin, pectate lyase, cellulase, SuSy, expansin, chitinase and UDP-glucose dehydrogenase. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.

Conclusion: The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.

Show MeSH
Related in: MedlinePlus