Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

Area of Science:

• Plant genomics
• Molecular biology
• Bioinformatics

Background:

• Conifer genomes are too large for full sequencing, making EST analysis the primary method for gene discovery.
• White spruce (Picea glauca) gene discovery and cDNA microarray development were objectives.

Purpose of the Study:

• To generate extensive expressed sequence tag (EST) collections and complementary DNA (cDNA) clones for white spruce.
• To support gene discovery and the creation of cDNA microarrays for white spruce.

Main Methods:

• Generated 16 cDNA libraries from various white spruce tissues and treatments.
• Partially sequenced 50,000 cDNA clones, assembling reads into 16,578 consensus sequences.
• Utilized sequence similarity searches, Gene Ontology, and Hidden Markov Models for functional annotation.

Main Results:

• Assembled 14,471 unique spruce transcripts, with 45% representing full-length inserts.
• Identified functional annotations for 70% of spruce transcripts.
• Discovered larger multigenic families in spruce compared to Arabidopsis and rice, notably in translationally controlled tumor protein and S-adenosylmethionine synthetase families.

Conclusions:

• Developed effective methods for large-scale gene discovery and annotation in conifers, distantly related to sequenced genomes.
• Created the SpruceDB database and associated search tools for efficient data mining.
• The generated sequence data and cDNA clones are a significant resource for conifer genetics and comparative genomics research.