Genomics Resources

Please click on the following links to learn more about the genomics resources being developed in this project:

We are also developing resources in these other components of our project:

 


cDNA Library Construction

We are constructing new cDNA libraries to support gene discovery with an emphasis on Sitka spruce defense against weevils.  Libraries will be from the following tissues:

  • Sitka spruce genotype H898 apical shoot bark treated with methyl jasmonate (WS036 SsH898 MeJA-N);
  • Apical shoot bark with wound treatment (WS037 SsH898Wound-N);
  • Apical shoot bark with weevil attack (WS038 SsH898Herbivory-N); and,
  • Lateral shoots, no treatment (WS039 Ss898MeJA-NN).


The genotype H898 was provided by the British Columbia Ministry of Forests and Range (BC MoFR) and has been identified as resistant to weevil attack.

New cDNA libraries to support gene discovery with an emphasis on cold hardiness and local adaptation will also be developed from Sitka spruce FB3-425 needle tissue.

In support of the FLcDNA sequencing activity, we use full-length enriched cDNA libraries from insect-induced Sitka spruce FB3-425.

 


EST Sequencing and Databasing 

We have sequenced ~ 50,000 new 3’ ESTs from Sitka spruce H898 cDNA libraries and ~ 25,000 new 3’ ESTs from Sitka spruce FB3-425 cDNA libraries. 

All sequencing is carried out at the Michael Smith Genome Sciences Centre (GSC) and then filtered, trimmed, and assembled by the bioinformatics team at the GSC.

 


Full Length cDNA Sequencing

We are continually sequencing Full Length cDNAs (FLcDNAs) and submitting them to GenBank. This activity is done in close collaboration with the sequencing and bioinformatics groups at the GSC, and involves bioinformatics and wet-lab development of an efficient clone selection and sequence finishing strategy.
     
Details of the clone selection strategy, sequence finishing, and the results from sequence analysis of a first set of 6,464 spruce FLcDNAs are in Ralph et al. (manuscript in preparation) and FLcDNA sequences to GenBank will be released as soon as the manuscript has passed peer review.  Associated 3’ and 5’ ESTs have already been released.  For more information, please contact Joerg Bohlmann.

 



EST and FLcDNA Annotation

Initial annotation of putative unique transcripts (PUTs) is done against 28,952 protein sequences in The Arabidopsis Information Resource (TAIR) and sequences from other higher plants in the NR division of GenBank.  We also do manual annotation based on expert knowledge and literature review for spruce EST and FLcDNA Sequences

We have established detailed gene annotations and pathway maps for spruce genes from 3,551 ESTs and 281 FLcDNAs representing almost all known genes and some large gene families involved in terpenoid and phenolic defense. Results of this annotation are described in Ralph et al. (manuscript in preparation) and will be made available on this webpage once the paper has passed peer-review. Clustering and assembly of 3’-end ESTs resulted in 19,941 contigs and 26,804 singletons, representing 46,745 PUTs.

 

Funding Institutions

UBC Genome Canada
Genome British Columbia