Databases

 Public Data Release

 

NCBI GenBank EST Sequence Submissions

As of July 2007, we have submitted a total of more than 250,000 spruce EST’s to NCBI Genbank for immediate release. These ESTs include ca. 184,000 EST’s from Treenomix I (finished within the Treenomix II project), and 67,753 new EST’s from Treenomix II.
 

  • Ralph SG, Kolosova N, Oddy C, Cooper D, Butterfield Y, Kirkpatrick R, Liu J, Palmquist D, Stott J, Barber S, Yang G, Babakaiff R, Brown-John M, Chand S, Featherstone R, Masson A, Mayo M, Moran J, Olson T, Wong D, Friedmann MF, Ritland CE, Siddiqui A, Holt R, Jones S, Marra M, Ellis BE, Douglas C, Ritland K and J Bohlmann. The spruce transcriptome: Analysis of expressed sequence tags from multiple cDNA libraries; ca. 184,000 ESTs generated in the Treenomix I project and finished in the Treenomix II project -  submitted to dbEST division of GenBank (accession numbers DR448912 to DR595214; CO203067 to CO258618) - Released.
  • Reid KE, Chun E, Ralph S, Gillan T, Jancsik S, Liao N, Moore R, Mayo M, Wagner S, Featherstone R, Roger J, Brown-John M, Tam B, Sze WK, Wilton J, Kirk H, Matsuo C, King J, Yanchuk A, Holt R, Jones S, Marra M, Ritland CE, Ritland K, Bohlmann J. Expressed sequence tags from Sitka Spruce. 18,237 ESTs submitted to dbEST division of GenBank (accession numbers ES244996 to ES263233) - Released.
  • Reid, K.E., Chun, E., Ralph, S., Gillan, T., Jancsik, Liao, N., Moore, R., Mayo, M., Wagner, S., Featherstone, R., Roger, J., Brown-John, M., Tam, B., Sze, W.K., Wilton, J., Kirk, H., Matsuo, C., King, J., Yanchuk, A., Holt, R., Jones, S., Marra, M., Ritland, C.E., Ritland, K., Bohlmann, J. (2007)  Expressed sequence tags from Sitka Spruce. 7,983 ESTs submitted to dbEST division of GenBank (accession numbers ES659089 to ES667071) - Released.
  • Reid, K.E., Chun, E., Liao, N., Holliday, J., Thomas, D., Gillan, T., Moore, R., Mayo, M., Wagner, S., Featherstone, R., Roger, J., Brown-John, M., Tam, B., Sze, W.K., Wilton, J., Kirk, H., Matsuo, C., King, J., Yanchuk, A., Holt, R., Jones, S., Marra, M., Ritland, C.E., Aitkens, S., Ritland, K., Bohlmann, J. (2007) Expressed sequence tags from Sitka Spruce. 4,822 ESTs submitted to dbEST division of GenBank (accession numbers ES667072 to ES671893) - Released.
  • DiGuistini S, Ralph SG, Lim YW, Holt R, Jones S, Bohlmann J and Breuil C. Generation and annotation of lodgepole pine and oleoresin induced expressed sequences from the blue-stain fungus Ophiostoma clavigerum, a Mountain Pine Beetle associated pathogen; 5,974 ESTs submitted to dbEST division of GenBank (accession numbers EE724403 to EE730376) - Released.
  • Ralph S, Kolosova N, Oddy C, Chun E, Reid KE, Liao N, Jancsik S, Moore R, Mayo M, Wagner S, King J, Yanchuk A, Holt R, Jones S, Marra M, Ritland CE, Ritland K, Bohlmann J. Expressed sequence tags from multiple Spruce cDNA libraries. 27,737 ESTs submitted to dbEST division of GenBank (accession numbers ES852448 to ES880185). These are the 3' reads belonging to the full length libraries (WS027, WS028 and WS029) - ) - Released. 


NCBI GenBank FLcDNA Sequence Submissions

We have submitted more than 9,000 sequence-verified FLcDNA to GenBank and the complete set of FLcDNA sequences will be released as soon as our submitted manuscript has passed peer review (see below).

  • Ralph SG, Jancsik S, and J Bohlmann. Dirigent proteins in conifer defense II: Extended gene discovery, phylogeny, and constitutive and stress-induced gene expression in spruce (Picea spp.). (accession numbers EF643700 to EF643715) – Released
  • Ralph SG, Kirkpatrick R, Chun HJE, Palmquist D, Wynhoven B, Kolosova N, Cooper D, Oddy C, Jancsik S, Ritland CE, Douglas CJ, Butterfield YSN, Liu J, Stott J, Yang G, Barber S, Holt RA, Siddiqui A, Jones SJM, Marra MA, Ritland K and Bohlmann J. The spruce transcriptome: Analysis of ca. 6,500 sequence-verified full-length cDNAs; submitted to non-redundant division of GenBank (accession numbers EF087932 to EF081469). Held for release until manuscript (submitted to Plant Physiology on June 25, 2007) has passed peer-review.
  • Ralph, S.G., Chun, H.J.E., Liao, N., Ali, J., Reid, K.E. Kolosova, N., Cooper, N., Cullis, C., Jancsik, S., Moore, R., Mayo, M., Wagner, S., Holt, R.A., Jones, S.J.M., Marra, M.A., Ritland, C.E., Ritland, K., and Bohlmann, J.  Full length cDNA sequences from Sitka Spruce (Picea sitchensis). 2,644 cDNA sequences submitted to non-redundant division of GenBank (accession numbers EF676105 to EF678748). Held for release until manuscript has passed peer-review.



NCBI GEO Microarray Data Submissions

  • Holliday JA, Ralph SG, White R, Bohlmann J, Aitken SN. Global monitoring of autumn gene expression within and among populations of Sitka spruce. GEO accession number GSE8370. Held for release until manuscript (under revision for New Phytologist, June 22 2007) has passed peer-review.
  • Ralph SG, Keeling CI, Jancsik S, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Chun HJE, Palmquist D, Wynhoven B, Butterfield YSN, Liu J, Stott J, Yang G, Barber S, Siddiqui A, Holt RA, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J. A high-quality full-length cDNA and EST resource for spruce and its utility for conifer gene annotation and characterization of insect-induced defenses.  GEO accession numbers GSE8363 and GSE8378. Held for release until manuscript (submitted to Plant Physiology, June 25 2007) has passed peer-review.

 

 

Funding Institutions

UBC Genome Canada
Genome British Columbia