Sequencing of Sitka spruce (Picea sitchensis) cDNA libraries constructed from autumn buds and foliage reveals autumn-specific spruce transcripts
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Substantial efforts have been invested in recent years to characterize the expressed genome of major North American spruce species, namely Sitka spruce (Picea sitchensis), white spruce (Picea glauca) and interior spruce (Picea engelmanii × glauca). To date, more than 550,000 spruce expressed sequence tags (ESTs) have been publically deposited, most of which were constructed from various tissue collected during active primary growth. Here we report EST sequencing of dormant foliage and bud tissue collected from Sitka spruce. Both normalized and standard libraries were employed, with tissue collected at two autumn time points. A total of 30,681 ESTs were generated then assembled into 9,400 putative unique transcripts, or unigenes, with an average length of 779 bp. These autumn specific Sitka spruce ESTs were combined with autumn specific white spruce ESTs and compared with all spruce ESTs currently available. In total, 12,307 ESTs were unique to the autumn libraries, which assembled into 11,121 unigenes. Functional categorization suggests a role for some of these genes in bud dormancy and adaptation to freezing stress. Our results show that dormant tissue harbours a large number of transcripts not found in the same tissue during the growing season, and this sequence resource will therefore support ongoing studies of adaptive traits in spruce.
KeywordsExpressed sequence tag EST Picea Cold hardiness Bud dormancy
We would like to thank Tristan Gillan for technical assistance with plant maintenance. This research was funded by Genome British Columbia and Genome Canada supporting the Treenomix project (grant to JB and SA), the SMarTForests project (grant to JB) and the AdapTree project (grant to SA) and by a University of British Columbia Graduate Fellowship and NSERC Postgraduate Scholarship to JH. JB has been supported, in part, by the Distinguished University Scholars program of the University of British Columbia.
Data archiving statement
High-quality EST reads were submitted to NCBI under accession numbers ES667072 to ES671893, FD740103 to FD748148, GH280265 to GH291091 and GT120725 to GT127710. This resulting contig builds described here have been submitted to the Transcriptome Shotgun Assembly at DDBJ/EMBL/GenBank under the accession GACG00000000.
- Ahuja MR, Neale DB (2005) Evolution of genome size in conifers. Silvae Genetica 54(3):126–137Google Scholar
- Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29PubMedCrossRefGoogle Scholar
- Cho SK, Kim JE, Park JA, Eom TJ, Kim WT (2006) Constitutive expression of abiotic stress-inducible hot pepper CaXTH3, which encodes a xyloglucan endotransglucosylase/hydrolase homolog, improves drought and salt tolerance in transgenic Arabidopsis plants. FEBS Lett 580(13):3136–3144PubMedCrossRefGoogle Scholar
- Joosen RVL, Lammers M, Balk PA, Bronnum P, Konings M, Perks M, Stattin E, Van Wordragen MF, van der Geest AHM (2006) Correlating gene expression to physiological parameters and environmental conditions during cold acclimation of Pinus sylvestris, identification of molecular markers using cDNA microarrays. Tree Physiol 26(10):1297–1313PubMedCrossRefGoogle Scholar
- Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210. doi: 10.1093/nar/gkr1090 PubMedCrossRefGoogle Scholar
- Liu Q, Kasuga M, Sakuma Y, Abe H, Miura S, Yamaguchi-Shinozaki K, Shinozaki K (1998) Two transcription factors, DREB1 and DREB2, with an EREBP/AP2 DNA binding domain separate two cellular signal transduction pathways in drought- and low-temperature-responsive gene expression, respectively, in Arabidopsis. Plant Cell 10(8):1391–1406PubMedGoogle Scholar
- Pavy N, Paule C, Parsons L, Crow JA, Morency MJ, Cooke J, Johnson JE, Noumen E, Guillet-Claude C, Butterfield Y, Barber S, Yang G, Liu J, Stott J, Kirkpatrick R, Siddiqui A, Holt R, Marra M, Seguin A, Retzel E, Bousquet J, MacKay J (2005) Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters. BMC Genomics 6:144Google Scholar
- Ralph SG, Chun HJE, Kolosova N, Cooper D, Oddy C, Ritland CE, Kirkpatrick R, Moore R, Barber S, Holt RA, Jones SJM, Marra MA, Douglas CJ, Ritland K, Bohlmann J (2008) A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9(484)Google Scholar