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Sequencing of Sitka spruce (Picea sitchensis) cDNA libraries constructed from autumn buds and foliage reveals autumn-specific spruce transcripts

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Abstract

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.

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Acknowledgments

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.

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Correspondence to J. A. Holliday.

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Communicated by L. Wegrzyn

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Table S1

Autumn cDNA libraries included in constructing the autumn-specific unigene set. (DOC 64 kb)

Table S2

Significantly overrepresented GO terms among combined autumn unigene set for both white spruce and Sitka spruce. (XLSX 141 kb)

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Reid, K.E., Holliday, J.A., Yuen, M. et al. Sequencing of Sitka spruce (Picea sitchensis) cDNA libraries constructed from autumn buds and foliage reveals autumn-specific spruce transcripts. Tree Genetics & Genomes 9, 683–691 (2013). https://doi.org/10.1007/s11295-012-0584-6

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