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Open Access Research article

Generation, functional annotation and comparative analysis of black spruce (Picea mariana) ESTs: an important conifer genomic resource

Ishminder K Mann1, Jill L Wegrzyn3 and Om P Rajora12*

Author Affiliations

1 Forest Genetics and Biotechnology Group, Department of Biology, Life Sciences Centre, Dalhousie University, 1355 Oxford Street, Halifax, NS B3H 4J1, Canada

2 Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, P.O. Box 44000, Fredericton, NB E3B 5A3, Canada

3 Department of Plant Sciences, University of California at Davis, One Shields Avenue MC4, Davis, California 95616, USA

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BMC Genomics 2013, 14:702  doi:10.1186/1471-2164-14-702

Published: 11 October 2013

Abstract

Background

EST (expressed sequence tag) sequences and their annotation provide a highly valuable resource for gene discovery, genome sequence annotation, and other genomics studies that can be applied in genetics, breeding and conservation programs for non-model organisms. Conifers are long-lived plants that are ecologically and economically important globally, and have a large genome size. Black spruce (Picea mariana), is a transcontinental species of the North American boreal and temperate forests. However, there are limited transcriptomic and genomic resources for this species. The primary objective of our study was to develop a black spruce transcriptomic resource to facilitate on-going functional genomics projects related to growth and adaptation to climate change.

Results

We conducted bidirectional sequencing of cDNA clones from a standard cDNA library constructed from black spruce needle tissues. We obtained 4,594 high quality (2,455 5' end and 2,139 3' end) sequence reads, with an average read-length of 532 bp. Clustering and assembly of ESTs resulted in 2,731 unique sequences, consisting of 2,234 singletons and 497 contigs. Approximately two-thirds (63%) of unique sequences were functionally annotated. Genes involved in 36 molecular functions and 90 biological processes were discovered, including 24 putative transcription factors and 232 genes involved in photosynthesis. Most abundantly expressed transcripts were associated with photosynthesis, growth factors, stress and disease response, and transcription factors. A total of 216 full-length genes were identified. About 18% (493) of the transcripts were novel, representing an important addition to the Genbank EST database (dbEST). Fifty-seven di-, tri-, tetra- and penta-nucleotide simple sequence repeats were identified.

Conclusions

We have developed the first high quality EST resource for black spruce and identified 493 novel transcripts, which may be species-specific related to life history and ecological traits. We have also identified full-length genes and microsatellite-containing ESTs. Based on EST sequence similarities, black spruce showed close evolutionary relationships with congeneric Picea glauca and Picea sitchensis compared to other Pinaceae members and angiosperms. The EST sequences reported here provide an important resource for genome annotation, functional and comparative genomics, molecular breeding, conservation and management studies and applications in black spruce and related conifer species.

Keywords:
Picea mariana; Expressed sequence tag; Gene discovery; Gene expression; Gene ontology; Microsatellites