Building References For Functional Genomics Of Conifer Development: Deep Sequencing and Comparative Gene Expression In Reproductive Tissues and Seeds Of Loblolly Pine

We are building conifer transcriptome references through extensive sequencing of loblolly pine (Pinus taeda) and sugar pine (P. lambertiana) RNA.  Assembled transcript profiles represent a wide array of contrasting tissue collections, and sequences are analyzed for homology across plants, enabling annotation of reference genomes presented in this workshop.  Preliminary results estimate completeness of the current loblolly pine genome draft, and also overall gene activity in the relatively large genomes of conifers.

Estimates based on embryo ESTs suggest that gymnosperms and angiosperms share approximately 70% overall gene content¹.  Phylogenomic reconstructions^2,3 estimate that ~300 genes contribute to defining the gymnosperm lineage.  These also corroborate the finding^4,5 that among other functions, differences in small RNA regulation of DNA methylation and gene silencing may be key factors distinguishing gymnosperms and angiosperms at the genomic level.  Reproductive mechanisms separate gymnosperms from angiosperms with respect to both gamete-producing structures and fertilization processes⁶.  Our molecular perspective of seed plant reproductive development derives mostly from angiosperms, and available datasets of genes expressed in gymnosperm strobili and their seeds are far from complete. Until gene activities can be comparatively assessed with the use of comprehensive references, our understanding of conifer development will remain limited.  Here we highlight results from massively parallel strand-specific sequencing of loblolly pine strobili, megagametophyte and embryo transcripts.  We discuss the extents to which pine references are improved for functional genomics studies.  Our findings have broad implications for advancing research, from studies of floral innovation to predicting parent-of-origin traits in conifer breeding.

1 Cairney, J., et al., 2006.  Plant Mol. Biol. 62: 485

2 Cibrián-Jaramillo, A., et al., 2010.  Genome Biol. Evol. 2: 225

3 Lee, E.K., et al., 2011.  PLoS Genet. 7: e1002411

4 Morin, R.D., et al., 2008.  Genome Res. 18: 571

5 Dolgosheina, E.V., et al., 2008.  RNA 14: 1508

6 Frohlich, M.W., 2003.  Nature Rev. Genet. 4: 559