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Expressed Sequence Tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis

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Abstract

The process of embryogenesis in gymnosperms differs in significant ways from the more widely studied process in angiosperms. To further our understanding of embryogenesis in gymnosperms, we have generated Expressed Sequence Tags (ESTs) from four cDNA libraries constructed from un-normalized, normalized, and subtracted RNA populations of zygotic and somatic embryos of loblolly pine (Pinus taeda L.). A total of 68,721 ESTs were generated from 68,131 cDNA clones. Following clustering and assembly, these sequences collapsed into 5,274 contigs and 6,880 singleton sequences for a total of 12,154 non-redundant sequences. Searches of a non-identical amino acid database revealed a putative homolog for 9,189 sequences, leaving 2,965 sequences with no known function. More extensive searches of additional plant sequence data sets revealed a putative homolog for all but 1,388 (11.4%) of the sequences. Using gene ontologies, a known function could be assigned for 5,495 of the 12,154 total non-redundant sequences with 13,633 associations in total assigned. When compared to ∼72,000 sequences in a collated P. taeda transcript assembly derived from >245,000 ESTs derived from root, xylem, stem, needles, pollen cone, and shoot ESTs, 3,458 (28.5%) of the non-redundant embryo sequences were unique and thereby provide a valuable addition to development of a complete loblolly pine transcriptome. To assess similarities between angiosperm and gymnosperm embryo development, we examined our EST collection for putative homologs of angiosperm genes implicated in embryogenesis. Out of 108 angiosperm embryogenesis-related genes, homologs were present for 83 of these genes suggesting that pine contains similar genes for embryogenesis and that our RNA sampling methods were successful. We also identified sequences from the pine embryo transcriptome that have no known function and may contribute to the programming of gene expression and embryo development.

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Acknowledgements

This work was supported through a grant from the National Science Foundation Plant Genome Research Program to J. Cairney and C.R. Buell (DBI-0217594). The assistance of the J. Craig Venter Joint Technology Center, the TIGR Sequencing Facility and the TIGR IT Group are acknowledged. All cDNA clones can be obtained from The Institute for Genomic Research.

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Authors and Affiliations

  1. School of Biology and Institute of Paper Science and Technology, Georgia Institute of Technology, 500, 10th Street, NW, Atlanta, GA, 30332-0620, USA

    John Cairney, Gerald S. Pullman, Yiting Zhang & Thomas Oh

  2. The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD, 20850, USA

    Li Zheng, Allison Cowels, Joseph Hsiao, Victoria Zismann, Jia Liu, Shu Ouyang, Francoise Thibaud-Nissen, John Hamilton, Kevin Childs & C. Robin Buell

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  1. John Cairney
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  2. Li Zheng
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  3. Allison Cowels
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  14. C. Robin Buell
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Correspondence to C. Robin Buell.

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John Cairney, Li Zheng—These authors contributed equally to this work.

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Cairney, J., Zheng, L., Cowels, A. et al. Expressed Sequence Tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. Plant Mol Biol 62, 485–501 (2006). https://doi.org/10.1007/s11103-006-9035-9

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