title: Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis.
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 approximately 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.
authors.affiliation: School of Biology and Institute of Paper Science and Technology, Georgia Institute of Technology, 500, 10th Street, NW, Atlanta, GA 30332-0620, USA.
authors.forename: John
authors.initials: J
authors.lastname: Cairney
authors.forename: Li
authors.initials: L
authors.lastname: Zheng
authors.forename: Allison
authors.initials: A
authors.lastname: Cowels
authors.forename: Joseph
authors.initials: J
authors.lastname: Hsiao
authors.forename: Victoria
authors.initials: V
authors.lastname: Zismann
authors.forename: Jia
authors.initials: J
authors.lastname: Liu
authors.forename: Shu
authors.initials: S
authors.lastname: Ouyang
authors.forename: Francoise
authors.initials: F
authors.lastname: Thibaud-Nissen
authors.forename: John
authors.initials: J
authors.lastname: Hamilton
authors.forename: Kevin
authors.initials: K
authors.lastname: Childs
authors.forename: Gerald S
authors.initials: GS
authors.lastname: Pullman
authors.forename: Yiting
authors.initials: Y
authors.lastname: Zhang
authors.forename: Thomas
authors.initials: T
authors.lastname: Oh
authors.forename: C Robin
authors.initials: CR
authors.lastname: Buell
mesh_terms: D000595:Amino Acid Sequence; D018076:DNA, Complementary; D020224:Expressed Sequence Tags; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D028223:Pinus / Q000196:embryology / Q000235:genetics*; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D012639:Seeds / Q000235:genetics*; D017386:Sequence Homology, Amino Acid
chemical_list: D018076:DNA, Complementary; D010940:Plant Proteins