P0510 An Exploration Into the Structure of Conifer Genomes Via Sequencing of Bacterial Artificial Chromosomes

Kermit Ritland , University of British Columbia
Nima Farzaneh , University of British Columbia
Claire Cullis , University of British Columbia
Agnes Yuen , University of British Columbia
Michelle Tang , University of British Columbia
Joël Fillon , University of British Columbia
Sarah Chao , University of British Columbia
Daniel G. Peterson , Institute for Genomics, Biocomputing & Biotechnology - Mississippi State University, Mississippi State, MS
Carol Ritland , University of British Columbia
Using BAC libraries from both white spruce and loblolly pine, we sequenced and compared 96 random BACs from these two species, and also sequenced an apparent homologous region containing the lignin biosynthesis gene, CCoAMT.  These efforts will aid in the assembly of conifer genomes and identify the potential for synteny among conifer genomes to aid assembly.  Using 454 technology, about 10MB were sequenced in each of spruce and pine.  Based upon protein BLASTs to Genbank, among the BACs we identified 24 functional genes in pine and 33 in spruce.  Estimates of gene number were 46,500 in pine and 75,500 in spruce; probably overestimates, but suggests spruce has a more complex genome.  Transposition has been ongoing at comparable rates in both species since their divergence (over 120 MYA), but in both species, there seems to be a peak at the start of the Cenozoic era (65 MYA), corresponding to climate change.  Classes of transposon gene families were also identified and compared between spruce and pine.  After several efforts, we found an apparent homologue for CCoAMT; coding regions were almost 100% identical (reflecting known conservation of gene evolution in conifers), but flanking regions showed low homology, but more than between random BACs, suggesting that only coding genes can assist the syntenic assembly of conifer genomes.
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