Towards decoding the conifer giga-genome

Abstract

Several new initiatives have been launched recently to sequence conifer genomes including pines, spruces and Douglas-fir. Owing to the very large genome sizes ranging from 18 to 35 gigabases, sequencing even a single conifer genome had been considered unattainable until the recent throughput increases and cost reductions afforded by next generation sequencers. The purpose of this review is to describe the context for these new initiatives. A knowledge foundation has been acquired in several conifers of commercial and ecological interest through large-scale cDNA analyses, construction of genetic maps and gene mapping studies aiming to link phenotype and genotype. Exploratory sequencing in pines and spruces have pointed out some of the unique properties of these giga-genomes and suggested strategies that may be needed to extract value from their sequencing. The hope is that recent and pending developments in sequencing technology will contribute to rapidly filling the knowledge vacuum surrounding their structure, contents and evolution. Researchers are also making plans to use comparative analyses that will help to turn the data into a valuable resource for enhancing and protecting the world's conifer forests.

The Evolutionary Genetics of the Genes Underlying Phenotypic Associations for Loblolly Pine (Pinus taeda, Pinaceae)

“…The observation that average levels of linkage disequilibrium varied across sets of amplicons defined as being associated with certain phenotypic traits is consistent with this conclusion (File S1), as is the observation that autocorrelation in values of nucleotide diversity and divergence occurred at the centimorgan scale ( Figure S9; autocorrelation .0 extended upward of 3 cM for each measure, results not shown). Further studies on a genome-wide scale with larger samples, however, are needed to resolve the issue fully with regard to patterns of linkage disequilibrium and recombination (see Mackay et al 2012).Genome-wide levels of nucleotide divergence were also as expected given recent estimates of the divergence times among pine species (Gernandt et al 2008;Parks et al 2009). For example, the per site divergence of loblolly relative to radiata pine was 0.72%, and although severalfold greater than nucleotide diversity, was relatively low.…”

“…The observation that average levels of linkage disequilibrium varied across sets of amplicons defined as being associated with certain phenotypic traits is consistent with this conclusion (File S1), as is the observation that autocorrelation in values of nucleotide diversity and divergence occurred at the centimorgan scale ( Figure S9; autocorrelation .0 extended upward of 3 cM for each measure, results not shown). Further studies on a genome-wide scale with larger samples, however, are needed to resolve the issue fully with regard to patterns of linkage disequilibrium and recombination (see Mackay et al 2012).…”

Haploids in Conifer Species: Characterization and Chromosomal Integrity of a Maritime Pine Cell Line

“…Molecular markers used to validate the presence of all chromosome arms. The position of each marker on the Oria 6 genetic map [29] as well as the allelic state of the mother tree (Oria 6) and L5 line (callus) are shown.…”

“…SNPs were genotyped by sequencing a region of 200-400 bp flanking each targeted site amplified by PCR using specific primers. Primers (available as supplementary material Table S1) were designed based on a BLAST search of the sequences used to build the genotyping array, which was used to construct the Oria 6 genetic map [29]. PCRs were performed in 25 μL containing 10 ng of DNA; 1× Pfu buffer (Fermentas, ON, Canada), 0.2 mM of each dNTP, 1.5 mM MgSO4, 1.25 U Pfu DNA polymerase (Fermentas, ON, Canada), and 0.2 μM of each primer.…”

“…As a result, several collaborative initiatives to sequence the genome of this species have been launched in the last few years [29]. In previous work, Arrillaga et al generated some maritime pine haploid cell lines [19], one of which (L5) was considered a good candidate to be used as a template for maritime pine genome sequencing [30].…”