High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

Abstract

Background: Benefits from high-throughput sequencing using 454 pyrosequencing technology may be most apparent for species with high societal or economic value but few genomic resources. Rapid means of gene sequence and SNP discovery using this novel sequencing technology provide a set of baseline tools for genome-level research. However, it is questionable how effective the sequencing of large numbers of short reads for species with essentially no prior gene sequence information will support contig assemblies and sequence annotation.

Results: With the purpose of generating the first broad survey of gene sequences in Eucalyptus grandis, the most widely planted hardwood tree species, we used 454 technology to sequence and assemble 148 Mbp of expressed sequences (EST). EST sequences were generated from a normalized cDNA pool comprised of multiple tissues and genotypes, promoting discovery of homologues to almost half of Arabidopsis genes, and a comprehensive survey of allelic variation in the transcriptome. By aligning the sequencing reads from multiple genotypes we detected 23,742 SNPs, 83% of which were validated in a sample. Genome-wide nucleotide diversity was estimated for 2,392 contigs using a modified theta (theta) parameter, adapted for measuring genetic diversity from polymorphisms detected by randomly sequencing a multi-genotype cDNA pool. Diversity estimates in non-synonymous nucleotides were on average 4x smaller than in synonymous, suggesting purifying selection. Non-synonymous to synonymous substitutions (Ka/Ks) among 2,001 contigs averaged 0.30 and was skewed to the right, further supporting that most genes are under purifying selection. Comparison of these estimates among contigs identified major functional classes of genes under purifying and diversifying selection in agreement with previous researches.

Conclusion: In providing an abundance of foundational transcript sequences where limited prior genomic information existed, this work created part of the foundation for the annotation of the E. grandis genome that is being sequenced by the US Department of Energy. In addition we demonstrated that SNPs sampled in large-scale with 454 pyrosequencing can be used to detect evolutionary signatures among genes, providing one of the first genome-wide assessments of nucleotide diversity and Ka/Ks for a non-model plant species.

Figure 1

Proportion of E. grandis unigenes with homology to gene models. Proportion of E. grandis unigenes (contigs + singlets) without (-) and with homology to the Arabidopsis (A), Populus (P), Oryza (O) gene models. (a) Effect of the sequence length on the proportion of homology to gene models (E value 10^-5). (b) Proportion of E. grandis unigenes longer than 100 bp with and without homology to gene models at three different E values (10^-5, 10^-10 and 10^-20).

Figure 2

Proportion of GO categories found in the E. grandis unigenes. Proportion of categories of each Gene Ontology (GO) sampled by the E. grandis unigene sequences compared with the proportions found in the Arabidopsis genome annotation.