The Pinus taeda genome is characterized by diverse and highly diverged repetitive sequences

Abstract

Background: In today's age of genomic discovery, no attempt has been made to comprehensively sequence a gymnosperm genome. The largest genus in the coniferous family Pinaceae is Pinus, whose 110-120 species have extremely large genomes (c. 20-40 Gb, 2N = 24). The size and complexity of these genomes have prompted much speculation as to the feasibility of completing a conifer genome sequence. Conifer genomes are reputed to be highly repetitive, but there is little information available on the nature and identity of repetitive units in gymnosperms. The pines have extensive genetic resources, with approximately 329000 ESTs from eleven species and genetic maps in eight species, including a dense genetic map of the twelve linkage groups in Pinus taeda.

Results: We present here the Sanger sequence and annotation of ten P. taeda BAC clones and Genome Analyzer II whole genome shotgun (WGS) sequences representing 7.5% of the genome. Computational annotation of ten BACs predicts three putative protein-coding genes and at least fifteen likely pseudogenes in nearly one megabase of sequence. We found three conifer-specific LTR retroelements in the BACs, and tentatively identified at least 15 others based on evidence from the distantly related angiosperms. Alignment of WGS sequences to the BACs indicates that 80% of BAC sequences have similar copies (> or = 75% nucleotide identity) elsewhere in the genome, but only 23% have identical copies (99% identity). The three most common repetitive elements in the genome were identified and, when combined, represent less than 5% of the genome.

Conclusions: This study indicates that the majority of repeats in the P. taeda genome are 'novel' and will therefore require additional BAC or genomic sequencing for accurate characterization. The pine genome contains a very large number of diverged and probably defunct repetitive elements. This study also provides new evidence that sequencing a pine genome using a WGS approach is a feasible goal.

Figure 1

Pinus taeda BAC12 (clone Pt314B2) illustrates several new trends found in the pine genome. (A) The length of BAC12 is shown along the horizontal axis. Shown above the axis are tracks of annotated genes (dicot and monocot parameters), similarity hits to Repbase [RM (blastx); DNA transposons; Non-LTR retroelements; ERV (endogenous retroviruses); LTR retroelements, copia; LTR retroelements, gypsy], and other elements identified in this study (simple repeats, tandem repeats, ORF elements, pairs of direct repeats, and regions of similarity among BACs). The bottom two tracks indicate WGS coverage at ≥ 75% identity and at ≥ 99% identity (B) Genes were annotated with both dicot and monocot parameters. The annotations generally differed in gene structure. (C) Coverage is similar between coverage tracks for active and relatively abundant retroelements in the pine genome such as this nested PtIFG7.

Figure 2

Comparison of repeat content among twelve sequenced genomes and Pinus taeda.