Computational Annotation of the Pecan Genome

Pecans (Carya illinoinensis) are large deciduous trees native to North and Central America. Pecan trees produce nutrient rich edible seeds and the trees can produce nuts for hundreds of years after planting. Pecans are a recently domesticated crop and have successfully been introduced to geographically and environmentally diverse areas including both arid and humid regions. An annotated pecan genome is necessary for genetic studies in pecan and molecular marker assisted breeding and is not yet available. Computational genome annotation predicts novel genes by identifying potential exons and introns via aligning transcripts, protein sequences, and known genes of other species to the target genome sequence. We report the preliminary annotation of an Illumina generated genome sequence from a USDA clonal germplasm repository pecan seedling accession that originated in Mexico (87MX3-2.11). MAKER software was used to annotate the 87MX3-2.11 genome. Plant genomes exhibit high rates of pseudogenization, contain both coding and noncoding sequences, and show unusually high numbers of transposable elements. The longest assembled contigs of the pecan genome were annotated for putative genes based on a pecan embryo transcriptome and protein homology based on the reference proteome of Populus trichocarpa. Noncoding sequences were also inferred by homology to noncoding RNA genes in other plants. Additionally, ab initio genes were predicted by using SNAP that was trained on genes identified by sequence alignment in the previous step. Knowledge of the annotated pecan genome will generate novel insights on the genetics of this species.