Development and Analysis of Genomic Resources for the Saguaro Cactus (Carnegiea gigantea) and Other Cactaceae

Cactaceae are spectacular examples of an adaptive radiation throughout the New World and have evolved morphological features (e.g. spines, stem succulence) and physiological functions (e.g. CAM photosynthesis) that allow them to proliferate in extreme environments. Of note, cacti are also the third most endangered taxonomic group among plants, and until now there have been no genomic resources available for this family.

Here we present a genome assembly and annotation of Carnegiea gigantea i.e. the saguaro cactus, together with draft assemblies of three other columnar cacti (the giant cardón – Pachycereus pringlei, senita – Lophocereus schottii and organ pipe – Stenocereus thurberi) and one representative of the most basally-branching genus of Cactaceae, Pereskia humboldtii. Sequencing four Illumina libraries, we assembled the ~1.4 Gb saguaro nuclear genome into 107,828 scaffolds spanning 980 Mb, with a scaffold N50 of 61.5 kb and a contig N50 of 20.4 kb. To characterize the genome, we developed five RNA-Seq datasets and an assembly-independent repeat library. About 28,300 genes were identified and more than half of the genome is composed of transposons and other repetitive elements. The other species were sequenced at lower coverage, enabling the assembly of the gene space fraction of each genome, which allowed us to perform genome-wide evolutionary and comparative analyses among different species of the family.

In addition, new orthogonal datasets that include population resequencing and the detection of differential gene expression across growth stages and organs will be presented.