First draft of the nuclear genome assembly and annotation of the multi-stress tolerant desert giant milkweed Calotropis procera

Abiotic stresses can intensely affect plant survival and productivity. The comprehension of the molecular mechanisms underlying stress responses in tolerant plant species is critical for the breeding of stress-adapted plant cultivars. The giant milkweed Calotropis procera (Apocynaceae) is a wild xerophytic shrub that is well adapted to extreme desert environments and has a broad gene reserve for stress tolerance. De novo genome assembly and its associated analyses were carried out in this highly tolerant but underexploited xerophyte, to decode its genetic structure. Paired-end (PE) and mate-pair (MP) libraries with an insert size of 350 bp and 5 kb, respectively, were constructed. An estimated genome size of 0.238 Gb was calculated based on the k-mer frequency of the read data. A high-quality draft assembly was generated via the short reads obtained using the Illumina sequencing technology and the ∼68.5 GB of genomic sequencing data that were acquired utilizing the two libraries with insert sizes of 350 bp and 5 kb. The assembly of the genome comprised 221 Mb of 24,374 scaffolds with an N50 of 655 kb. A gene prediction analysis performed using an ab initio gene annotation pipeline identified 20,660 coding sequences, including those related to transposable elements. The analysis of the functional annotation of the genome coding sequences reported genes involved in tolerance, photoacclimation, vacuole membrane transport, and nitrogenous compound detoxification. This is the first draft of the genome of C. procera, which will provide a deeper understanding of abiotic stress tolerance and contribute to the investigation of the biosynthesis of secondary metabolites particular to this milkweed.