De novo Sequencing of the Pineapple Genome

Pineapple (Ananas comosus var. comosus) is the most produced tropical fruit after banana and citrus.  The crop is easily propagated worldwide due to its CAM photosynthesis system and water efficiency properties. In the endeavour to produce an elite pineapple cultivar, genomic information is crucial but currently unavailable for the crop. In the light of advancements in sequencing technology, we have sequenced and assembled the pineapple genome (from the MD-2 pineapple hybrid variety) using two highly renowned platforms i.e. Illumina and PacBio, each with coverage of 180X and 28X, respectively.  The Illumina short reads were used to error-correct the PacBio long sequencing reads by using the SMRTCorrector tool from Novocraft. Consensus calling was done after the short reads had been aligned to the long read sequences.  Several approaches were performed to reduce the redundancy introduced due to the highly heterozygous nature of pineapple genome.  The final assembly was performed with only 16X of error-corrected long PacBio reads using the Celera assembler. This first draft of the pineapple genome covered 97.8% of the estimated 526 Mbp genome in 12,127 scaffolds with an N50 of 105,209 bp.  More than 99% of 108,136 transcripts from in-house RNASeq data (Illumina) and long RNA Iso-Seq (PacBio) read sequences were successfully mapped to the genome.  In addition, an assessment of the genome using CEGMA showed complete homology to 224 (90.32%) CEG sequences, while 246 (99.19%) CEGs had at least partial similarity to our assembly.  The availability of the pineapple genome sequences, and for being the first species under the Bromeliaceae family to be sequenced, will enable further exploration on the evolutionary processes of this non-climacteric fruit and will lead towards the improvement of the crop.