Sequencing of the Pineapple Genome with Short and Long Reads Sequencing Technology

Pineapple (Ananas comosus var. comosus) cultivation is largely based on a single cultivar, Smooth Cayenne. The narrow gene pool has made variety improvement a very difficult task for pineapple breeders particularly when using classical breeding approaches. Thus, genetic information of the pineapple is crucial in order to identify important economic traits to expedite breeding purposes.  With this motivation, we sequenced the genome of the MD2 pineapple hybrid by using two different platforms i.e. Illumina short-reads for high coverage, and the PacBio long reads to tackle the problem of high heterozygosity rate and repeats in the genome.  The genome was sequenced paired-ended at three different insert sizes: 250 bp and 550 bp using HiSeq Illumina technology with a read length of 100 bp, and 750 bp insert size with the latest MiSeq Sequencing Kit V3 of 300 bp pair-end.   All of the sequence reads were trimmed to a Q-value of 30 and jellyfish kmer analysis at 17 was performed for in-silico genome survey.  The histogram of the kmer distribution clearly indicted the characteristic double-peak and a long tail at the high kmer coverage, which accentuated the problem of its heterozygosity and repeats.  Initial assembly with SOAPdenovo2 with kmer of 23 produced an assembly of N50 with 6,122 bp.  On the other hand, the CLC Genomic Workbench® produced an assembly with an N50 of 3,981bp.  The current method to solve repeats and heterozygosity in de novo genomic assembly is to use the mate-pair technology of Illumina. Nevertheless, as an alternative, we undertook to use third-generation sequencing using PacBio RS II to generate longer reads in order to improve the assembly.  Here, we present the assembly produced using PacBio RS II and Illumina reads of the pineapple genome.