The Draft Genome of the MD-2 Pineapple

Abstract

With the advancement in sequencing technology, it is now possible to decode complex plant genomes with high accuracy. For many years, short-read sequencers were the dominant reads used for assembling genomes until the introduction of third-generation long-read sequencing machines. Long reads are able to extend through complex regions of repeats avoiding erroneous collapse which causes a reduction in the genome assembly size. However, the low accuracy of the long reads is a cause of concern, and this hinders its direct application in de novo assemblies of large genomes. Here, we report on the whole-genome assembly of the MD-2 pineapple using a hybrid sequencing approach. We used the Illumina short reads to correct the systematic errors of the long PacBio reads. The error-corrected long reads were then used to de novo assemble the MD-2 pineapple genome using multiple assembly software and strategies. The most optimal accuracy and contiguity were achieved in the de novo assembly of error-corrected long reads using Celera. The MD-2 pineapple genome achieved a N50 of 153,084 bp with 8448 scaffolds and a total assembly size of 524.07 Mb. In addition, 245 out of the 248 ultra-conserved CEGs were found in the genome, indicating completeness of more than 98%. Furthermore, 87% of the mapped transcripts were identified in the genome with coverages of more than 90%, while another 12% were mapped with coverages of more than 80%. This MD-2 pineapple genome provides a high-quality draft for gene prediction and further downstream applications in pineapple.