Ananas comosus Assembly and Gene Annotation

About Ananas comosus

Pineapple (Ananas comosus) is a fruit crop originated and domesticated in South America. It is the most economically important plant in the family Bromeliaceae. Ananas is unique in the family for its syncarpic fruit; in fact it means 'excellent fruit' in Guaraní language. Pineapple was domesticated over 6 thousand years ago and distributed to Mesoamerica over 2,500 years ago. Cultivated pineapple is a clonally propagated, self-incompatible diploid (2n=2x=50) with CAM photosynthesis.

Assembly

The genome of pineapple variety F153 was sequenced and assembled using 400× Illumina reads, 2× Moleculo synthetic long reads, 1× 454 reads, 5× PacBio single-molecule long reads and 9,400 BACs. Because of self-incompatibility, pineapple has high levels of heterozygosity and is cultivated through clonal propagation. To overcome the difficulties in assembling this highly heterozygous genome, we applied a genetic approach to reduce the complexity of the genome using a cross between F153 and the CB5 A. bracteatus accession. The haploid genomes of the F1 plants were used for haplotype phasing to improve the assembly. Using this approach substantially improved the initial Illumina-only assembly and spanned 382 Mb, 72.6% of the estimated 526 Mb of the pineapple genome.
A more recent CB5 chromosome level assembly and the distribution of Gypsy LTR-RT elements around centromeres were used to further improve the F153 assembly (F153 v.7), in which LG01 was separated into AccChr1 and AccChr24, while LG24 and LG25 were linked together into AccChr25.

Annotation

MAKER was used for gene annotation, obtaining 27,024 gene models, 89% of which were categorized as complete. In total 10,151 alternative splicing events were identified, with intron retention accounting for 62.8%.

Repeated sequences were called with the Repeat Detector, which is part of the Ensembl Genomes repeat feature pipelines. Repeats length: 126480149 - Repeats content: 40.04%

References

1. The bracteatus pineapple genome and domestication of clonally propagated crops.
   LY Chen, R VanBuren, M Paris et al.. 2019. Nature Genetics. 51:154958.
2. The pineapple genome and the evolution of CAM photosynthesis.
   Ming R, VanBuren R, Wai CM et al. 2015. Nature Genetics. 47:1435-42.

Picture credit: Suniltg CC BY 3.0

More information

General information about this species can be found in Wikipedia.