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Team Digs Into Pineapple Genome for Clues to Water-Efficient Photosynthesis

NEW YORK (GenomeWeb) – The pineapple plant's use of a water-conserving form of photosynthesis called crassulacean acid metabolism (CAM) appears to have stemmed from changes to genes involved in C3 photosynthesis, according to a new genome sequencing study in Nature Genetics.

An international team led by investigators in China and the US produced genome sequences for two cultivated varieties of pineapple, Ananas comosus, as well as one wild pineapple accession from the A. bracteatus species, and re-sequenced almost 100 hybrids.

Comparing these sequences to one another and to existing plant genomes, the group got a glimpse at the evolutionary events along the pineapple lineage as well as insights into the plant's current biological features. Along with the roots of CAM-based photosynthesis, for example, it uncovered ties between CAM and the regulatory mechanisms policing the pineapple plant's circadian clock — a connection that may reflect the altered timing with which plants take up carbon dioxide in CAM photosynthesis.

"This is the first time scientists have found a link between regulatory elements of CAM photosynthesis genes and circadian clock regulation," co-first author Ray Ming, a genomics, biotechnology, and plant biology researcher affiliated with the Fujian Agriculture and Forestry University and the University of Illinois at Urbana-Champaign, said in a statement.

"This makes sense, because CAM photosynthesis allows plants to close the pores in their leaves during the day and open them at night," Ming explained. "This contributes to pineapple's resilience in hot, arid climates, as the plant loses very little moisture through its leaves during the day."

In an effort to better understand CAM and other pineapple features, the researchers used a combination of Illumina, Moleculo, PacBio, and bacterial artificial chromosome sequencing to put together a pineapple genome based on DNA from a Del Monte-cultivated variety called P153.

The assembly of the genome — which covered almost 73 percent of the plant's roughly 526 million bases — was helped along with haplotype phasing done using sequences from the hybrid of the F153 plant and a wild pineapple species from Brazil called A. bracteatus CB5.

To that, the team added transcript sequence data from nine pineapple tissues, RNA-sequence data on leaf tissue taken over time from field-grown pineapples, and genome re-sequencing data on 93 more A. comosus-A. bracteatus hybrids.

Along with transposable element sequences spanning some 44 percent of the assembled pineapple genome, this data pointed to the presence of more than 27,000 predicted protein-coding genes and 10,151 alternatively spliced transcripts in the F153 pineapple plant. Using the hybrid plant sequences, the team identified almost 300,000 SNPs in F153.

A more detailed SNP comparison was possible when the researchers did de novo genome assembly on A. bracteatus CB5 and on the A. comosus accession MD2, a widely grown pineapple variety produced through hybridization over several generations.

By comparing the three pineapple genome assemblies to sequences from rice, sorghum, and other plants, they were able to peer back at past whole-genome duplications in the pineapple lineage, which split from the lineage leading to grass plants some 100 million years ago.

Their cross-plant comparisons also pointed to gene family functions, expansions, and homologous genes in various plants and plant types — an analysis that yielded more than three-dozen potential players in the carbon-fixing phase of CAM photosynthesis in pineapple.

Based on such results, the study's authors argued that "[a]ll plants contain the necessary genes for CAM photosynthesis, and the evolution of CAM simply required the re-routing of preexisting pathways."

"This work provides the first detailed analysis of the expression and regulation patterns of genes associated with CAM," they explained, "and could ultimately be used to engineer better [water-use efficiency] and drought tolerance in crop plants."