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Durian Genome Informs Smelly Fruit Features

Durio zibethinus

NEW YORK (GenomeWeb) – Researchers from Singapore, Hong Kong, and Malaysia have sequenced and started analyzing a draft genome assembly for a tropical plant with infamously smelly, spine-covered fruit: the durian, Durio zibethinus.

The team used a combination of short- and long-read sequencing paired with chromosome contact mapping to put together a draft genome assembly for the Musang King cultivar of durian. It also generated transcriptome sequences representing fruit and non-fruit tissues from the D. zibethinus plant.

Based on sequence and expression profiles in the plant, the researchers delved into features related to the fruit's characteristic aroma. In that regard, they narrowed in on enhanced expression of pathways related to sulfur, ethylene, and lipid production, as well as polyploidization-based expansions affecting genes that contribute to volatile sulfur compound (VSC) or ethylene production. The group published its findings online today in Nature Genetics.

"Our analysis revealed that VSC production is turbocharged in durian fruits, which fits with many people's opinions that durian smell has a 'sulphury' aspect," co-senior author Patrick Tan, a cancer researcher affiliated with Thorn Biosystems, Duke-NUS Medical School, Singapore's National Heart Centre, and the National University of Singapore, said in a statement.

Although it remains an important tropical fruit crop, the durian "is banned from public transportation and many hotels because of its characteristic and pungent smell," he and his co-authors noted, "described by some detractors as 'turpentine and onions, garnished with a gym sock.'"

The foul-smelling D. zibethinus fruit plantis one of 30 documented Durio species, the team explained, belonging to the same Malvales plant order as plants that produce cocoa beans and cotton. Likewise, there are hundreds of durian cultivars, each known for slightly different textures, flavors, scents, and desirability in the Southeast Asian countries where the plant is grown.

"Distinct regional demands for different cultivars reflect local idiosyncrasies in consumer tastes: pungent and bitter varieties are prized in Malaysia and Singapore (for example, Musang King), whereas sweeter cultivars with a mild odor are popular in Thailand (for example, Monthong)," the authors wrote. "The distinctive odors of different durian cultivars have also been biochemically studied and characterized as a complex suite of odor-active compounds, including sulfur volatiles, esters, alcohols, and acids."

The researchers started by doing long read sequencing on the durian genome, using the Pacific Biosciences RSII platform and genomic DNA from fruit stalk samples of a Musang King plant. To those long reads, the team added paired-end genome sequences generated with the Illumina HiSeq 2500. The latter instrument was also used to do RNA sequencing on several fruit aril and non-fruit samples from plants in the Musang King, Monthong, and Puang Manee cultivars.

The researchers found that their 738 million base durian genome, scaffolded with Dovetail's Chicago and H-C approaches, contained an estimated 45,335 protein-coding genes. More than 43,100 of those were also represented in transcript sequence data from the Musang King plants.

When the team analyzed the durian draft genome alongside sequences from several other plants — ranging from cacao and coffee to grape, papaya, soybean, and rice — it saw signs that the lineage leading to D. zibethinus underwent a whole-genome duplication shared with the cotton plant lineage. It also narrowed in on more than 600 gene families that appeared to be specific to durian.

Along with a phylogenetic assessment of plant relationships, the researchers folded in gene expression information to pick up evidence of sulfur, ripening, and flavor pathway genes in the durian fruit. Some of the upregulated genes, including those coding for enzymes contributing to VCS and ethylene production, appear to have gone through gene expansions in the plant as well, providing insight into the plant's pungent sulfur smell and fruit ripening features. 

"Certain plants whose primary dispersal vectors are primates with more advanced olfactory systems show a shift in odor at ripening," the authors wrote. "Similarly, durian — by emanating an extremely pungent odor at ripening — appears to have the characteristic of a plant whose main dispersal vectors are odor-enticed primates rather than visually enticed animals."