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With Chromosome-Scale Resolution, Draft Durian Genome Explains Smelly Fruit

Thursday, November 2, 2017

Photo by مانفی

Scientists in Singapore, Hong Kong, and Malaysia recently reported the high-quality draft genome assembly of Durio zibethinus, a type of durian fruit commonly eaten in southeast Asia. The team used SMRT Sequencing and chromosome mapping techniques to produce the assembly, which will be an important tool for agricultural monitoring.

The draft genome of tropical fruit durian (Durio zibethinus)” was published in Nature Genetics from lead authors Bin Tean Teh, Kevin Lim, Chern Han Yong, Cedric Chuan Young Ng, senior author Patrick Tan, and collaborators at the Duke-NUS Medical School and other institutions. They chose to study durian — a tropical fruit best known for its strong sulfuric smell — because it represents an economically important food crop in the region. “In 2016 alone, durian imports into China accounted for about $600 million, as compared to $200 million for oranges, one of China’s other main fruit imports,” the authors note. Until this project, however, there has been little genomic research into the plant or even its close relatives.

The scientists used PacBio sequencing to 153-fold coverage and applied both FALCON and FALCON-unzip to generate a haplotig-merged assembly. The 738 Mb genome was then enhanced using Chicago and Hi-C methods, increasing scaffold N50 lengths to 22.7 Mb. “The final reference assembly comprised chromosome-scale pseudomolecules, with 30 pseudomolecules greater than 10 Mb in length,” the team reports.

A comparison to gene families in other plants led the scientists to conclude that durian is most closely related to cotton and cacao, and probably shares an ancestral whole genome duplication (WGD) event with cotton. That finding means that “other subfamilies within Malvaceae … are also likely to have the cotton-specific WGD” and that the duplication event “may also have been involved in driving the evolution of unique durian traits.”

Speaking of unique durian traits, the team’s gene expression analysis of the plant revealed upregulated sulfur-related pathways as well as “durian-specific gene expansions … associated with production of volatile sulfur compounds.” Both findings offer new insight into the fruit’s odor and even suggest the biological reason for it: “Certain plants whose primary dispersal vectors are primates with more advanced olfactory systems show a shift in odor at ripening,” the authors write. “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.”

The team concludes that the availability of this genome resource will have important agricultural implications. “As an example, rapid commercialization of durian has led to the proliferation of cultivars with a wide discrepancy in prices and little way to verify the authenticity of the fruit products at scale,” they write. “A high-quality genome assembly may aid in identifying cultivar-specific sequences, including SNPs related to important cultivar-specific traits (such as taste, texture, and odor), and allow molecular barcoding of different durian cultivars for rapid quality control.” They also hope the work will fuel studies of other durian varieties to characterize the plant’s natural biodiversity.

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