Meet the scientists who sequenced the durian genome

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Durian Fruit

1. Why are the cancer researchers interested in sequencing the durian genome?

All scientists possess an innate interest and curiosity in understanding and figuring out how the world works, regardless of the specific field they are concentrating on. Throughout South East Asia, durian is widely known as the “king of fruits” for its very distinctive features, including its unique smell, flavour, and formidable spiny appearance, and most of us have been durian aficionados from a very young age. Driven by this strong scientific curiosity, the almost mythological status of durian, and the availability of new sequencing technologies, we felt it would be a meaningful contribution to science, and also a great challenge, to unlock the mysteries of durian by deciphering its genome.

2. What prompted the team to conduct this research?

We felt that the timing was perfect to crack the durian genome. First, new technologies like long-read sequencing and chromosome conformation mapping were just introduced which are ideal for studying plant genomes, that are very complex. Second, we were fortunate to receive funding support by an anonymous durian lover who was also fascinated by the mysteries of durian. There was a sense that as a team, we could indeed pull this off, and in the attempt we would also would learn a lot from the venture.

3. The team is the first to decipher the genetic blueprint of durian. What exactly did you discover?

Using state-of-the-art sequencing platforms, the team mapped the genome of a particular durian variety called Musang King (“Mao Shan Wang” in Chinese).

The team’s analysis revealed that the durian genome comprises approximately 46,000 genes – almost double that in humans who have about 23,000 genes. Based on the newly generated genomic data, the team also studied the evolution of durian and traced its relationship 65 million years back to the cacao plant which produces chocolate.

The team focused their analysis on genes that might control durian’s notorious smell. By combining the durian genetic map with genes activated in ripening fruits, they identified a class of genes called MGLs (methionine gamma lyases) that regulate the production of odor compounds called volatile sulphur compunds (VSCs). Unlike other plant species that typically have only one or two copies of MGL, our analysis revealed that durians have four copies, demonstrating that VSC production is turbocharged in durian fruits. The team speculates that in the wild, the ability of durians to produce high VSC levels and a pungent smell may be important in attracting animals to eat and disperse durian seeds to other regions.

4. Were there any surprises in the sequence?

The team found that durian and cotton both shared a whole genome duplication (WGD) event, before the two lineages diverged. This same WGD may explain how durian and cotton evolved such distinct traits.

5. How does the study shed light on the taste profiles and degree of pungency of different cultivars of durian? Eg. what does it tell us about the Monthong variety compared with the Musang King variety?

Our analysis of gene expression between different durian cultivars showed that genes involved in sulfur and flavor pathways were more active in Musang King versus other cultivars. This may help to explain why Musang King has the strongest (most pungent) taste and smell among the different cultivars.

Inside the Durian

6. What is the next-generation sequencing technology used in this study?

The team applied 3 different sequencing techniques:

1) long reads sequencing technology (Pacific Biosciences),

2) short reads sequencing technology (Illumina), and

3) in vitro proximity ligation technology that integrates long-range genomic information with next-generation sequencing output (Dovetail Genomics).

The team integrated sequencing data from the 3 platforms to generate a high-resolution and contiguous genome assembly of the organism at chromosomal level. They also generated transcriptomic data to annotate the genome, and to study the plant’s gene expression.

This high-resolution and contiguous durian genome assembly gives important insights into the plant’s genetic make-up and its relationship with other agriculturally-important relatives.

Long reads sequencing technology has been used locally to sequence smaller and simpler genomes, such as viral or bacterial genomes. The team is the first in the region to integrate these multiple platforms to generate such a high-resolution and contiguous genome assembly of a complex plant genome.

7. Can the expertise in next-generation sequencing technology that was developed in this study be applied to other plants? Can you cite examples?

Indeed, the expertise developed in this project can be applied to study the genomes of other plants. Besides Durio zibethenus which was sequenced in the current study, there are at least 30 other Durio species – some edible, some inedible, and some with many other unique features. In Singapore, there is also a D. singaporensis! Unfortunately, several of these species are currently endangered – we hope to work with experts in the region to characterize the genomes of these other Durio species, to protect their biodiversity and to gain further insights into these fascinating plants. Our platforms can also be expanded to plant biodiversity efforts in South East Asia, one of the most important biodiversity hotspots.

8. What are the main practical benefits of having the durian genome sequence?

The durian genome sequence will be a useful resource for durian agronomy research: for example, identifying genes involved in disease resistance, drought tolerance, fertilizer requirements, and flavour profiles, will be useful in breeding cultivars with such traits. In addition, it may be feasible to change or modify some of the traits of durian. For example, we could potentially can create a low-sugar durian that may be for suitable for diabetics.

9. Just how different can various durian cultivars be, in terms of flavor and smell?

The various durian cultivars can be very different, especially in terms of taste, smell, and texture. Moreover, different regions have distinct demands for different cultivars, reflecting local idiosyncracies in consumer tastes. For example, many consumers in Singapore and Malaysia prefer the pungent and soft texture of Musang King and D24, and they consider the more mild and hard-textured Monthong cultivar to be bland. On the other hand, consumers in Thailand prefer the Monthong cultivar, and they consider the pungent and softer varieties to be overripe and potentially rotten!

10. When did the project start? How long did it take for the team to make the discovery?

The project started in early 2015. The team took about 3 years to complete the present study. However, this is only the beginning, there are many more things we can do as described above.

The scientists from National Cancer Centre Singapore and Duke-NUS Medical School,
Singapore
From Left to Right (Top Row): Prof Patrick Tan, Prof Teh Bin Tean
From Left to Right (Bottom Row): Dr Yong Chern Han, Mr Cedric Ng, Dr Kevin Lim

11. How did the scientific teamwork on this research, even though they did not have plant biology knowledge?

The members in the team did a fair bit of self-learning, including reading plant-related papers and approaches used by other plant scientists. In addition, they also consulted and discussed with plant experts especially those specialized in durian. They also attended conferences to learn about the latest DNA sequencing technologies used in the field.