Plant Genome Sequencing

I have always wanted to write a post on this topic. Last week, Iattended an informal talk on oil palm genomics. On the same week, Sime Darby announced that they have completed oil palm genome sequencing. This means that another private company has completely sequenced the most important crop in Malaysia. A few years back, there was a debate of whether Malaysia should sequence this plant. Many people don't see the importance to sequence this crop. But, we can understand why.

One major problem in plant genome sequencing is high cost. The sequencing projects are usually joint-collaboration from several sequencing centers, research institutes and universities research groups. Together, they formed a consortium and held meetings on regular basis. Most of the time, one group will be in charge of sequencing one or more chromosomes. Priority will be given to chromosomes that are known to possess desired traits or have most genic region. The difficulties of plant genome sequencing lies in the complexity and large genome size. Some plants are polypoidy. Plant genomes consists a lot of repetitive elements that can be hard to resolved.

The main goal of a plant genome sequencing project is often crop improvement (with the exception of model crops). The first three years involves genome sequencing, assembly and annotation. Re-sequencing and finishing efforts can take a few more years. After the genome is completed, 3 years are required to develop Marker-Assisted Selection (MAS) using high throughput markers such as SNPs. Association mapping and QTL mapping can be carried. The timeframe from genome sequencing to successful phenotypic selection can take at least 9 years.

Joint Genome Institute under US Department of Energy has been actively involved in many sequencing projects. JGI community sequencing programme offers genome sequencing grants . The organism sequenced must be related to energy issues. Basically, this rule is applicable to all microbes and plants because they can produce biomass... which can be converted to biofuel. The catch? Every project must involve US collaborator.

So where does the future lies with researchers from developing countries who can't afford to sequence the whole genome? Here's my suggestion: use a related species as your reference genome. Publications using EST will give you some ideas how genomic studies were carried out in the past. So, keep working with the Poor Man's genome until... genome sequencing become much more affordable.

Complete Genomics has targeted $1000 for a human genome (3.2Gb) this year. That is a few times the size of most crops (Bear in mind that oil palm is 1.8Gb). Whether they can achieve that is another issue. The thing is...Next Generation Sequencing is transforming genomics at a fast pace now. How far is $1000 plant genome from now?