NEW YORK (GenomeWeb News) – An international team led by investigators affiliated with centers in China, the US, and Denmark has produced a high-quality draft genome for watermelon, using the sequence as a jumping-off point for more extensive genomic and transcriptomic analyses of the plant.
For the study, appearing online yesterday in Nature Genetics, researchers started by sequencing the genome of watermelon, Citrullus lanatus, using DNA from an East Asian watermelon cultivar called 97103. From there, they re-sequenced plants from 20 more accessions stretching across three watermelon sub-species — an analysis that helped to reveal haplotype and genetic diversity patterns in the commercially valuable fruit plant, as well as watermelon population structure.
Together with transcriptome sequence analyses on watermelon vascular and fruit tissues, study authors reported, the new genomic data offers insights into watermelon's biology, evolutionary history, and relationships with other plants in the Cucurbitaceae family such as cucumber, pumpkin, and melon.
"The high-quality genomic sequence opens a new way for the further studies of watermelon," co-first author Jianguo Zhang, a researcher affiliated with BGI-Shenzhen and Fudan University, said in a statement. "The data resources could serve as a robust tool for better exploring the mechanisms underlying significant economic traits and regulatory networks and further for breeding improvement."
The team initially tackled the 425 million base watermelon genome using the Illumina GAII platform and genomic DNA from watermelon in the inbred Chinese elite line 97103.
In addition to putting together a draft genome sequence that covers around 83 percent of the watermelon genome at an average depth of almost 109-fold, the researchers went on to re-sequence the genomes of plants from 20 more watermelon accessions at average depths of between five- and 16-fold apiece.
These accessions were selected to represent three watermelon sub-species, study authors said: an ancient, wild watermelon sub-species called lanatus that is native to southern Africa; a "semi-wild" mucosospermus sub-species that includes plants with large, edible seeds; and vulgaris, the sub-species from which domestic, cultivated watermelon was developed.
On top of that, the team performed transcriptome sequencing on phloem sap and vascular tissue from watermelon, cucumber, and pumpkin plants with the Illumina HiSeq 2000, as well as HiSeq 2000 sequencing of transcripts from the 97103 watermelon fruit and rind samples at four stages of development.
The team's analyses of the initial draft genome uncovered almost 160 million bases of transposable element sequences, making up some 45 percent of the assembled genetic blueprint.
The genome also housed hundreds of ribosomal RNA, transfer RNA, small nuclear RNA, and microRNA genes, researchers reported, along with 23,440 high-confidence protein-coding genes — a protein-coding repertoire on par with that of the related cucumber plant. Across the sequences from all 21 watermelon accessions, they also identified nearly 6.8 million potential SNPs and more than 965,000 small insertions and deletions.
Whereas several commonly cultivated watermelon accessions seem to have fairly low genetic diversity, the diversity within wild watermelon plants remains quite high, they found, suggesting that these plants might serve as a source to augment the genetic wherewithal of watermelon crops.
Such improvements may be especially important for building up pathogen resistance in watermelon, since many modern watermelon cultivars are prone to crop diseases.
By scouring the watermelon genome for sequences from three main resistance gene groups, for instance, the team tracked down clusters of pathogen-resistance genes suspected of arising from past duplication events. But comparisons of plants from domestic, semi-wild, and wild watermelon sub-species hinted that resistance genes have been lost from cultivated accessions during domestication.
From comparisons between the watermelon genome and sequences for cucumber, melon, and grape plants, meanwhile, the team was able to tease apart syntenic regions within the plant genomes and gain insights into their evolutionary relationships.
For example, that analysis indicated that the watermelon plant's 11 chromosomes originated from a set of seven chromosomes in a eudicot ancestor plant that expanded to 21 chromosomes before undergoing extensive fission and fusion events to get whittled back down to 11.
Finally, through transcriptomic analyses, the team was able to begin delving into the nature of the so-called sieve tubes that help circulate nutrients and signaling molecules through cucurbit plants — and to explore some of the regulatory features contributing to watermelon fruit development and quality.
"The unique metabolic and regulatory networks in developing watermelon fruit identified from our functional genomics study represent an initial genomics-enabled milestone for the understanding and genetic improvement of crucial nutritional attributes, including sugar and amino acid contents," the study authors said.