With next-generation sequencing technologies dropping in price and increasing in throughput, it’s not surprising to find multiple genomes published every week in scientific journals. Most of these articles don’t qualify for publication in the top tier of journals like they did at the onset of the next-generation sequencing boom, but some genome sequencing projects, such as the potato genome, are high profile enough to warrant publication in top tier journals.
In the July 14th issue of the journal Nature, a draft of the potato (Solanum tuberosum) genome was described in a paper authored by the Potato Genome Sequencing Consortium – a huge group of researchers from 26 institutions.
The potato is the world’s fourth most consumed food crop, the most commonly grown vegetable crop, and a member of the economically important Solanaceae family –otherwise known as the nightshades – which include tomato, peppers, aubergine (eggplant if you live in the United States), tobacco, and petunia. Widely distributed in western South America, tuber forming Solanum species are highly morphologically diverse and easily cross with other varieties for breeding purposes.
It’s been a bumpy road sequencing the potato genome since the project was started in 2006. The potato genome is an extremely heterozygous autotetraploid, which translates to four highly variable copies of each of the 12 chromosomes. It’s also the first sequenced Eudicot genome in the Asterid clade, so there are no close genetic relatives to provide the basis for a guided genome assembly.
The consortium began the sequencing by creating a bacterial artificial chromosome (BAC) library of 78,000 clones from a well studied diploid line providing high quality potatoes, named RH89-039-16. The group used the BAC library and 10,000 AFLP markers to create more than 7000 contigs which were constructed into a physical map. The group then identified up to 150 BACs for every chromosome on the potato genome, and verified their locations using fluorescent in situ hybridization.
Heterozygosity was so high in the RH line that after thorough sequencing the group hit an impasse with the assembly of the genome. In an attempt to complement the sequencing of the RH line, the consortium began sequencing a doubled monoploid potato clone, DM1-3 516R44, derived from a diploid wild South America accession. The DM line has a simpler genome than the RH line and is highly homozygous.
Using both the Illumina Genome Analyzer II and Roche 454 pyrosequencing platforms, and supplementing this data with traditional Sanger sequencing, approximately 96 Gb of data was acquired for the DM line. The group then used the SOAPdenovo computer program to assemble the reads with a final assembly of 727 Mb for the DM line and a final estimation of 844 Mb for the genome.
The consortium generated more than 31 Gb of transcriptome data from both the DM and RH line libraries. These 48 libraries represented major tissue types, developmental stages, and included various responses to abiotic and biotic stresses. All the reads from the RNA-Seq libraries were mapped to the assembled DM genome. Using gene prediction methods, along with protein and EST data, the potato genome was predicted to contain 39,000 protein coding genes, an amount which is in agreement with other plant genomes. Within these genes, there were an estimated 2,642 asterid-specific and 3,372 potato-lineage-specific genes. Some of the predicted asterid-specific genes include many novel transcription factors, self-incompatibility factors, and defence-related proteins. The draft assembly of the genome consists of more than 60% repeated elements. The largest class of the transposable elements is the long terminal repeat retrotransposons (LTRs) which are estimated at 30% of the potato genome.
The potato is notorious for being susceptible to many pathogens and pests. This well known susceptibility was one of the priorities for sequencing the genome and determining genes responsible for disease resistance and pathogen defense. The DM genome assembly contains more than 800 putative R genes, responsible for conferring disease resistance, including 408 NBS-LRR-encoding genes, 57 Toll/interleukin-1 receptor (TIR) domains, and 351 non-TIR type resistance genes. An extreme number of pseudogenes – attributed to indels, frameshift mutations, and misplaced stop codons –were identified within known R gene motifs, which possibly explains the potato’s inability to fight off some specific diseases.
One such well known disease, Late Blight, caused by Phytophthora infestans, was responsible for the Irish Potato Famine in the 1840s.. Using information from this genome sequencing project and other studies, we now know the variety brought to Europe in the late 16th century happens to lack specific disease resistance genes for Phytophthora infestans. One could speculate that unbridled transposon jumping caused the inactivation of many R genes in this potato variety.
Unique for the potato is the formation of tubers (the actual potatoes) through the modification of a stolon. The tomato is very closely related to potato, but does not produce stolons or modified tubers. The group used transcript data from both potato and tomato to address genetic regulation of the formation of stolons and the transition of stolons to tubers. Quite interestingly, the formation of stolons and tubers coincides with an up-regulation of genes associated with starch biosynthesis, protein storage, and Kunitz protease inhibitor genes associated with pests and pathogens.
Possibly due to extremely high levels of heterozygosity, it has been difficult to improve the potato through traditional breeding efforts. It’s estimated that there is a worldwide economic loss of 4.5 billion US dollars to potato crops from diseases each year. Just to attempt to suppress these diseases copious amounts of pesticides and fungicides are applied to potato crop land each year. The potato cyst nematode, for example, is an important pest that researchers hope to improve resistance to via breeding initiatives. Having this draft potato genome sequence will aid in the characterization of existing germplasm collections and description of allelic variance in breeding efforts to avoid diseases. The potato genome will also serve as a resource for breeders wanting to improve the quality of other economically important Solanaceous plants such as tomato, pepper, eggplant, and tobacco.