Genome sequence and analysis of the tuber crop potato

Abstract

Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.

The oyster genome reveals stress adaptation and complexity of shell formation

“…NGS technology has been successfully applied for de novo genome sequencing and assembly using whole-genome shotgun strategies [9][10][11][12][13] . We initially generated 155-fold Illumina whole-genome shotgun reads (Supplementary Table 1), but could not adequately assemble them owing to high levels of polymorphism and abundant repetitive sequences (Supplementary Text B2 and Supplementary Fig.…”

The tomato genome: implications for plant breeding, genomics and evolution

“…Rapid progress in the development of new sequencing technology and bioinformatic tools in recent years has allowed faster and more efficient sequencing, and assembly of genomes at lower cost. As many as 20 plant genomes have been sequenced and assembled in the last two years [6-25]. Genome sequences of plants belonging to different groups, such as two plants from the early land plant clades (a moss Physcomitrella patens and a spikemoss Selaginella moellendorffii ) and numerous economically important monocots (Box 1), such as rice, maize, sorghum, and so on, have now been decoded [4,5,25-28] (Figure 1).…”

“…Genome sequences of many members of group Eurosids, such as Arabidopsis , grape, poplar, medicago, cucumber, and so on, have already been published [3,13,29-31]. However, members of the group Euasterids, which has many plants of economic importance, were not represented in the list of known plant genome sequences until the release of the potato ( Solanum tuberosum ) genome belonging to the family Solanaceae [6]. The recently decoded genome sequences of tomato ( Solanum lycopersicum ) and its close wild relative ( Solanum pimpinellifolium ) are significant additions to published Euasterid genomes [7].…”

“…Solanaceous crop genomics is in an exciting phase of development following the recent sequencing of the potato and tomato genomes [6,7]. Tomato ( Solanum lycopersicum L.), originated in South America, and was spread around the world to become one of the most extensively used vegetable crops.…”

“…With the recently decoded tomato and potato genomes (both belonging to the family Solanaceae), plant biologists have just started to explore the genome sequences of Euasterids for both applied and basic research [6,7]. To promote large-scale genomic studies in Euasterids, more species belonging to this group need to be sequenced to match the plethora of sequence information from Eurosids.…”