The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Abstract

Papaya, a fruit crop cultivated in tropical and subtropical regions, is known for its nutritional benefits and medicinal applications. Here we report a 3x draft genome sequence of 'SunUp' papaya, the first commercial virus-resistant transgenic fruit tree to be sequenced. The papaya genome is three times the size of the Arabidopsis genome, but contains fewer genes, including significantly fewer disease-resistance gene analogues. Comparison of the five sequenced genomes suggests a minimal angiosperm gene set of 13,311. A lack of recent genome duplication, atypical of other angiosperm genomes sequenced so far, may account for the smaller papaya gene number in most functional groups. Nonetheless, striking amplifications in gene number within particular functional groups suggest roles in the evolution of tree-like habit, deposition and remobilization of starch reserves, attraction of seed dispersal agents, and adaptation to tropical daylengths. Transgenesis at three locations is closely associated with chloroplast insertions into the nuclear genome, and with topoisomerase I recognition sites. Papaya offers numerous advantages as a system for fruit-tree functional genomics, and this draft genome sequence provides the foundation for revealing the basis of Carica's distinguishing morpho-physiological, medicinal and nutritional properties.

Figure 1. Alignment of co-linear regions from Arabidopsis (green), papaya (magenta), poplar (blue) and grape (red)

‘Vv chr16r’ is an unordered ultracontig that has been assigned to grape chromosome 16. Triangles represent individual genes with transcriptional orientations. Several Arabidopsis regions belong to previously identified duplication segments (α3, α11, α20, β6, γ7, shown to the right). The whole syntenic alignment supports four distinct whole-genome duplication events: α, β within the Arabidopsis lineage, an independent duplication in poplar, and γ which is shared by all four eudicot genomes. Co-linear regions can be grouped into three γ sub-genomes based on Camin–Sokal parsimony criteria.

Figure 2. Comparison of gene numbers in transcription-factor tribe or related tribes from Arabidopsis and papaya

Most transcription factors are represented by fewer genes in papaya than Arabidopsis. Transcription-factor names are given, with values after the names corresponding to: number of tribes with genes assigned to transcription factor group, number of tribes with smaller counts in papaya than Arabidopsis, number of tribes with equal counts in papaya and Arabidopsis, number of tribes with larger counts in papaya, and number of tribes with zero members in papaya. Supporting data are provided in Supplementary Table 8.