Papaya Genome: A Model for Tropical Fruit Trees and Beyond

Papaya, Carica papaya L., a major fruit crop of the tropics, is featured in a series of articles in this, the first “special issue” of Tropical Plant Biology. One of the goals of TPB is to publish occasional special issues highlighting breakthroughs on a particular plant species or unifying problem of significance in plant tropical biology. It is fitting and with pride that we devote this first special issue of TPB to one of our personally favorite tropical plants, papaya. The timing of this particular special issue is based on the April 2008 report that the papaya genome has been sequenced [2] and the release of a large set of publicly available data, which is subsequently responsible for interesting and informative research such as that being reported in this issue. This special issue highlights specific examples of how a new and interesting plant genome sequence can open new avenues to better understand angiosperm genome evolution. Papaya belongs to the order Brassicales that comprises 17 families including Caracacae, which contains papaya, and Brassicacae, the mustard or cabbage family known for its large and diverse collection of species (more than 3700 according to the Key Royal Botanical Gardens) including the model plant Arabidopsis thaliana. The placement of papaya and Arabidopsis deep within the order Brassicales allows one to use the extensive data and concepts developed extensively in Arabidopsis to discover possible gene function in papaya. More importantly, having the genome sequences of the closely related species provides information from one to help resolve unanswerable questions in the other. For example, which of the completely annotated genes of Arabidopsis are orthologs to which papaya genes? Analysis of syntenic blocks between Arabidopsis and papaya show that for single papaya genes there might be four corresponding genes in Arabidopsis [1]. The lack of multiple whole genome duplication events (polyploidy) in papaya make it a simple system for analysis and can help explain the course of genome evolution of orthologous genes in Arabidopsis. Papaya, the fifth flowering plant to be sequenced, is also the first transgenic eukaryotic organism sequenced. Having the full genome sequence of a transgenic plant allows for detailed characterization of insert size, number, site, and function for a better understanding of genetic transformation on whole genome structure and function [7]. Among the plants sequenced, papaya has the fewest functional genes, apparently as the result of undergoing only one ancient genome triplication shared by most eudicots during its evolution. Compared to the other four sequenced plant genomes, the papaya genome count of 24,746 genes is 20% fewer than that of Arabidopsis, 34% fewer than rice, 46% fewer than poplar, and 19% fewer than grape. The streamlined genome of papaya is already proving to be an excellent resource for comparative and functional analysis of both genes and repetitive elements and may provide clues about the minimum set of genes that are needed to be a flowering plant. The relative simplicity of the papaya genome makes it ideal for detailed analysis of subsets of protein coding genes that may be involved in specific physiological and biochemical processes, anatomical and morphological characteristics, or environmental sensing pathways. Each Tropical Plant Biol. (2008) 1:179–180 DOI 10.1007/s12042-008-9025-y