Physical Map of Papaya Genome

Abstract

Bacterial artificial chromosome (BAC)-based fingerprinted physical maps have been proven to be a powerful tool in genomic and genetic studies. A BAC-based physical map of papaya was developed from the hermaphrodite papaya BAC library using the high-information-content fingerprinting approach to assist the whole-genome shotgun sequence assembly. The entire library of the hermaphrodite papaya BAC library was fingerprinted, and a total of 30,824 high-quality fingerprints were used to assemble fingerprinted contigs. The assembled physical map consists of 963 contigs, representing 9.4× genome equivalents. The papaya physical map was integrated with the genetic map and genome sequence by mapping microsatellite markers derived from BAC end sequences (BES) and the whole-genome shotgun sequences. The genome coverage of the physical map is estimated to be about 95.8 %, while 72.4 % of the genome was aligned to the genetic map. In addition, a total of 1,181 high-quality short overlapping oligonucleotide (overgo) probes representing conserved sequences in Arabidopsis and genetically mapped loci in Brassica were anchored on the physical map, which provides a foundation for comparative genomics in the Brassicales. The integrated genetic and physical map aligned with the genome sequence revealed recombination hot spots and regions of suppressed recombination across the genome, particularly on the recently evolved sex chromosomes. The integrated map facilitated the genomic draft sequence assembly and has been a valuable resource for papaya sex chromosome research and, perhaps more importantly, for comparative genomics and map-based cloning of agronomically and economically important genes.