Details of the record

TitleA physical map of the papaya genome with integrated genetic map
and genome sequence
AuthorsQingyi Yu1, Eric Tong, Rachel L Skelton, John E Bowers, Meghan R Jones,
Jan E Murray, Shaobin Hou, Peizhu Guan, Ricelle A Acob, Ming-
Cheng Luo, Paul H Moore, Maqsudul Alam, Andrew H Paterson and
Ray Ming
PublicationBMC Genomics 2009, 10:371
AbstractBackground: Papaya is a major fruit crop in tropical and subtropical regions worldwide and has primitive sex
chromosomes controlling sex determination in this trioecious species. The papaya genome was recently sequenced
because of its agricultural importance, unique biological features, and successful application of transgenic papaya for
resistance to papaya ringspot virus. As a part of the genome sequencing project, we constructed a BAC-based physical
map using a high information-content fingerprinting approach to assist whole genome shotgun sequence assembly.
Results: The physical map consists of 963 contigs, representing 9.4x genome equivalents, and was integrated with the
genetic map and genome sequence using BAC end sequences and a sequence-tagged high-density genetic map. The
estimated genome coverage of the physical map is about 95.8%, while 72.4% of the genome was aligned to the genetic
map. A total of 1,181 high quality overgo (overlapping oligonucleotide) 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 hotspots as well as regions suppressed for recombination across the genome, particularly on the
recently evolved sex chromosomes. Suppression of recombination spread to the adjacent region of the male specific
region of the Y chromosome (MSY), and recombination rates were recovered gradually and then exceeded the genome
average. Recombination hotspots were observed at about 10 Mb away on both sides of the MSY, showing 7-fold increase
compared with the genome wide average, demonstrating the dynamics of recombination of the sex chromosomes.
Conclusion: A BAC-based physical map of papaya was constructed and integrated with the genetic map and genome
sequence. The integrated map facilitated the draft genome assembly, and is a valuable resource for comparative genomics
and map-based cloning of agronomically and economically important genes and for sex chromosome research.

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.: 2009 :: Barry Marler :: Plant Genome Mapping Laboratory :: University of Georgia