Research article

A physical map of the papaya genome with integrated genetic map and genome sequence

Qingyi Yu¹ , Eric Tong¹ , Rachel L Skelton¹ , John E Bowers² , Meghan R Jones¹ , Jan E Murray^1,3 , Shaobin Hou⁴ , Peizhu Guan⁵ , Ricelle A Acob⁵ , Ming-Cheng Luo⁶ , Paul H Moore⁷ , Maqsudul Alam⁴ , Andrew H Paterson² and Ray Ming^1,3

¹  Cellular and Molecular Biology Research Unit, Hawaii Agriculture Research Center, Aiea, HI 96701, USA

²  Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA

³  Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

⁴  Center for Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI 96822, USA

⁵  Department of Molecular Bioscience and Bioengineering, University of Hawaii, Honolulu, HI 96822, USA

⁶  Department of Plant Sciences, University of California, Davis, CA 95616, USA

⁷  USDA-ARS, Pacific Basin Agricultural Research Center, Hilo, HI 96720, USA

author email corresponding author email

BMC Genomics 2009, 10:371doi:10.1186/1471-2164-10-371

Published:	7 August 2009

Abstract

Background

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 9.4× 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.