ArticleBMC genomics2009
A physical map of the papaya genome with integrated genetic map and genome sequence.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
35 citing papers in PubMed, 94 citations in OpenAlex.
- ZW sex chromosome structure in Amborella trichopoda.Nature plants · 2024Article
- Sex chromosome cycle as a mechanism of stable sex determination.Journal of biochemistry · 2024Review
- Puzzle Hi-C: An accurate scaffolding software.PloS one · 2024Article
- Evolution of plant sex and molecular mechanisms underlying plants sex separation.Forestry research · 2023Review
- Descriptive Genomic Analysis and Sequence Genotyping of the Two Papaya Species (Vasconcellea pubescens and Vasconcellea chilensis) Using GBS Tools.Plants (Basel, Switzerland) · 2022Article
- The contributions of Nettie Stevens to the field of sex chromosome biology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2022Review
- Genomic characterization of a rare Carica papaya X chromosome mutant reveals a candidate monodehydroascorbate reductase 4 gene involved in all-hermaphrodite phenomenon.Molecular genetics and genomics : MGG · 2021Article
- Fruit crops in the era of genome editing: closing the regulatory gap.Plant cell reports · 2021Review
- The Diversity of Plant Sex Chromosomes Highlighted through Advances in Genome Sequencing.Genes · 2021Review
- Linkage mapping and quantitative trait loci analysis of sweetness and other fruit quality traits in papaya.BMC plant biology · 2019Article
- The development of functional mapping by three sex-related loci on the third whorl of different sex types of Carica papaya L.PloS one · 2018Article
- Bioinformatics Approach in Plant Genomic Research.Current genomics · 2016Article
- A polymorphic pseudoautosomal boundary in the Carica papaya sex chromosomes.Molecular genetics and genomics : MGG · 2015Article
- The Evolutionary Tempo of Sex Chromosome Degradation in Carica papaya.Journal of molecular evolution · 2015Article
- Recombination in the human Pseudoautosomal region PAR1.PLoS genetics · 2014Article
- Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.).Functional & integrative genomics · 2014Article
- Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.).PloS one · 2013Article
- Integrated consensus genetic and physical maps of flax (Linum usitatissimum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2012Article
- Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information.BMC genomics · 2012Article
Corrections and comments
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Authors and funding
14 authors at 7 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPapaya 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.
resultsThe 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.
conclusionA 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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