ArticleMolecular genetics and genomics : MGG2006
Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome.
Article in Molecular genetics and genomics : MGG, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 73 citations in OpenAlex.
- In Silico Approach for Characterization and Comparison of Repeats in the Genomes of Oil and Date Palms.Bioinformatics and biology insights · 2017Article
- A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition.BMC genomics · 2016Article
- Article
- BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution.Plant molecular biology · 2013Article
- First insights into the large genome of Epimedium sagittatum (Sieb. et Zucc) Maxim, a Chinese Ttaditional medicinal plant.International journal of molecular sciences · 2013Article
- A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin.Plant molecular biology · 2013Article
- A comparative survey of genetic diversity among a set of Caricaceae accessions using microsatellite markers.SpringerPlus · 2013Article
- Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple.BMC genomics · 2012Article
- Construction of physical maps for the sex-specific regions of papaya sex chromosomes.BMC genomics · 2012Article
- Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.Molecular biology reports · 2012Article
- Characterizing the walnut genome through analyses of BAC end sequences.Plant molecular biology · 2012Article
- Narrowing down the apricot Plum pox virus resistance locus and comparative analysis with the peach genome syntenic region.Molecular plant pathology · 2011Article
- Analysis of BAC-end sequences in rainbow trout: content characterization and assessment of synteny between trout and other fish genomes.BMC genomics · 2011Article
- Physical mapping and BAC-end sequence analysis provide initial insights into the flax (Linum usitatissimum L.) genome.BMC genomics · 2011Article
- Analysis of BAC-end sequences (BESs) and development of BES-SSR markers for genetic mapping and hybrid purity assessment in pigeonpea (Cajanus spp.).BMC plant biology · 2011Article
- An overview of the Phalaenopsis orchid genome through BAC end sequence analysis.BMC plant biology · 2011Article
- Construction of papaya male and female BAC libraries and application in physical mapping of the sex chromosomes.Journal of biomedicine & biotechnology · 2011Article
- Genome-wide BAC-end sequencing of Cucumis melo using two BAC libraries.BMC genomics · 2010Article
- An examination of targeted gene neighborhoods in strawberry.BMC plant biology · 2010Article
- A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
13 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We present the analysis of 4.7% of the papaya genome based on BAC end sequences (BESs) representing 17 million high-quality bases. Microsatellites discovered in 5,452 BESs and flanking primer sequences are available to papaya breeding programs at http://www.genomics.hawaii.edu/papaya/BES . Sixteen percent of BESs contain plant repeat elements, the vast majority (83.3%) of which are class I retrotransposons. Several novel papaya-specific repeats were identified. Approximately 19.1% of the BESs have homology to Arabidopsis cDNA. Increasing numbers of completely sequenced plant genomes and BES projects enable novel approaches to comparative plant genomics. Paired BESs of Carica, Arabidopsis, Populus, Brassica and Lycopersicon were mapped onto the completed genomes of Arabidopsis and Populus. In general the level of microsynteny was highest between closely related organisms. However, papaya revealed a higher degree of apparent synteny with the more distantly related poplar than with the more closely related Arabidopsis. This, as well as significant colinearity observed between peach and poplar genome sequences, support recent observations of frequent genome rearrangements in the Arabidopsis lineage and suggest that the poplar genome sequence may be more useful for elucidating the papaya and other rosid genomes. These insights will play a critical role in selecting species and sequencing strategies that will optimally represent crop genomes in sequence databases.
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