Progress 09/15/04 to 09/14/07
Outputs
In January of 2006, the current status of the papaya BAC end sequence analysis work was presented by graduate student Jeffrey Lai in the form of a poster at the Plant and Animal Genome Meeting in San Diego, CA. On 22 September of 2006, the papaya BAC end sequence analysis project was presented by the PI at the 42nd ANNUAL HAWAII PAPAYA INDUSTRY ASSOCIATION CONFERENCE in Honolulu, HI. This presentation also highlighted some of the anticipated benefits of the papaya genome sequencing project and provided an opportunity for approximately 60 growers and marketers of papaya to interact with the genomics community. The PI of this project, Gernot Presting, delivered an invited presentation on the BAC end sequence analysis to an audience of about 200 attendees of the "Fruit and Nut Workshop" at the Annual Plant and Animal Genome Meeting in San Diego, CA, in January 2007.
Impacts
The impact of this project is reflected in the number of citations it has received since publication of the major findings resulting from this work in the journal "Molecular Genetics and Genomics" in July 2006: 1) Freeling M, Rapaka L, Lyons E, et al. G-Boxes, Bigfoot Genes, and Environmental Response: Characterization of Intragenomic Conserved Noncoding Sequences in Arabidopsis. PLANT CELL 19: 1441-1457 MAY 2007 2) Cheung F, Town CD. A BAC end view of the Musa acuminata genome. BMC PLANT BIOLOGY 7: Art. No. 29 JUN 11 2007 3) Yu QY, Hou SB, Hobza R, et al. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. MOLECULAR GENETICS AND GENOMICS 278 (2): 177-185 AUG 2007 4) Telgmann-Rauber A, Jamsari A, Kinney MS, et al. Genetic and physical maps around the sex-determining M-locus of the dioecious plant asparagus. MOLECULAR GENETICS AND GENOMICS 278 (3): 221-234 SEP 2007 5) Eustice M, Yu Q, Lai CW, et al. Development and application of
microsatellite markers for genomic analysis of papaya. TREE GENETICS AND GENOMES DOI 10.1007/s11295-007-0112-2 JUL 2007 Note that the citation list does not yet include the report on the whole genome sequencing, assembly and analysis of papaya (which will be published shortly), and of which the generation and analysis of the papaya BAC end sequence data was an integral component. This project has had impacts both on the applied field (e.g. by providing thousands of microsatellite marker sequences to the papaya breeding community) as well as on the basic research (e.g. by shedding light on plant genome evolution).
Publications
- No publications reported this period
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Progress 10/01/05 to 09/30/06
Outputs
During this report period, the papaya BAC end sequence data was further analyzed to assess the co-linearity between papaya and other completely sequenced plant genomes (Arabidopsis, Populus and rice). To do this, single copy BAC end sequence pairs (i.e. forward and reverse sequence of the same papaya BAC) were mapped onto the chromosomes of the heterologous crop. If both BAC end sequences mapped to within 300 kb on the heterologous genome, the BAC and the heterologous genome region were considered to be colinear. Significantly, the papaya genome was found to exhibit higher colinearity with the more distantly related Populus than the more closely related Arabidopsis genome.
Impacts
Colinearity of genomes can be exploited to efficiently clone genes from heterologous genomes based on location. The extent to which colinearity can be thus utilized depends on the degree and frequency of rearrangements in each genome. Our analysis indicates that the Populus, peach and papaya genomes exhibit relatively high levels of colinearity, and supports recent observations of frequent genome rearrangements in the Arabidopsis lineage. Together these observations suggest that the Populus genome may be more suitable for the assembly of 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. Furthermore, the BAC end sequence data generated and analyzed in this project should greatly facilitate the assembly of shotgun sequence data in the on-going whole genome project of papaya.
Publications
- Lai CW, Yu Q, Hou S, Skelton RL, Jones MR, Kanako LTJ, Murray J, Eustice M, Agbayani R, Guan P, Moore P, Ming R, Presting G. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Gen. Genomics 276:1-12.
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Progress 10/01/04 to 09/30/05
Outputs
Papaya (Carica papaya L.) is a major tree fruit crop of tropical and subtropical regions with an estimated genome size of 372 Mbp. We have completed sequencing of 50,661 BAC ends from 26,017 individual papaya BAC clones. Analysis of the sequence yielded 17,483,563 high quality bases that represent 4.7% of the papaya genome. A total of 7,456 microsatellites of at least 12 bases length were discovered in 5,452 BESs, and primer pairs were generated for 2,575 of these SSRs. Sixteen percent of BESs contained plant repeat elements, the vast majority of which were class I retrotransposons (83.3%). Approximately 19.1% of the low-copy BES had homology to Arabidopsis thaliana cDNA. A total of 53, 167, and 11 BAC end sequence pairs could be mapped to co-linear regions in the Arabidopsis thaliana, Populus trichocapa and Oryza sativa genomes, respectively. Several new papaya-specific repeats were identified. Detailed analysis results are available in a searchable web database at
(http://www.genomics.hawaii.edu/papaya/BES).
Impacts
We provide thousands of microsatellite marker sequences that are already being used in papaya breeding projects. BAC end sequence tags that are searchable on our web page provide easy avenues for candidate gene cloning. The sequences that have been obtained and analyzed in detail for this project will be critical for an on-going whole-genome shotgun sequencing project of papaya and will substantially increase the value of the papaya physical map that is being constructed independently. Finally, these sequences have already provided significant insight into the genome organization of papaya in relation to that of three other sequenced plant genomes: Arabidopsis, rice and poplar.
Publications
- http://www.genomics.hawaii.edu/papaya/BES/. 2005.
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Progress 10/01/03 to 09/30/04
Outputs
No progress to report. This project started on September 15, 2004.
Impacts
No impact to report. This project started on September 15, 2004.
Publications
- No publications reported this period
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