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The Hawaii Papaya Genome Project
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An integrative Multi-Institutional Genomics and Bioinformatic Project
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Welcome to the Hawaii Papaya Genome Project at the University of Hawaii.
We are developing the resources necessary to map and clone papaya genes in an effort to improve the economic value and efficiency of agricultural cultivation, and to discover new applications for one of the most important fruit crops of the tropical and subtropical regions.
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Update
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You can access the new Genome Browser page
here
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Status of the Papaya Genome Project
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Estimated genome completion date:
Total papaya genome size:
Total number of chromosomes:
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December 2007
372 Mb (Millions of base pairs)
9
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Statistics
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Genome size done:
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1980.30 Mb (estimate based on 6x pass)
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Total reactions done:
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2829004
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Ave. Read Length:
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700
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In 2004 the UH Center for Genomics, Proteomics and Bioinformatics Research Initiative (CGPBRI) formed an integrative multi-institutional consortium including the Maui High Performance Computing Center (MHPCC, http://www.mhpcc.edu/ ), Hawaii Agricultural Research Center (HARC, http://www.hawaiiag.org/harc/), US Department of Agriculture (USDA http://pbarc.ars.usda.gov/), the Pacific Telehealth & Technology Hui (http://www.pacifichui.org/), and Nankai University, China, to determine the DNA sequence of the papaya tree genome as the first significant step towards improving the quality and productivity of tropical fruit trees and to increase our basic knowledge of higher plant biology.
Papaya offers several features that make it highly suitable from a scientific point of view for a project of this magnitude in Hawaii, which includes a comparatively small genome (372 Mb; approximately 86% of the rice genome).
This will allow rapid elaboration of the genome organization and sequencing for the identification of agronomically important genes.
Papaya also displays biological features of a “living fossil” among plants and provides an exceptional opportunity to study sex chromosome evolution (http://www.ncbi.nlm.nih.gov...) and sex determination (http://www.genetics.org...). The biological significance of this achievement is that this will be the first genome of a fruit species to be sequenced.
Importance to Hawaii
Papaya was endemic to central America where it was extensively cultivated prior to European settlement.
In the wake of Spanish colonization during the 16th century it was rapidly distributed to many tropical areas, partly because of an abundance of seed of relatively long viability.
Papaya (he’i’) was consequently not among the plants that were brought to the islands by early Polynesian voyagers (here) and did not arrive in Hawaii until the early 1800’s.
(http://www.dole5aday.com/...).
Papaya is one of the few plant species which fruit throughout the year and can produce ripe fruit in as little as 9 months from planting.
A papaya tree may live for 25 years or longer, bearing continuously with one or more fruit in each leaf axil.
Papaya is a principal fruit crop in many tropical and subtropical regions world wide and a major export commodity, generating an annual revenue of $ 17 million in Hawaii (2001).
Expected benefits of the Hawaii Papaya Genome Project
Depending on the variety, papaya trees produce varying proportions of male, female, and hermaphrodite seeds.
Only hermaphrodite trees are used in commercial fruit production because female trees produce variably sized fruit that require a greater container volume and do not hold up as well in shipping as the more compact and slender pear-shaped fruit of the hermaphrodite trees (http://www.extento.hawaii.edu...).
Papaya fields are established by planting five to ten seedlings in a single hole, which have to be grown for three to four months before they can be sexed and thinned to remove the female trees.
This system of over-planting followed a few months later by thinning to a single tree is labor intensive and wasteful of seed, water and fertilizer, and leaves non-producing gaps in the field.
Sequencing and analyzing the papaya genome will aid the identification of sex determining genes and facilitate the development of a propagation technique that will allow “genetic sexing” of papaya seedlings and establish true breeding hermaphrodite varieties.
This will significantly reduce the cost for establishing fields, and lead to earlier fruit harvests.
Improvement of pest and disease resistance
The continuous growing season in Hawaii allows pests and pathogens to maintain high, crop damaging populations.
Failure to maintain adequate, year-round pest and disease control measures results in reduced yields and quality, and a diminished ability to export the papaya fruit.
Pests and pathogens are commonly fought by the application of pesticides, which is both costly and has environmental side effects.
In addition, pesticides are effective only against certain pathogens.
Papaya farmers have been plagued by a devastating disease caused by the papaya ringspot virus (PRV), which almost wiped out the entire papaya industry on the Big Island of Hawaii in the early 1990’s.
A transgenic strain carrying a fragment of the virus coat-protein gene was subsequently developed, which is resistant to the virus (http://www.afaa.com...).
This strain is the first tropical crop rendered resistant to a devastating disease using recombinant DNA technology.
Today, “Rainbow” comprises over 60% of papaya grown and exported from Hawai’i.
The ready accessibility of large-scale sequence information on these strains will significantly aid and accelerate the deregulation process of transgenic papaya varieties and thus provide the local agriculture with an important marketing tool.
Other uses of papaya
Papaya is also used in a wide range of medical, biotechnological and cosmetic applications that can be further developed once a complete picture of the genomic sequence is obtained.
Many of these uses are based on the proteolytic enzyme papain, the most widely studied and utilized member of a large family of cysteine proteases.
In food biotechnology, papain is used in the tenderization of meat by its action on connective tissue and muscle proteins.
It is also used in beer brewing for chill proofing, in the preparation of fish protein concentrates for animal feed, the development of roast beef-like flavors by partial hydrolysis of proteins, and for production of dehydrated pulses and beans.
The enzyme is used also to improve the protein dispersibility index of soya flour.
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