Comparative Genomics of Papaya Chromosomes

番木瓜（Carica Papaya L.）是全球热带和亚热带地区的主要水果作物。番木瓜果是夏威夷的主要出口商品，在佛罗里达州、德克萨斯州的大河谷和南加州也有生产。种植番木瓜树是为了获取果实和木瓜蛋白酶，木瓜蛋白酶是一种具有商业价值的蛋白质水解酶。木瓜是为数不多的一年四季都有果实的植物之一，在种植后的短短9个月内就能结出成熟的果实。一棵番木瓜树可以存活25年或更长时间，每个叶腋连续结出一个或多个果实。木瓜有雄性、雌性和雌雄同体，具有原始的Y染色体，为研究性染色体进化和性别决定提供了独特的机会。动物的性染色体很古老——大约有3亿年的历史，而y染色体在基因上被侵蚀了。开花植物大约出现在1.3 -2亿年前，植物性染色体的进化更晚。据估计，Silene属具有2000 - 2500万年的祖先，通常被认为包含真核生物中已知的最新进化的XY系统。然而，在Silene中，90%的Y染色体退化并抑制重组。最近在木瓜中发现的原始Y染色体有一个小的男性特定区域，仅占Y染色体的10%左右。这个男性特异性区域（MSY）表现出更温和的退化和重组抑制。因此，木瓜系统似乎是迄今为止已知的最新进化的XY系统，为性染色体的进化如何开始的问题提供了潜在的见解。揭示植物性别决定过程将直接应用于木瓜、芦笋、菠菜、黑胡椒、山药和开心果等农作物的生产。这个项目旨在探索早期性染色体的本质。木瓜MSY和相应的x特异性区域将被测序和表征。为了估计非重组区域的古老程度，将计算X和Y基因对沿该区域的发散程度，特别注意用于性别决定的候选基因。比较X和Y DNA序列及其周围环境将揭示染色体重排的类型和程度以及转座因子在MSY变性中的作用。MSY与原始Y染色体着丝粒的相对位置将通过粗线素和纤维荧光原位杂交（FISH）分析来澄清。预计该项目将为木瓜研究界产生性别决定和胚胎致死的候选基因。获取项目成果的dna序列数据和跟踪文件将存入基因库，项目数据将在夏威夷农业研究中心（http://www.hawaiiag.org/harc）和佐治亚大学（http://www.plantgenome.uga.edu/）的网站上提供。细菌人工染色体（BAC）克隆将由佐治亚大学植物基因组定位实验室分发，并存放在公共BAC分发中心。

Papaya (Carica papaya L.) is a principal fruit crop of tropical and subtropical regions worldwide. Papaya fruit is a major export commodity in Hawaii, and is also in production in Florida, the Rio Grande Valley of Texas, and southern California. Papaya trees are grown for both fruit and papain, a commercially valuable proteolytic enzyme. Papaya is one of the few plant species which fruit throughout the year and can produce ripe fruit in as little as nine 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 has male, female, and hermaphrodite sexes, with a primitive Y chromosome that provides a unique opportunity to study sex chromosome evolution and sex determination. Sex chromosomes in animals are ancient - about 300 million years old, and Y-chromosomes are genetically eroded. Flowering plants appeared about 130-200 million years ago and plant sex chromosomes evolved more recently. The Silene genus with its estimated 20 - 25 million-year ancestry has generally been thought to contain the most recently evolved XY system known in eukaryotes. Yet 90% of the Y chromosome in Silene is degenerated and suppressed for recombination. The recently discovered primitive Y chromosome in papaya has a small male specific region that comprises only about 10% of the Y chromosome. This male specific region (MSY) shows much more moderate degeneration and suppression of recombination. Thus the papaya system appears to be the most recently evolved XY system known to date, offering potential insights into the question of how evolution of the sex chromosome began. Unraveling plant sex determination processes will have direct applications in production of crop plants such as papaya, asparagus, spinach, black pepper, yam, and pistachio. This project seeks to explore the nature of incipient sex chromosomes. The papaya MSY and the corresponding X-specific region will be sequenced and characterized. To estimate the antiquity of the non-recombining region, the extent of divergence of X and Y gene pairs along the region will be calculated, giving special attention to candidate gene(s) for sex determination. Comparing the X and Y DNA sequences and their surroundings will reveal types and extent of chromosomal rearrangements and the role of transposable elements in the degeneration of MSY. The relative position of MSY to the centromere of the primitive Y chromosome will be clarified by pachytene and fiber Fluorescent In Situ Hybridization (FISH) analyses. It is expected that this project will generate candidate genes for sex determination and embryo lethality for the papaya research community.Access to project outcomesDNA sequence data and trace files will be deposited in GenBank, and project data made available at the websites of Hawaii Agriculture Research Center (http://www.hawaiiag.org/harc) and University of Georgia (http://www.plantgenome.uga.edu/). Bacterial Artificial Chromosome (BAC) clones will be distributed by the Plant Genome Mapping Laboratory at the University of Georgia and also deposited in a public BAC distribution center.