Genomics of Comparative Seed Evolution.

该项目旨在为基因发现目的探索自然对生物多样性植物物种的基因组进行修补的机制，以使种子等重要经济性状得以进化。 这种方法涉及到科学家的独特合作，这些科学家在物种进化、基因组学和生物信息学方面具有不同领域的专业知识，他们位于纽约的姐妹机构：纽约大学、纽约植物园、美国自然历史博物馆和冷泉港实验室。该方法包括鉴定一种特征首先进化的关键植物物种，以及随后对这些基因组的大部分编码区进行测序。 下一步是开发和使用生物信息学工具，使大量的基因保守的一组物种之间的相互比较，并与他们最接近的物种谁不具有该性状的性状进行比较。 这种方法使得能够鉴定其DNA历史与包含该性状的物种的进化相关的基因和基因性状。候选基因，然后测试它们的作用，在确定性状的生物多样性物种的基因表达的比较研究，并在模式物种，如拟南芥突变分析。 这种方法的工作例子是识别使种子进化成为可能的基因组，这是植物中一项重要的进化创新，对农业具有重要意义。 这涉及到对地球上自中生代以来最原始的种子植物（不开花的裸子植物）的部分基因组进行测序。 这项研究超越并结合了基因组学和系统学，对种子进化有了更深入的了解，同时揭示了参与种子发育的重要农艺性状的基因。这些发现将对提高种子质量产生影响，因为今天的农业-从食品到纺织品-都依赖于种子产品。 该项目也有系统学家和基因组学家共同努力，培养一批新的生物学家，他们在这两个互补领域拥有跨学科的专业知识。 最后，本项目开发的方法和生物信息学工具将适用于任何物种、植物或动物的功能基因组比较研究。

This project aims to exploit for gene discovery purposes the mechanisms by which nature has tinkered with the genomes of biodiverse plant species to enable the evolution of important economic traits, such as seeds. This approach involves a unique collaboration of scientists with diverse areas of expertise in species evolution, genomics and bioinformatics located at sister institutions in New York: New York University, The New York Botanical Garden, The American Museum of Natural History, and Cold Spring Harbor Laboratories. The approach involves the identification of key plant species in which a trait first evolved and the subsequent sequencing of large portions of the coding regions of these genomes. The next step is to develop and use bioinformatics tools that enable the comparison of large numbers of genes conserved across a set of species which have the trait compared to each other and to their closest related species who do not have the trait. This approach enables the identification of genes and gene characters whose DNA history correlates with the evolution of the species containing the trait. The candidate genes are then tested for their role in determining the trait using comparative studies of gene expression in the biodiverse species, and by mutant analysis in model species such as Arabidopsis. The working example of this approach is to identify the sets of genes that enabled the evolution of seeds, an important evolutionary innovation in plants with important implications for agriculture. This involves the sequencing of portions of the genomes of the most primitive living seed plants, the non-flowering Gymnosperms, on earth since the Mesozoic era. This research transcends and unites genomics and systematics to produce a deeper understanding of seed evolution, while revealing genes involved in important agronomic traits involved in seed development. The findings will have implications for improving seed quality, as much of today's agriculture - from food to textiles- depends on seed products. This project also has systematicists and genomicists working together to train a new class of biologists with interdisciplinary expertise in these two complementary areas. Finally, the approaches and bioinformatics tools developed in this project will be applicable to comparative functional genomic studies in any species, plant or animal.