Genomics of Comparative Seed Evolution.

这个项目的目的是利用基因发现的目的，利用大自然修补生物多样性植物物种基因组的机制，使重要的经济性状（如种子）得以进化。这种方法涉及到在物种进化、基因组学和生物信息学等不同专业领域的科学家的独特合作，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。该方法包括鉴定一个性状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域进行测序。下一步是开发和使用生物信息学工具，使在一组物种中保存的大量基因能够相互比较，这些物种具有相互比较的特征，并与它们最接近的不具有该特征的物种进行比较。这种方法能够鉴定出DNA历史与含有该性状的物种的进化相关的基因和基因特征。然后，通过生物多样性物种的基因表达比较研究以及拟南芥等模式物种的突变分析，测试候选基因在决定性状中的作用。这种方法的一个有效的例子是识别使种子进化的一组基因，这是植物进化中的一项重要创新，对农业具有重要意义。这涉及到对中生代以来地球上现存的最原始种子植物——不开花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，同时揭示了与种子发育有关的重要农艺性状相关的基因。这一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——很大程度上依赖于种子产品。这个项目也有系统学家和基因组学家共同努力，在这两个互补的领域培养具有跨学科专业知识的新一类生物学家。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，植物或动物的比较功能基因组研究。

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.