RaMP: Collaborative: From genome assembly to genomic novelty to phenotype: an integrated training framework

整个生命之树的全基因组测序表明，新基因在进化过程中频繁出现。然而，相对而言，人们对这些基因在新表型衍生中的功能或进化重要性知之甚少。该项目将招募学士学位后的学员参与一个队列项目，描述尚未得到充分研究的物种的基因组，并在这些基因组中识别潜在的新基因。此外，学员将在实验室网络中参与个人项目，以表征新基因组元件的功能及其与不同分类群新性状的潜在联系。这些研究项目将促进分子生物学和计算生物学的综合研究机会。该项目将支持培训30名不同的本科后学员，为未来在STEM领域取得成功提供支持，这些学员来自生物学领域代表性不足的群体。该计划的组成部分是更广泛的影响，包括对pi和联合导师进行导师培训；培训、指导和社交机会；关于基因组的公共宣传；以及跨部门、机构和行业的联系。生物学的一个主要挑战是确定基因组中编码的信息如何产生个体表型，以及这些信息的差异如何导致独特的表型结果。比较基因组研究发现了一个高度保守的发育基因“工具包”，它早于主要进化支的多样化。形态新颖性产生的一种方式是通过对这些古老工具箱基因的调节修补。最近，比较研究已经确定了大量新的“分类限制基因”，这可能在表型新颖性的起源中也很重要。基因组新颖性在不同分类群和生物学不同子领域的功能表征将成为一个新的学士学位后研究培训计划的智力焦点。个别研究项目将解决有关不同分类群中新基因功能的具体问题。总的来说，这些项目解决了关于新基因在进化和发展中的作用的更广泛的问题。基因组的测序、组装和注释将与区域伙伴机构的研究人员合作完成。该项目将有助于建立跨机构的研究网络，为学员提供生物信息学培训，并传播基因组学培训材料。培训计划将部署个性化的指导网络、队列培训研讨会、专业发展和网络机会，以及与pi、导师、同行和近同行的互动，以帮助受训者确定并实现他们的职业目标。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Whole genome sequencing across the tree of life has shown that new genes arise frequently in evolution. However, relatively little is known about the function or evolutionary importance of these genes in the derivation of novel phenotypes. This project will recruit postbaccalaureate trainees to engage in a cohort project to describe the genomes of species that are not well studied and to identify potentially new genes in these genomes. In addition, trainees will engage in individual projects in a network of labs to characterize the function of novel genomic elements and their potential links to new traits in diverse taxa. These research projects will promote integrated research opportunities in molecular and computational biology. The program will support the training of a diverse set of 30 postbaccalaureate mentees, enriched for members from groups underrepresented in biology, for future success in STEM. Integral to the program are the broader impacts that include mentor training for PIs and co-mentors; training, mentoring, and networking opportunities; public outreach about genomes; and connections across departments, institutions, and industry. A major challenge in biology is determining how information encoded in the genome generates individual phenotypes and thus how differences in that information lead to unique phenotypic outcomes. Comparative genomic studies identified a highly conserved ‘toolkit’ of developmental genes that predates the diversification of major clades. One way that morphological novelty originates is through regulatory tinkering with these ancient toolkit genes. More recently, comparative studies have identified a profusion of new ‘taxon-restricted genes,’ which may also be important in the origin of phenotypic novelty. The functional characterization of genomic novelty in diverse taxa and diverse subfields of biology will be leveraged as the intellectual focal point for a new postbaccalaureate research training program. Individual research projects will address specific questions about the function of new genes in diverse taxa. Collectively, these projects address broader question about the role of new genes in evolution and development. Sequencing, assembly, and annotation of genomes will be done in collaboration with researchers at regional partner institutions. This project will help build a cross-institutional research network, provide trainees with bioinformatics training, and disseminate training materials for genomics. The training program will deploy individualized mentoring networks, cohort training workshops, professional development and networking opportunities, and interactions with PIs, mentors, peers and near-peers to help trainees identify and meet their professional goals.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.