DISSERTATION RESEARCH: Genomic architecture as a species delimitation tool: validating a novel approach using rDNA variation for discovering species boundaries in ground beetles.

论文研究：基因组结构作为物种界定工具：验证使用 rDNA 变异发现地面甲虫物种边界的新方法。

• 批准号: 1702080
• 负责人: David Maddison
• 金额: $ 1.66万
• 依托单位: Oregon State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-05-01 至 2018-10-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1702080&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Genomic; architecture; species

With millions of undiscovered or undescribed species estimated, new techniques that increase scientists' ability to discover species is urgently needed. Recognizing biodiversity is important not only for comparative biology, but also because it provides an important decision-making framework for very diverse applied disciplines related to biology, such as agriculture, bioremediation, biophysics, biomedicine (among others). This research proposes to develop a new, widely applicable approach to identifying species using ground beetles (genus Bembidion) as a model. Preliminary data show that species in this group can have large differences in some aspects of the structure of their genomes despite being very closely related. These differences in genome structure are revealed by examining a set of genes (ribosomal DNA (rDNA) genes) with modern sequencing techniques. This analysis of 'rDNA fingerprints' costs little to obtain and has potential to help discover new species more efficiently than more traditionally used methods. Results from this research will be used for training opportunities for undergraduate students, as well as a community outreach project involving high school students. The use of rDNA fingerprints as a species delimitation tool will be validated by profiling additional specimens through low-coverage Illumina sequencing and comparing patterns in rDNA fingerprints to existing species concepts that are built on five gene trees and morphological analysis. The extent of variation in rDNA fingerprints across a wider group of carabid beetles will be explored using a real-time PCR assay followed by additional sequencing of relevant specimens. Finally, the mechanism of copy number inflation within the rDNA cistron will be explored through comparative fluorescent in situ hybridization (FISH), to test the hypothesis that many copies of fragments of rDNA have been transferred to heterochromatic DNA near its boundary with euchromatin.

由于估计数以百万计的未被发现或未描述的物种，因此迫切需要提高科学家发现物种能力的新技术。认识生物多样性不仅对比较生物学也很重要，还因为它为与生物学相关的非常多样化的应用学科提供了重要的决策框架，例如农业，生物修复，生物物理学，生物医学（以及其他）。这项研究建议开发一种新的，广泛的方法，用于使用甲虫（bembidion属）作为模型来识别物种。初步数据表明，尽管密切相关，但该组中的物种在其基因组结构的某些方面可能存在很大差异。通过检查一组具有现代测序技术的基因（核糖体DNA（rDNA）基因），可以揭示基因组结构上的这些差异。对“ rDNA指纹”的分析几乎没有花费，并且具有比传统上使用的方法更有效地发现新物种的潜力。这项研究的结果将用于本科生的培训机会，以及涉及高中生的社区外展项目。将rDNA指纹用作物种划界工具的使用将通过通过低覆盖的Illumina测序分析其他标本来验证，并将rDNA指纹中的模式与五个基因树建立的现有物种概念和形态分析进行比较。将使用实时PCR测定法探索更广泛的甲壳虫甲虫的rDNA指纹变化程度，然后再进行相关标本的其他测序。最后，将通过比较的荧光原位杂交（FISH）探索rDNA cistron内部拷贝数膨胀的机理，以检验以下假设：rDNA片段的许多副本已转移到与正染色素边界附近的异质DNA中。