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.

估计有数百万未发现或未描述的物种，迫切需要提高科学家发现物种能力的新技术。认识到生物多样性不仅对比较生物学很重要，而且还因为它为与生物学有关的各种应用学科提供了重要的决策框架，如农业、生物修复、生物物理学、生物医学等。本研究提出了一种新的，广泛适用的方法来识别物种使用地面甲虫（属Bembidion）作为模式。初步数据显示，这组物种在基因组结构的某些方面可能存在很大差异，尽管它们非常接近。基因组结构的这些差异通过用现代测序技术检查一组基因（核糖体DNA（rDNA）基因）来揭示。这种对“rDNA指纹”的分析成本很低，并且有可能比传统方法更有效地帮助发现新物种。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。将通过低覆盖率Illumina测序对更多标本进行分析，并将rDNA指纹模式与建立在五个基因树和形态分析基础上的现有物种概念进行比较，从而验证rDNA指纹作为物种划界工具的用途。rDNA指纹在更广泛的一组步甲的变化程度将探讨使用实时PCR检测，然后通过额外的测序相关标本。最后，rDNA顺反子内的拷贝数膨胀的机制将通过比较荧光原位杂交（FISH）进行探讨，以测试的假设，即许多拷贝的rDNA片段已被转移到异染色质DNA的边界附近的常染色质。