Evolutionary Genomics of Supersized Mitochondrial Genomes

超大线粒体基因组的进化基因组学

• 批准号: 7479188
• 负责人: ANDREW J ALVERSON
• 金额: $ 4.96万
• 依托单位: TRUSTEES OF INDIANA UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-07-20 至 2010-07-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7479188
• 关键词: Address; Angiosperms; Animals; Bacterial Genome; Binding Sites; Bioinformatics; Chloroplast DNA; Chloroplasts; Cucumber; Cucurbitaceae; DNA; Data; Disease; Environment; Eukaryota; Eukaryotic Cell; Event; Evolution; Family; Figs - dietary; Fostering; Genes; Genetic Processes; Genetic Recombination; Genome; Genomics; Genus Cucumis; Goals; Growth; Horizontal Gene Transfer; Human; Initiator Codon; Intergenic DNA; Intergenic Sequence; Introns; Laboratories; Mission; Mitochondria; Mitochondrial DNA; Morphologic artifacts; Mutation; Nuclear; Nucleotides; Numbers; Pattern; Phylogenetic Analysis; Plants; Population; Process; Production; Property; RNA Splicing; Range; Rate; Restriction fragment length polymorphism; Sampling; Series; Source; Squash; Structure; Technology; Testing; Time; United States National Institutes of Health; Variant; Watermelon; Work; age related; comparative; driving force; genome sequencing; insight; knowledge base; mitochondrial DNA mutation; mitochondrial genome; plant growth/development; pressure; size; theories; transcription factor

DESCRIPTION (provided by applicant): Plant mitochondrial genomes are extremely large and variably sized (200-2,400 kb) compared to other eukaryotes (typically 15-60 kb). Remarkably, most of the inordinate size range in plants is encompassed by a single family, the Cucurbitaceae, whose mitochondrial genomes vary in size from 330 to 2,400 kb. One common and frustrating theme in plant mitochondrial genomics is that the overwhelming majority of size variation is due to large amounts of intergenic DNA with no identifiable homology to known sequences. This is also true in cucurbits, where 65-87% of the mitochondrial DNA (mtDNA) is of unknown origin. Discovering the source of these enigmatic sequences is one of the major challenges in mitochondrial genomics and represents a primary goal of this project. Beyond identifying the source of these sequences, a further goal is to identify the general processes facilitating the growth of plant mitochondrial genomes. A recent study proposed that similar population genetic processes govern the evolution of nuclear and organellar genome size and concluded that the disparity in mitochondrial genome size between plants and animals reflects their drastically different mitochondriaI mutation rates. That is, the vast amounts of noncoding sequence in plant mitochondrial genomes owe to the near-universally low mutation rate observed in plant mtDNA. By extension, the largest cucurbit mitochondrial genomes are predicted to have the lowest nucleotide substitution rates. Data from this project will provide the first empirical test of this hypothesis. The Cucurbitaceae offer an exciting opportunity both to address longstanding problems in plant mitochondrial genomics and to test provocative new hypotheses on genome evolution in the broad sense. I propose to fully sequence the mitochondrial genomes for 6-10 cucurbit plants and use a complementary set of experimental and bioinformatic approaches to test explicit hypotheses about the expansion and contraction of these exceptional mitochondrial genomes. In addition to forwarding the NIH mission to foster creative scientific discovery and expand our basic scientific knowledge base, this project has broader significance to the field of mitochondrial genomics. In humans, mitochondrial DNA mutations retard energy production and contribute to a number of age-related diseases. These mtDNA mutations accumulate 50- 100 faster in animals than in plants! Therefore, a full understanding of this disparity could benefit our understanding of age-related disease and illness. Comparative genomic studies like this one provide a powerful and efficient way to characterize "enviable" genomic properties (i.e., the extraordinarily low nucleotide substitution rate of plants) and identify the processes that underlie them.

描述（由申请人提供）：与其他真核生物（通常为15-60 kb）相比，植物线粒体基因组非常大且大小不一（200- 2，400 kb）。值得注意的是，植物中大部分的过度大小范围都包含在一个单一的家族中，葫芦科，其线粒体基因组的大小从330到2,400 kb不等。植物线粒体基因组学中一个常见且令人沮丧的主题是，绝大多数大小变异是由于大量的基因间DNA与已知序列没有可识别的同源性。瓜类也是如此，其中65-87%的线粒体DNA（mtDNA）来源不明。发现这些神秘序列的来源是线粒体基因组学的主要挑战之一，也是该项目的主要目标。除了确定这些序列的来源之外，另一个目标是确定促进植物线粒体基因组生长的一般过程。最近的一项研究提出，类似的群体遗传过程控制着细胞核和细胞器基因组大小的进化，并得出结论，植物和动物之间线粒体基因组大小的差异反映了它们截然不同的线粒体突变率。也就是说，植物线粒体基因组中大量的非编码序列归因于在植物mtDNA中观察到的几乎普遍的低突变率。通过扩展，预测最大的葫芦科线粒体基因组具有最低的核苷酸取代率。来自该项目的数据将为这一假设提供第一个实证检验。葫芦科提供了一个令人兴奋的机会，既解决长期存在的问题，植物线粒体基因组学和测试挑衅性的新假设基因组进化的广义。我建议对6-10种葫芦科植物的线粒体基因组进行完全测序，并使用一组互补的实验和生物信息学方法来测试关于这些特殊线粒体基因组的扩展和收缩的明确假设。除了推进NIH的使命，以促进创造性的科学发现和扩大我们的基础科学知识基础，该项目具有更广泛的意义，线粒体基因组学领域。在人类中，线粒体DNA突变会阻碍能量的产生，并导致许多与年龄有关的疾病。这些mtDNA突变在动物中的积累速度比在植物中快50- 100倍！因此，充分了解这种差异有助于我们了解与年龄有关的疾病和疾病。像这样的比较基因组研究提供了一种强大而有效的方法来表征“令人羡慕的”基因组特性（即，植物中极低的核苷酸替换率），并确定它们背后的过程。