Nuclear integrations of mitochondrial DNA in great apes

类人猿线粒体 DNA 的核整合

• 批准号: 7254610
• 负责人: NICOLA M ANTHONY
• 金额: $ 22.47万
• 依托单位: UNIVERSITY OF NEW ORLEANS
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-04-01 至 2011-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7254610
• 关键词: Acute; Address; African; Bacterial Artificial Chromosomes; Bacteriophages; Blast Cell; Cell Nucleus; Classification; DNA; DNA Databases; DNA Sequence; DNA Sequence Databases; Data; Databases; Diagnosis; Diagnostic; Eukaryota; Eukaryotic Cell; Evaluation; Event; Evolution; Frequencies; Future; Gene Duplication; Generations; Genes; Genetic Markers; Genetic Polymorphism; Genetic Recombination; Genetic Variation; Genome; Genomic Instability; Genomic Library; Genomics; Gorilla gorilla; Hand; Hereditary Disease; High Prevalence; Hominidae; Human; In Vitro; Lead; Left; Libraries; Location; Maps; Mitochondria; Mitochondrial DNA; Mitochondrial Diseases; Molecular; Nuclear; Nucleotides; Pan Genus; Pan troglodytes; Paper; Pattern; Phase; Phylogenetic Analysis; Phylogeny; Plant Roots; Pongidae; Population; Population Genetics; Prevalence; Purpose; Rate; Recording of previous events; Relative (related person); Research; Site; Sorting - Cell Movement; Sperm Head; Surveys; Taxon; Taxonomy; Time; Transcript; Work; base; comparative; design; genome database; insight; mitochondrial genome; tool

DESCRIPTION (provided by applicant): - This is a proposal to examine Numts (mtDNA genes translocated to the nucleus) in humans and great apes. It will involve blast searches for hypervariable 1 gene (HV1) from mtDNA transcripts, inserted into nuclear genomes. These have elevated frequencies in gorillas, and hundreds have been described for humans. The fact that there is recombination even in vitro suggests that the phenomenon may not be all that rare. First, the strategy is (1) to screen Numts from chimpanzee and gorilla BAC libraries for nuclear insertions, as well as to search nuclear-enriched DNA phage libraries from sperm heads from several chimpanzees and gorillas. Then, these sequences will be compared with the pre-existing BLAST surveys of those species. Human Numts will be drawn from BLAST searches. Te comparative work is motivated by four questions: (a) Are HV1 integrants elevated in gorillas? (b) Is the rate of integration constant over time, or are there phylogenetic bursts? (c) Do rates of nucleotide evolution differ for mitochondrial and nuclear-integrated copies? (d) How well do the Numts match up with the classic gorilla subspecific taxonomy. Second, the idea is to map the insertion sites, using nuclear flanking sequences and mtDNA break sites for identification, and to determine whether there has been subsequent gene duplication in the nucleus, addressing three questions: (a) Are the sites of integration random, or are they sequence-regular? (b) What is the fraction of post-integration duplication? (c) Are there specific sequence motifs that are particularly prone to mobilization or to insertion? Third, an attempt will be made to use the Numts to reconstruct gorilla population history, since there are a great many in hand from the 1st phase of the study, addressing two questions: (a) Can we use polymorphic Numts to reconstruct gorilla population history? (b) Are the major gorilla subspecific clades evident in the HV1 data in the mitochondrion also evident in the Numts? The basic intent is twofold: (a) to explore the sorts of inferential difficulty caused by our inability to detect Numts in previous work, and (b) to determine the extent to which they can used to advantage for taxonomic or population genetic purposes.

描述（由申请人提供）：-这是一个研究人类和类人猿Numts（线粒体DNA基因易位到细胞核）的建议。它将涉及从mtDNA转录本中快速搜索插入核基因组的高变1基因（HV 1）。这些在大猩猩中的频率升高，并且已经描述了数百种人类。事实上，即使在体外也存在重组，这表明这种现象可能并不罕见。首先，策略是（1）从黑猩猩和大猩猩BAC文库中筛选用于核插入的Numt，以及从几种黑猩猩和大猩猩的精子头中搜索核富集的DNA噬菌体文库。然后，将这些序列与这些物种的预先存在的BLAST调查进行比较。将从BLAST检索中提取人类Numt。比较工作的动机是四个问题：（a）HV 1整合体在大猩猩中升高？(b)整合的速率是随时间而恒定的，还是存在系统发育的爆发？(c)线粒体和核整合拷贝的核苷酸进化速率不同吗？(d)Numts与经典的大猩猩亚种分类学的匹配程度如何？其次，我们的想法是绘制插入位点，使用核侧翼序列和mtDNA断裂位点进行鉴定，并确定是否有随后的基因复制在核中，解决三个问题：（a）整合位点是随机的，还是它们是序列规则的？(b)整合后重复的比例是多少？(c)是否有特定的序列基序特别倾向于移动或插入？第三，将尝试使用Numts重建大猩猩的人口历史，因为有很多手从第一阶段的研究，解决两个问题：（一）我们可以使用多态Numts重建大猩猩的人口历史？(b)大猩猩亚种的主要分支在HV 1数据中是明显的吗？基本意图有两个方面：（a）探索我们在以前的工作中无法检测到Numts而导致的各种推理困难，（B）确定它们在分类学或种群遗传学目的中的优势程度。

项目成果

A comparative approach shows differences in patterns of numt insertion during hominoid evolution.

• DOI: 10.1007/s00239-009-9243-4
• 发表时间: 2009-06
• 期刊: JOURNAL OF MOLECULAR EVOLUTION
• 影响因子: 3.9
• 作者: Jensen-Seaman, M. I.;Wildschutte, J. H.;Soto-Calderon, I. D.;Anthony, N. M.
• 通讯作者: Anthony, N. M.

Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.

• DOI: 10.1016/j.ympev.2014.08.018
• 发表时间: 2014-12
• 期刊: MOLECULAR PHYLOGENETICS AND EVOLUTION
• 影响因子: 4.1
• 作者: Dario Soto-Calderon, Ivan;Clark, Nicholas Jonathan;Wildschutte, Julia Vera Halo;DiMattio, Kelly;Jensen-Seaman, Michael Ignatius;Anthony, Nicola Mary
• 通讯作者: Anthony, Nicola Mary

Factors affecting the relative abundance of nuclear copies of mitochondrial DNA (numts) in hominoids.

影响类人猿线粒体 DNA (numts) 核拷贝相对丰度的因素。

• DOI: 10.1007/s00239-012-9519-y
• 发表时间: 2012
• 期刊: Journal of molecular evolution
• 影响因子: 3.9
• 作者: Soto-Calderon,ID;Lee,EJ;Jensen-Seaman,MI;Anthony,NM
• 通讯作者: Anthony,NM

Admixture between historically isolated mitochondrial lineages in captive Western gorillas: recommendations for future management.

圈养西方大猩猩历史上分离的线粒体谱系之间的混合：未来管理的建议。

• DOI: 10.1093/jhered/esv006
• 发表时间: 2015
• 期刊: The Journal of heredity
• 作者: Soto-Calderón,IvánD;Dew,JLarry;Bergl,RichardA;Jensen-Seaman,MichaelI;Anthony,NicolaM
• 通讯作者: Anthony,NicolaM