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人族各支系基因组的染色体结构性差异

本帖最后由 Ryan 于 2013-7-18 13:47 编辑

为考虑人族内的 生殖隔离问题,开一个资料收集贴。
人类基因组计划的研究结果在测序的水平上证实,人类第2号染色体是由古猿的两个染色体融合而来的,这点证实了人类与黑猩猩的同源性。
本帖最后由 Ryan 于 2013-7-18 13:45 编辑

PLoS Genet 1(4): e56. doi:10.1371/journal.pgen.0010056

Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies
Lars Feuk,Jeffrey R MacDonald,Terence Tang,  Andrew R Carson,Martin Li,Girish Rao, Razi Khaja,Stephen W Scherer

Abstract

With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans. The goal of this study was to investigate chromosomal regions that are inverted between the chimpanzee and human genomes. Using the net alignments for the builds of the human and chimpanzee genome assemblies, we identified a total of 1,576 putative regions of inverted orientation, covering more than 154 mega-bases of DNA. The DNA segments are distributed throughout the genome and range from 23 base pairs to 62 mega-bases in length. For the 66 inversions more than 25 kilobases (kb) in length, 75% were flanked on one or both sides by (often unrelated) segmental duplications. Using PCR and fluorescence in situ hybridization we experimentally validated 23 of 27 (85%) semi-randomly chosen regions; the largest novel inversion confirmed was 4.3 mega-bases at human Chromosome 7p14. Gorilla was used as an out-group to assign ancestral status to the variants. All experimentally validated inversion regions were then assayed against a panel of human samples and three of the 23 (13%) regions were found to be polymorphic in the human genome. These polymorphic inversions include 730 kb (at 7p22), 13 kb (at 7q11), and 1 kb (at 16q24) fragments with a 5%, 30%, and 48% minor allele frequency, respectively. Our results suggest that inversions are an important source of variation in primate genome evolution. The finding of at least three novel inversion polymorphisms in humans indicates this type of structural variation may be a more common feature of our genome than previously realized.

生物通的报道:
http://www.ebiotrade.com/newsf/2005-11/200511393031.htm


来自HHMI霍德华休斯医学院的研究人员通过比较人类和人类血缘最近的“亲戚”—黑猩猩的基因组发现基因倒位现象(inversions)并不如科学家之前所认为的那么少见,这也许解释了这两个物种之间的许多进化之谜,也为人类疾病发生找到了部分根源。这一研究成果公布在10月28号的美国科学公共图书馆遗传学版上(Public Library of Science Genetics ,PLoS Genetics)。

基因倒位(inversions)是指染色体在两个点发生断裂后,产生三个区段,中间的区段发生180度的倒转,与另外两个区段重新接合而引起变异的现象。倒位杂合体形成的配子大多是异常的,从而影响了个体的育性。倒位纯合体通常也不能和原种个体间进行有性生殖,但是这样形成的生殖隔离,为新物种的进化提供了有利条件。例如,普通果蝇的第3号染色体上有三个基因按猩红眼—桃色眼—三角翅脉的顺序排列(St—P—Dl);同是这三个基因,在另一种果蝇中的顺序是St—Dl—P,仅仅这一倒位的差异便构成了两个物种之间的差别。

虽然人类和黑猩猩在6百万年以前就分别朝着不同的方向进化了,但是这两种物种在DNA水平上有将近98%的相似性。利用今年公布的黑猩猩基因组序列,研究人员比较了人类和黑猩猩染色体上的大区域结构变化,尤其是基因倒置现象,结果分析得到了这两个物种间1,576个假定的基因倒置区,其中有33个区域跨度很大—超过100,000个bp。而且通过进一步将黑猩猩与大猩猩(gorilla)基因组比对,发现有效倒置现象中有一半在人类进化历程中时常会翻个筋斗,掉转过来或者过去。

更加吸引科学家的是在这一研究中发现了一个倒位簇的多态性--这意味着人类仍然在进化:通过对23个经实验验证的倒位点的分析,研究人员发现一些人群有两个等位基因或者说基因配对子倒位,而其他人则有一个人类等位基因倒位和一个猩猩正常序列的等位基因。而有趣的是在这个倒位簇上检测到了一个结肠癌基因,这也就是说有可能个体倒位点的进化增加了患上结肠癌的风险。不过这一结论仍需要更多的实验验证。

(生物通记者:张迪)
本帖最后由 Ryan 于 2013-7-17 22:49 编辑

PLoS ONE 7(7): e40224. doi:10.1371/journal.pone.0040224

Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis
Jianzhong Ma mail,   Christopher I. Amos

Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1:1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.
本帖最后由 Ryan 于 2013-7-18 13:29 编辑

Genome Biol. 2007;8(10):R230.

On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

Marques-Bonet T, Sànchez-Ruiz J, Armengol L, Khaja R, Bertranpetit J, Lopez-Bigas N, Rocchi M, Gazave E, Navarro A.
SourceUnitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Catalonia, Spain. tomas.marques@upf.edu

Abstract

BACKGROUND:
     The role that chromosomal rearrangements might have played in the speciation processes that have separated the lineages of humans and chimpanzees has recently come into the spotlight. To date, however, results are contradictory. Here we revisit this issue by making use of the available human and chimpanzee genome sequence to study the relationship between chromosomal rearrangements and rates of DNA sequence evolution.

RESULTS:
     Contrary to previous findings for this pair of species, we show that genes located in the rearranged chromosomes that differentiate the genomes of humans and chimpanzees, especially genes within rearrangements themselves, present lower divergence than genes elsewhere in the genome. Still, there are considerable differences between individual chromosomes. Chromosome 4, in particular, presents higher divergence in genes located within its rearrangement.

CONCLUSION:
     A first conclusion of our analysis is that divergence is lower for genes located in rearranged chromosomes than for those in colinear chromosomes. We also report that non-coding regions within rearranged regions tend to have lower divergence than non-coding regions outside them. These results suggest an association between chromosomal rearrangements and lower non-coding divergence that has not been reported before, even if some chromosomes do not follow this trend and could be potentially associated with a speciation episode. In summary, without excluding it, our results suggest that chromosomal speciation has not been common along the human and chimpanzee lineage.

http://genomebiology.com/content/8/10/R230

转自《科学时报》的报道:

http://www.biosino.org/news-2003/200308/03080410.htm

人类和黑猩猩之所以成为不同的物种是由于生活的地理环境隔绝而导致的,一般的教科书都持上述观点。然而,现在有科学家对此提出了异议。一支研究队伍通过比较人类和黑猩猩的DNA,得出结论认为人类和黑猩猩的区别在于染色体内在的区别,而不是仅仅由于非洲大草原的地理隔离。
  该研究有力地支持了这样一种理论,即人类祖先的染色体在复制时偶然发生了重排,并且这种重排最终导致了远古人类与远古猩猩之间遗传上的“不可交换”区域。虽然远古人类和远古猩猩之间有可能还可以杂交,并且互补染色体部分也可能交换基因,但是在非互补区之内具有突出优点的任何突变都只能保留在一个物种中而不能互换。
  位于巴塞罗那的珀姆派·法布瑞大学的阿萨迪·那维若说:“这种现象最终导致了那些区域不可交换,因此它们成为分离基因的最佳区域。”他与艾丁堡大学的尼克·巴藤一起分析了相关的DNA。
  上述发现的含义是重大的。首先,这意味着人类和黑猩猩的分化过程比以前所认为的要缓慢得多。与地理隔绝所造成的快速分离完全不同的是,人类和黑猩猩的共同祖先能够彼此杂交一直到它们的染色体不再互补为止
  其次,更具挑战性的一点是,它意味着这两个物种的共同祖先虽然生活在同一块土地上,但是却逐渐演化成了截然不同的物种。伦敦自然历史博物馆的克里斯托福·索利根说:“这就解释了人类学中数据和地点的分歧。它意味着人类和黑猩猩有着比我们原先所想象的要长得多的杂交期。”
  与黑猩猩相比,人类染色体中有10条染色体进行了不同的重排。其中有9条发生了中心粒倒位——即着丝粒周围的两个大染色体片段发生了互换。并且第10条染色体是由两条小染色体融合而成,但是在黑猩猩中这两条染色体仍是分离的。
  那维若和巴藤比较了115个基因的DNA,其中一半来自人类和黑猩猩不同的重排染色体区域,而另一半来自它们染色体相同的区域。虽然这两个区域中基因突变的概率是相同的,但是科学家们发现突变在重排区域中的保留率要高出两倍。换句话说,重排区域成为有用突变的避难所,使之能够维持并发展下去,成为不同物种发展的遗传动力。那维若说:“它们有可能就是那些使两个物种变得不互补并不再能杂交的基因。”
  其它研究人员在探索染色体隔绝作为不同物种发展的证据时未能成功。那维若认为这是由于他们错误地认为染色体重排要么是致命的,要么就会导致不育。然而事实上,在果蝇和向日葵中的实验表明,具有重排染色体的个体不仅能够生存,而且还能够将此特性遗传下去。
  染色体的分歧最终导致两者的基因不能交换,并使它们成为完全分离的两个物种。索利根说:“上述发现首次对在没有地理隔绝的情况下发生的物种分离现象给出了一个比较合理的解释。”
本帖最后由 Ryan 于 2013-7-18 13:22 编辑

动物学研究 2012, 33(1) 108-118 DOI:   10.3724/SP.J.1141.2012.01108   
灵长类比较基因组学的研究进展

廖承红1, 宿兵2

1. 海南大学 农学院, 海口 570288;
2. 中国科学院昆明动物研究所 遗传资源与进化国家重点实验室, 昆明 650223

摘要:
随着人类和黑猩猩全基因组测序工作宣布完成, 以及其他灵长类基因组测序工作的逐步开展, 目前已经积累了大量的灵长类基因组数据, 一个崭新的研究领域——灵长类比较基因组学应运而生。该文主要通过对人类和其他非人灵长类系统关系和基因组结构的比较, 从系统进化、基因组结构和基因表达调控等方面评述该领域的研究进展, 阐述人类、黑猩猩与其他非人灵长类之间的主要生物学差异, 揭示人类进化的生物学机制。


关键词: 灵长类   比较基因组   进化

http://www.zoores.ac.cn/CN/abstract/abstract3108.shtml#

PDF全文:http://www.bioline.org.br/request?zr12018
我觉得长臂猿和人类特别是M168-L3 系的主流人群的脸型颅型最接近,是否测过他们的基因?
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