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首页> 外文学位 >Assembly and analysis of an Sp185/333 gene cluster from the purple sea urchin: Putative evidence for microsatellite-mediated gene and segmental duplication.
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Assembly and analysis of an Sp185/333 gene cluster from the purple sea urchin: Putative evidence for microsatellite-mediated gene and segmental duplication.

机译：紫海胆Sp185 / 333基因簇的组装和分析：微卫星介导的基因和节段重复的公认证据。

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摘要

Recent studies have shown that the immune system of the sea urchin, Strongylocentrotus purpuratus, is more complex than previously thought. Exemplifying this is the Sp185/333 gene family, which is upregulated in immunologically challenged animals. The Sp185/333 genes are small (2kb) with two exons and are members of a large diverse family composed of greater than 40 genes. The current S. purpuratus genome (v2.1), however, contains only six Sp185/333 genes. This underrepresentation could be due to the difficulties that large gene families present in shotgun assembly, where multiple similar genes can be collapsed into a single consensus gene. Therefore, to understand the genomic spatial organization of the Sp185/333 gene family, a BAC containing Sp185/333 genes was assembled, paying careful attention to artifacts that may result from very similar genes. Twelve candidate BAC assemblies were generated with varying parameters to account for potential gene collapse or artificial duplication/expansion. PCR, restriction digests, and subclone sequencing were used to identify and validate the optimal assembly. The validated assembly contained six Sp185/333 genes ranging in size from 1.3 to 1.8 kb. These genes were clustered in a 34 kb region at one end of the BAC with five of the six genes tightly clustered within 20 kb. The Sp185/333 genes in this cluster were no more similar to each other than to previously sequenced Sp185/333 genes isolated from three different animals. This was unexpected given their proximity and putative effects of gene homogenization in closely linked, similar genes. All six genes displayed significant similarity including both 5' and 3' flanking regions, which were bounded by microsatellites. Three of the Sp185/333 genes and their flanking regions were tandemly duplicated such that each repeated segment consisted of a gene plus 0.7 kb 5' and 2.4 kb 3' of the gene (4.5 kb total). Both edges of the segmental duplications were characterized by the presence of microsatellites. The three genes not associated with the tandem duplication displayed smaller conserved flanking regions ranging from 400 to 600 nt 5' and 400 nt 3' of each gene. The high sequence similarity of the Sp185/333 genes and flanking regions, suggests that the microsatellites promote genomic instability and increase the rate of gene duplication of this family, thereby contributing to its extraordinary diversity.
机译：最近的研究表明，海胆紫斑病菌的免疫系统比以前想象的要复杂。 Sp185 / 333基因家族就是一个例证，该家族在受到免疫攻击的动物中被上调。 Sp185 / 333基因很小（小于2kb），带有两个外显子，是一个由40多个基因组成的大家族的成员。但是，当前的紫癜链球菌基因组（v2.1）仅包含六个Sp185 / 333基因。代表性不足的原因可能在于shot弹枪装配中存在较大的基因家族，在该家族中多个相似的基因可以折叠成一个共有基因。因此，为了了解Sp185 / 333基因家族的基因组空间组织，组装了一个包含Sp185 / 333基因的BAC，并特别注意可能由非常相似的基因产生的伪像。生成十二个具有不同参数的BAC候选组件，以说明潜在的基因崩溃或人为复制/扩展。 PCR，限制性酶切和亚克隆测序用于鉴定和验证最佳装配。经过验证的程序集包含六个Sp185 / 333基因，大小从1.3到1.8 kb不等。这些基因聚集在BAC末端的34 kb区域，六个基因中的五个紧密聚集在20 kb内。该簇中的Sp185 / 333基因彼此之间的相似性与从三只不同动物中分离出的先前测序的Sp185 / 333基因彼此之间的相似性更高。考虑到它们在紧密相连的相似基因中的接近性和基因均质化的假定作用，这是出乎意料的。所有六个基因都显示出显着相似性，包括由微卫星界定的5'和3'侧翼区域。串联复制了三个Sp185 / 333基因及其侧翼区域，以使每个重复的片段由一个基因加上该基因的0.7 kb 5'和2.4 kb 3'（共4.5 kb）组成。节段重复的两个边缘都以微卫星的存在为特征。与串联重复无关的三个基因显示每个基因较小的保守侧翼区域，其范围从每个基因的400至600 nt 5'和400 nt 3'。 Sp185 / 333基因和侧翼区域的高度序列相似性表明，微卫星促进了基因组的不稳定性，并增加了该家族的基因重复率，从而促进了其非同寻常的多样性。

著录项

  • 作者

    Miller, Chase.;

  • 作者单位

    The George Washington University.;

  • 授予单位 The George Washington University.;
  • 学科 Biology Genetics.Biology Bioinformatics.
  • 学位 M.S.
  • 年度 2010
  • 页码 70 p.
  • 总页数 70
  • 原文格式 PDF
  • 正文语种 eng
  • 中图分类
  • 关键词

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