SNPs and Hox gene mapping in Ciona intestinalis.
SNPs and Hox gene mapping in Ciona intestinalis.
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DOI：
10.1186/1471-2164-9-39
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发表时间：
2008-01-25
期刊：
影响因子：
4.4
通讯作者：
Sordino, Paolo
中科院分区：
文献类型：
--
作者：
Caputi, Luigi;Borra, Marco;Andreakis, Nikos;Biffali, Elio;Sordino, Paolo
被囊玻璃海鞘（Enterogona，Ascidiacea）是脊索动物进化和发育遗传学的主要模式系统。为了评估种内和种间遗传变异的程度，我们报告了C。SNP（单核苷酸多态性）标记。使用SNP子集来确定Hox-5和-10基因之间的遗传距离。从C.黑齿藓A.在8 Kb的DNA中共发现了128个SNPs和32个1 bp的indel。编码区中的SNP引起4个同义和12个非同义替换。在Hox 5和Hox 10基因内区域检测到最高的SNP频率。In C.然而，这两个基因已经失去了它们在簇内的原型拓扑结构，使得Hox 10位于Hox 4和Hox 5之间。使用上述引物的子集在C.黑刺蛾属B.在3614 bp内共检测到62个SNPs，其中非编码区41个，编码区21个。Hox-5和-10位点的遗传距离，计算结合经典的回交方法与SNP标记的应用，被认为是8.4 cM（Halfman的功能）。基于物理距离，1 cM对应于39.5 Kb。在回交世代中计算了上述位点之间的连锁不平衡。这里描述的SNP允许在C.神秘的物种。我们提供了第一个可靠的计算遗传距离在这个重要的模型脊索动物。后者的结果代表了一个重要的平台，为今后的研究Hox基因显示偏离原型拓扑结构。
The tunicate Ciona intestinalis (Enterogona, Ascidiacea), a major model system for evolutionary and developmental genetics of chordates, harbours two cryptic species. To assess the degree of intra- and inter-specific genetic variability, we report the identification and analysis of C. intestinalis SNP (Single Nucleotide Polymorphism) markers. A SNP subset was used to determine the genetic distance between Hox-5 and -10 genes. DNA fragments were amplified from 12 regions of C. intestinalis sp. A. In total, 128 SNPs and 32 one bp indels have been identified within 8 Kb DNA. SNPs in coding regions cause 4 synonymous and 12 non-synonymous substitutions. The highest SNP frequency was detected in the Hox5 and Hox10 intragenic regions. In C. intestinalis, these two genes have lost their archetypal topology within the cluster, such that Hox10 is located between Hox4 and Hox5. A subset of the above primers was used to perform successful amplification in C. intestinalis sp. B. In this cryptic species, 62 SNPs were identified within 3614 bp: 41 in non-coding and 21 in coding regions. The genetic distance of the Hox-5 and -10 loci, computed combining a classical backcross approach with the application of SNP markers, was found to be 8.4 cM (Haldane's function). Based on the physical distance, 1 cM corresponds to 39.5 Kb. Linkage disequilibrium between the aforementioned loci was calculated in the backcross generation. SNPs here described allow analysis and comparisons within and between C. intestinalis cryptic species. We provide the first reliable computation of genetic distance in this important model chordate. This latter result represents an important platform for future studies on Hox genes showing deviations from the archetypal topology.
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影响因子：
5.4
作者：
HILL W G;ROBERTSON A
通讯作者：
ROBERTSON A
DOI：
10.1073/pnas.0402177101
发表时间：
2004-08-31
影响因子：
11.1
作者：
Guindon, S;Rodrigo, AG;Huelsenbeck, JP
通讯作者：
Huelsenbeck, JP
影响因子：
7
作者：
Boffelli, D;Weer, CV;Rubin, EM
通讯作者：
Rubin, EM
影响因子：
0.9
作者：
Chiba, S;Sasaki, A;Satoh, N
通讯作者：
Satoh, N
影响因子：
64.8
作者：
Jeffery, WR;Strickler, AG;Yamamoto, Y
通讯作者：
Yamamoto, Y