Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species.
Genomic distribution of AFLP markers relative to gene locations for different eukaryotic species.
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DOI：
10.1186/1471-2164-14-528
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发表时间：
2013-08-01
期刊：
影响因子：
4.4
通讯作者：
Quesada H
中科院分区：
文献类型：
--
作者：
Caballero A;García-Pereira MJ;Quesada H
扩增片段长度多态性（AFLP）标记经常用于广泛的研究，如全基因组作图，群体遗传多样性估计，杂交和渐渗研究，系统发育分析，以及选择标记的检测。这些领域中的一些领域要解决的一个重要问题是标记在基因组中的分布，特别是与基因序列有关的标记。使用硅限制性片段分析的基因组的9个真核生物物种，我们将AFLP片段的分布在整个基因组，特别是在基因位置。首先，我们确定所有物种染色体上标记的物理位置。在某些物种中，观察到的着丝粒区域周围的片段积累是由重复序列产生的，当考虑AFLP条带而不是片段时，这种积累就消失了。其次，我们计算了AFLP标记位于基因序列内的百分比。对于典型的EcoRI/MseI酶对，这个范围在28%和87%之间，并且通常大于偶然预期的值，因为基因序列的GC含量相对于基因间序列更高。与此一致，使用具有富含GC的限制性位点的酶对大大增加了上述百分比。例如，使用酶系统SacI/HpaII，86%的AFLP标记位于A.在恶性疟原虫中的阳性率为100%。我们进一步发现，对于一个由50个平均大小的基因控制的典型性状，如果在一个研究中使用1000个AFLP，则距离任何基因1 kb距离内的AFLP的数量将仅为约1-2个，并且只有约50%的基因在该距离内具有标记。基因组中AFLP标记的高覆盖率以及基因序列内或附近标记的高比例使它们适合基因组扫描和检测基因组中的大分化岛。然而，对于特定的性状，AFLP标记接近基因的百分比可能相当小。因此，在许多情况下，针对搜索与所选基因座紧密连锁的标记的基因组扫描可能是一项艰巨的任务。
Amplified fragment length polymorphism (AFLP) markers are frequently used for a wide range of studies, such as genome-wide mapping, population genetic diversity estimation, hybridization and introgression studies, phylogenetic analyses, and detection of signatures of selection. An important issue to be addressed for some of these fields is the distribution of the markers across the genome, particularly in relation to gene sequences. Using in-silico restriction fragment analysis of the genomes of nine eukaryotic species we characterise the distribution of AFLP fragments across the genome and, particularly, in relation to gene locations. First, we identify the physical position of markers across the chromosomes of all species. An observed accumulation of fragments around (peri) centromeric regions in some species is produced by repeated sequences, and this accumulation disappears when AFLP bands rather than fragments are considered. Second, we calculate the percentage of AFLP markers positioned within gene sequences. For the typical EcoRI/MseI enzyme pair, this ranges between 28 and 87% and is usually larger than that expected by chance because of the higher GC content of gene sequences relative to intergenic ones. In agreement with this, the use of enzyme pairs with GC-rich restriction sites substantially increases the above percentages. For example, using the enzyme system SacI/HpaII, 86% of AFLP markers are located within gene sequences in A. thaliana, and 100% of markers in Plasmodium falciparun. We further find that for a typical trait controlled by 50 genes of average size, if 1000 AFLPs are used in a study, the number of those within 1 kb distance from any of the genes would be only about 1–2, and only about 50% of the genes would have markers within that distance. The high coverage of AFLP markers across the genomes and the high proportion of markers within or close to gene sequences make them suitable for genome scans and detecting large islands of differentiation in the genome. However, for specific traits, the percentage of AFLP markers close to genes can be rather small. Therefore, genome scans directed towards the search of markers closely linked to selected loci can be a difficult task in many instances.
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