随着测序技术的发展,多个物种基因组测序的完成,科学家们对基因的研究也越来越深入。在细菌的基因组中存在有很多基因插入和缺失的现象,基因的插入与缺失通常导致基因的缀块分布。评估基因存在和缺失的方法被广泛运用在细菌基因组进化的研究领域。
2007年Zhaxybayeva等科学家的研究表明,基因存在的错误诊断和未检测到的存在基因可能导致基因获得系统性过度评估。而最近,加拿大麦克马斯特大学的Weilong Hao和Golding研究认为,注释错误可能引起更多复杂的影响,而不一定是系统性的,当前的注释打分是研究基因缺失的最好方法。基因获得和丢失基因组评估并没有因为基因组注释中很小的不同而受到强烈影响,但受到相关基因家族数目的强烈影响。科学家通过使用不同的域值来评估基因插入和缺失率,结果显示,长度匹配的不同域值只能引起评估率的一些很小变化。但是新近分支的基因插入缺失率一样相对较高,这与长度匹配的域值无关。现有的数据表明,在最近转移的基因当中更趋向于基因截短,但基因截短的动力学过程还需要在基因组比较中进行更深入的研究。相关文章发表在爱思唯尔期刊《基因》(Gene)上。(生物谷Bioon.com)
生物谷推荐原始出处:
Gene,Volume 421, Issues 1-2, 15 September 2008, Pages 27-31,Weilong Hao,G. Brian Golding
High rates of lateral gene transfer are not due to false diagnosis of gene absence
Weilong Haoa and G. Brian Golding,
Department of Biology, McMaster University, Hamilton, Ontario, Canada L8S 4K1
Abstract
Methods for assessing gene presence and absence have been widely used to study bacterial genome evolution. A recent report by Zhaxybayeva et al. [Zhaxybayeva, O., Nesbo, C. L., and Doolittle, W. F., 2007. Systematic overestimation of gene gain through false diagnosis of gene absence. Genome. Biol. 8, 402] suggests that false diagnosis of gene absence or the presence of undetected truncated genes leads to a systematic overestimation of gene gain. Here (1) we argue that these annotation errors can cause more complicated effects and are not necessarily systematic, (2) we argue that current annotations (supplemented with BLAST searches) are the best way to consistently score gene presence/absence and (3) that genome wide estimates of gene gain/loss are not strongly affected by small differences in gene annotations but that the number of related gene families is strongly affected. We have estimated the rates of gene insertions/deletions using a variety of cutoff thresholds and match lengths as a way in which to alter the recognition of genes and gene fragments. The results reveal that different cutoffs for match length only cause a small variation of the estimated insertion/deletion rates. The rates of gene insertions/deletions on recent branches remain relatively high regardless of the thresholds for match length. Lastly (4), the dynamic process of gene truncation needs to be further considered in genome comparison studies. The data presented suggest that gene truncation tends to take place preferentially in recently transferred genes, which supports a fast turnover of recent laterally transferred genes. The presence of truncated genes or false diagnosis of gene absence therefore does not significantly affect the estimation of gene insertions/deletions rates, but there are several other factors that bias the results toward an under-estimation of the rate of gene insertion/deletion. All of these factors need to be considered.