隨著測(cè)序技術(shù)的發(fā)展,，多個(gè)物種基因組測(cè)序的完成，科學(xué)家們對(duì)基因的研究也越來(lái)越深入,。在細(xì)菌的基因組中存在有很多基因插入和缺失的現(xiàn)象,，基因的插入與缺失通常導(dǎo)致基因的綴塊分布。評(píng)估基因存在和缺失的方法被廣泛運(yùn)用在細(xì)菌基因組進(jìn)化的研究領(lǐng)域,。
2007年Zhaxybayeva等科學(xué)家的研究表明,，基因存在的錯(cuò)誤診斷和未檢測(cè)到的存在基因可能導(dǎo)致基因獲得系統(tǒng)性過(guò)度評(píng)估。而最近,，加拿大麥克馬斯特大學(xué)的Weilong Hao和Golding研究認(rèn)為,，注釋錯(cuò)誤可能引起更多復(fù)雜的影響，而不一定是系統(tǒng)性的,，當(dāng)前的注釋打分是研究基因缺失的最好方法,。基因獲得和丟失基因組評(píng)估并沒(méi)有因?yàn)榛蚪M注釋中很小的不同而受到強(qiáng)烈影響,，但受到相關(guān)基因家族數(shù)目的強(qiáng)烈影響,。科學(xué)家通過(guò)使用不同的域值來(lái)評(píng)估基因插入和缺失率,，結(jié)果顯示,，長(zhǎng)度匹配的不同域值只能引起評(píng)估率的一些很小變化。但是新近分支的基因插入缺失率一樣相對(duì)較高,，這與長(zhǎng)度匹配的域值無(wú)關(guān)?，F(xiàn)有的數(shù)據(jù)表明，在最近轉(zhuǎn)移的基因當(dāng)中更趨向于基因截短,，但基因截短的動(dòng)力學(xué)過(guò)程還需要在基因組比較中進(jìn)行更深入的研究,。相關(guān)文章發(fā)表在愛(ài)思唯爾期刊《基因》（Gene）上。（生物谷Bioon.com）
生物谷推薦原始出處：
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.
