Schrider Daniel R, Costello James C, Hahn Matthew W
Department of Biology and School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.
J Comput Biol. 2009 Oct;16(10):1419-27. doi: 10.1089/cmb.2009.0085.
The loss of previously established genes has been proposed as a major force in evolutionary change. While genome sequencing of many new species offers the opportunity to identify cases of gene loss, it is unclear which algorithms offer the greatest accuracy or sensitivity. A number of methods to identify gene losses rely on the presence of a pseudogene for each loss. If genes are deleted when lost, however, such methods will fail to identify these cases. As the fate of gene losses is still unclear, we identified gene losses through a method that does not require pseudogenes to identify human-specific gene losses. Of the several hundred probable gene losses initially identified, we were unable to find a single case of unambiguous gene loss via deletion. We were also able to identify a large number of previously unannotated genes in the human genome, some of which also had evidence for transcription. Though our results suggest that pseudogene-based methods for finding gene losses in humans will not miss many events, we discuss the dependence of these conclusions on the divergence times among the species considered. Supplementary Material is provided (see online Supplementary Material at www.liebertonline.com ).
先前已确立的基因丢失被认为是进化变化中的一股主要力量。虽然对许多新物种进行基因组测序为识别基因丢失的情况提供了机会，但尚不清楚哪种算法具有最高的准确性或灵敏度。许多识别基因丢失的方法依赖于每次丢失都存在一个假基因。然而，如果基因在丢失时被删除，此类方法将无法识别这些情况。由于基因丢失的命运仍不明确，我们通过一种不需要假基因来识别人类特异性基因丢失的方法来识别基因丢失。在最初识别出的数百个可能的基因丢失中，我们未能找到一例通过删除导致的明确基因丢失。我们还能够在人类基因组中识别出大量先前未注释的基因，其中一些也有转录证据。尽管我们的结果表明，基于假基因的人类基因丢失检测方法不会遗漏太多事件，但我们讨论了这些结论对所考虑物种之间分歧时间的依赖性。提供了补充材料（见在线补充材料，网址为www.liebertonline.com ）。
