Koutsovoulos Georgios, Kumar Sujai, Laetsch Dominik R, Stevens Lewis, Daub Jennifer, Conlon Claire, Maroon Habib, Thomas Fran, Aboobaker Aziz A, Blaxter Mark
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom;
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; The James Hutton Institute, Dundee DD2 5DA, United Kingdom;
Proc Natl Acad Sci U S A. 2016 May 3;113(18):5053-8. doi: 10.1073/pnas.1600338113. Epub 2016 Mar 24.
Tardigrades are meiofaunal ecdysozoans that are key to understanding the origins of Arthropoda. Many species of Tardigrada can survive extreme conditions through cryptobiosis. In a recent paper [Boothby TC, et al. (2015) Proc Natl Acad Sci USA 112(52):15976-15981], the authors concluded that the tardigrade Hypsibius dujardini had an unprecedented proportion (17%) of genes originating through functional horizontal gene transfer (fHGT) and speculated that fHGT was likely formative in the evolution of cryptobiosis. We independently sequenced the genome of H. dujardini As expected from whole-organism DNA sampling, our raw data contained reads from nontarget genomes. Filtering using metagenomics approaches generated a draft H. dujardini genome assembly of 135 Mb with superior assembly metrics to the previously published assembly. Additional microbial contamination likely remains. We found no support for extensive fHGT. Among 23,021 gene predictions we identified 0.2% strong candidates for fHGT from bacteria and 0.2% strong candidates for fHGT from nonmetazoan eukaryotes. Cross-comparison of assemblies showed that the overwhelming majority of HGT candidates in the Boothby et al. genome derived from contaminants. We conclude that fHGT into H. dujardini accounts for at most 1-2% of genes and that the proposal that one-sixth of tardigrade genes originate from functional HGT events is an artifact of undetected contamination.
缓步动物是小型土壤动物蜕皮动物，是理解节肢动物起源的关键。许多缓步动物物种可以通过隐生状态在极端条件下存活。在最近的一篇论文[布斯比·T·C等人（2015年）《美国国家科学院院刊》112(52):15976 - 15981]中，作者得出结论，杜氏高生熊虫（Hypsibius dujardini）有17%的基因来自功能性水平基因转移（fHGT），这一比例前所未闻，并推测fHGT可能在隐生进化中起了形成作用。我们独立对杜氏高生熊虫的基因组进行了测序。正如从全生物体DNA采样所预期的那样，我们的原始数据包含了来自非目标基因组的读数。使用宏基因组学方法进行过滤后，得到了一个135兆碱基的杜氏高生熊虫基因组草图组装，其组装指标优于之前发表的组装结果。可能仍存在其他微生物污染。我们没有找到支持广泛fHGT的证据。在23,021个基因预测中，我们确定了0.2%的来自细菌的fHGT强候选基因和0.2%的来自非后生动物真核生物的fHGT强候选基因。组装结果的交叉比较表明，布斯比等人基因组中绝大多数HGT候选基因来自污染物。我们得出结论，进入杜氏高生熊虫的fHGT最多占基因的1 - 2%，并且认为六分之一的缓步动物基因起源于功能性HGT事件的说法是未检测到的污染造成的假象。
