Roncal Julissa, Guyot Romain, Hamon Perla, Crouzillat Dominique, Rigoreau Michel, Konan Olivier N'Guessan, Rakotomalala Jean-Jacques, Nowak Michael D, Davis Aaron P, de Kochko Alexandre
Department of Biology, Memorial University of Newfoundland, 232 Elizabeth Avenue, St. John's, A1B 3X9, Canada.
UMR DIADE, IRD, B.P. 64501, 34394, Cedex 5 Montpellier, France.
Mol Genet Genomics. 2016 Feb;291(1):155-68. doi: 10.1007/s00438-015-1098-3. Epub 2015 Aug 1.
The completion of the genome assembly for the economically important coffee plant Coffea canephora (Rubiaceae) has allowed the use of bioinformatic tools to identify and characterize a diverse array of transposable elements (TEs), which can be used in evolutionary studies of the genus. An overview of the copy number and location within the C. canephora genome of four TEs is presented. These are tested for their use as molecular markers to unravel the evolutionary history of the Millotii Complex, a group of six wild coffee (Coffea) species native to Madagascar. Two TEs from the Gypsy superfamily successfully recovered some species boundaries and geographic structure among samples, whereas a TE from the Copia superfamily did not. Notably, species occurring in evergreen moist forests of eastern and southeastern Madagascar were divergent with respect to species in other habitats and regions. Our results suggest that the peak of transpositional activity of the Gypsy and Copia TEs occurred, respectively, before and after the speciation events of the tested Madagascan species. We conclude that the utilization of active TEs has considerable potential to unravel the evolutionary history and delimitation of closely related Coffea species. However, the selection of TE needs to be experimentally tested, since each element has its own evolutionary history. Different TEs with similar copy number in a given species can render different dendrograms; thus copy number is not a good selection criterion to attain phylogenetic resolution.
经济上重要的咖啡植物卡内弗拉咖啡（茜草科）的基因组组装完成后，使得利用生物信息学工具来识别和表征各种各样的转座元件（TEs）成为可能，这些转座元件可用于该属的进化研究。本文概述了四种TEs在卡内弗拉咖啡基因组中的拷贝数和位置。对这些TEs作为分子标记来揭示米洛蒂复合体进化历史的用途进行了测试，米洛蒂复合体是一组原产于马达加斯加的六种野生咖啡（咖啡属）物种。来自吉普赛超家族的两种TEs成功地恢复了样本间的一些物种界限和地理结构，而来自考皮亚超家族的一种TEs则没有。值得注意的是，马达加斯加东部和东南部常绿湿润森林中的物种与其他栖息地和地区的物种存在差异。我们的结果表明，吉普赛和考皮亚TEs的转座活性高峰分别发生在被测马达加斯加物种的物种形成事件之前和之后。我们得出结论，利用活跃的TEs在揭示近缘咖啡物种的进化历史和界定方面具有相当大的潜力。然而，TE的选择需要进行实验测试，因为每个元件都有其自身的进化历史。给定物种中具有相似拷贝数的不同TEs可能会产生不同的树状图；因此，拷贝数不是获得系统发育分辨率的良好选择标准。
