Department of Genetics, University of Georgia, Athens, GA, USA.
Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.
Mol Biol Evol. 2021 Aug 23;38(9):3664-3675. doi: 10.1093/molbev/msab133.
Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.
基因组资源有限是植物中 DNA 水平转移 (HT) 研究的瓶颈。为了解决这个问题，我们测试了 19 个先前未表征的 panicoid 禾本科植物的低深度测序数据在 HT 研究中的有用性。我们最初通过将 19 个样本序列与 115 个被子植物基因组序列进行比较，来搜索水平转移的 LTR-逆转录转座子。LTR-逆转录转座子在 panicoid 和水稻 (Oryza sativa) 之间频繁发生 HT。因此，我们将注意力集中在其他 Oryza 物种上，并对包括 panicoid 属 Echinochloa 在内的物种进行了非靶向 HT 调查，该属在第一轮分析中显示出最多的 HT。对 9 个 Echinochloa 样本和 10 个 Oryza 物种的比较，确定了在 Oryza 历史的不同时期，各种转座元件 (TE) 类型的反复 HT，但除了 TE 之外，没有确认的 HT 序列。在具有重叠地理分布的一个 Echinochloa 物种和一个 Oryza 物种中观察到一个 HT。物种间和数据集之间的差异突出了识别所有 HT 的困难，但我们的研究表明，样本序列分析可以揭示 HT 对植物 TE 库多样化的重要性。
