SOKENDAI, Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan.
Genome Biol Evol. 2018 Dec 1;10(12):3196-3210. doi: 10.1093/gbe/evy219.
We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampyrum roseum) are facultative parasites. By using reference genome sequences and/or transcriptomes of 14 species from Fabaceae and Poaceae, their major host families, we detected 106 horizontally transferred genes (HGT genes), only in the genomes of the two obligate parasites (22 and 84 for Oro. minor and Ae. indica, respectively), whereas none in the three facultative parasites. The HGT genes, respectively, account for roughly 0.1% and 0.2% of the coding genes in the two species. We found that almost all HGT genes retained introns at the same locations as their homologs in potential host species, indicating a crucial role of DNA-mediated gene transfer, rather than mRNA mediated retro transfer. Furthermore, some of the HGT genes might have transferred simultaneously because they located very closely in the host reference genome, indicating that the length of transferred DNA could exceed 100 kb. We confirmed that almost all introns are spliced in the current genome of the parasite species, and that about half HGT genes do not have any missense mutations or frameshift-causing indels, suggesting that some HGT genes may be still functional. Evolutionary analyses revealed that the nonsynonymous-synonymous substitution ratio is on average elevated on the lineage leading to HGT genes, due to either relaxation of selection or positive selection.
我们对列当科五种寄生虫的基因组进行了测序，以探索水平基因转移在植物进化中的作用。列当属的 Orobanche minor 和 Aeginetia indica 是专性寄生植物，没有光合作用，而另外三种（Pedicularis keiskei、Phtheirospermum japonicum 和 Melampyrum roseum）是兼性寄生植物。通过使用来自豆科和禾本科这两个主要寄生植物科的 14 个物种的参考基因组序列和/或转录组，我们在两个专性寄生植物（Oro. minor 和 Ae. indica 分别有 22 个和 84 个）的基因组中检测到 106 个水平转移基因（HGT 基因），而在三个兼性寄生植物中均未检测到。这些 HGT 基因分别占这两个物种编码基因的约 0.1%和 0.2%。我们发现，几乎所有的 HGT 基因在潜在宿主物种中的同源基因都保留了内含子，这表明 DNA 介导的基因转移，而不是 mRNA 介导的逆转录，发挥了关键作用。此外，一些 HGT 基因可能同时转移，因为它们在宿主参考基因组中非常接近，这表明转移的 DNA 长度可能超过 100kb。我们证实，几乎所有内含子都在寄生虫物种的当前基因组中进行了拼接，而且大约一半的 HGT 基因没有任何错义突变或导致移码的插入缺失，这表明一些 HGT 基因可能仍然具有功能。进化分析表明，由于选择放松或正选择，在导致 HGT 基因的进化支上，非同义-同义取代比平均升高。
