Vanderbilt University, Department of Biological Sciences, VU Station B 351364, Nashville, Tennessee 37235, and University of Hawaii at Mânoa, Botany Department, 3190 Maile Way, Room 101, Honolulu, Hawaii 96822.
Mycologia. 2013 Sep-Oct;105(5):1126-34. doi: 10.3852/12-390. Epub 2013 Aug 6.
At least five of the six genes of the bikaverin secondary metabolic gene cluster were shown to have undergone horizontal transfer (HGT) from a Fusarium donor to the Botrytis lineage. Of these five, two enzyme-encoding genes are found as pseudogenes in B. cinerea whereas two regulatory genes and the transporter remain intact. To reconstruct the evolutionary events leading to decay of this gene cluster and infer a more precise timing of its transfer, we examined the genomes of nine additional broadly sampled Botrytis species. We found evidence that a Botrytis ancestor acquired the entire gene cluster through an ancient HGT that occurred before the diversification of the genus. During the subsequent evolution and diversification of the genus, four of the 10 genomes appear to have lost the gene cluster, while in the other six the cluster is in various stages of degeneration. Across the Botrytis genomes, the modes of gene decay in the cluster differed between enzyme-encoding genes, which had higher rates of transition to or retention of pseudogenes and were universally inactivated, and regulatory genes (particularly the non-pathway-specific regulator bik4), which more frequently appeared intact. Consistent with these results, the regulatory genes bik4 and bik5 showed stronger evidence of transcriptional expression than other bikaverin genes under multiple conditions in B. cinerea. These results could be explained by pleiotropy in the bikaverin regulatory genes either through rewiring or their interaction with more central pathways or by constraints on the order of gene loss driven by the intrinsic toxicity of the pathway. Our finding that most of the bikaverin pathway genes have been lost or pseudogenized in these Botrytis genomes suggests that the incidence of HGT of gene cluster-encoded metabolic pathways might be higher than what is possible to be inferred from isolated genome analyses.
至少有六个比卡维因次生代谢基因簇的五个基因被证明经历了水平转移（HGT），从尖孢镰刀菌供体转移到 Botrytis 谱系。在这五个基因中，两个编码酶的基因在灰葡萄孢中是假基因，而两个调节基因和转运蛋白仍然完整。为了重建导致这个基因簇衰减的进化事件，并推断其转移的更精确时间，我们检查了另外九个广泛采样的 Botrytis 物种的基因组。我们发现，Botrytis 的一个祖先通过发生在属分化之前的古老 HGT 获得了整个基因簇。在属的随后进化和多样化过程中，10 个基因组中的 4 个似乎失去了基因簇，而在其他 6 个中，该基因簇处于不同的退化阶段。在整个 Botrytis 基因组中，基因簇中的基因衰减模式在编码酶的基因之间有所不同，这些基因向或保留假基因的转换率较高，并且普遍失活，而调节基因（特别是非途径特异性调节剂 bik4）则更频繁地保持完整。与这些结果一致，在灰葡萄孢中，在多种条件下，调节基因 bik4 和 bik5 的转录表达证据比其他比卡维因基因更强。这些结果可以通过比卡维因调节基因的多效性来解释，要么通过重新布线，要么通过与更中心的途径相互作用，要么通过途径固有毒性驱动的基因丢失顺序的约束。我们发现，这些 Botrytis 基因组中的大多数比卡维因途径基因已经丢失或失活，这表明基因簇编码代谢途径的 HGT 发生率可能高于从孤立的基因组分析中推断出的可能性。
