Gaborieau Lydiane, Brown Gregory G
Department of Biology, McGill University, 1205 Doctor Penfield Ave., Montreal, QC, H3A 1B1, Canada.
BMC Genomics. 2016 Oct 26;17(1):834. doi: 10.1186/s12864-016-3117-0.
The plant trait of cytoplasmically-inherited male sterility (CMS) and its suppression by nuclear restorer-of-fertility (Rf) genes can be viewed as a genetic arms race between the mitochondrial and nuclear genomes. Most nuclear Rf genes have been shown to encode P-type pentatricopeptide repeat proteins (PPRs). Phylogenetic analysis of P-class PPRs from sequenced plants genomes has shown that Rf-proteins cluster in a distinct clade of P-class PPRs, RFL-PPRs, that display hallmarks of positive evolutionary selection. Genes encoding RFL-PPRs (RFLs) within a given plant genome tend to be closely related both in sequence and position, but a detailed understanding of how such species-specific expansion occurs is lacking. In the canola, (oilseed rape) species Brassica napus, previous work has indicated the nuclear restorer genes for the two native forms of CMS, Rfn (for nap CMS) and Rfp (pol CMS), represent alternate haplotypes, or alleles, of a single nuclear locus.
Fine genetic mapping indicates that Rfn does indeed localize to the same genomic region as Rfp. We find this region is enriched in RFL genes, three of which, based on their position and expression, represent potential candidates for Rfn; one of these genes, designated PPR4, is a preferred candidate in that it is not expressed in the nap CMS line. Comparison of the corresponding regions of the genomes of B. rapa, B. oleracea, Arabidopsis thaliana and A. lyrata provides insight into the expansion of this group of RFL genes in different lines of evolutionary descent.
Unlike other nuclear restorer loci containing multiple RFL genes, the RFL genes in the Rf region of B. napus are not present in tandem arrays but rather are dispersed in genomic location. The genes do not share similar flanking non-coding regions and do not contain introns, indicating that they have duplicated primarily through a retrotransposition-mediated process. In contrast, segmental duplication has been responsible for the distribution of the 10 sequences we annotated as RFL genes in the corresponding region of the A. lyrata genome. Our observations define the Brassica Rf locus and indicate that different mechanisms may be responsible for the proliferation of RFL genes even among closely related genomes.
细胞质遗传雄性不育（CMS）这一植物性状及其被核育性恢复基因（Rf）抑制的现象，可被视为线粒体基因组与核基因组之间的一场基因军备竞赛。大多数核Rf基因已被证明编码P型五肽重复蛋白（PPR）。对已测序植物基因组中的P类PPR进行系统发育分析表明，Rf蛋白聚集在P类PPR的一个独特分支RFL-PPR中，该分支显示出正进化选择的特征。给定植物基因组中编码RFL-PPR的基因（RFL）在序列和位置上往往密切相关，但对于这种物种特异性扩增如何发生，仍缺乏详细了解。在油菜（甘蓝型油菜）物种甘蓝型油菜中，先前的研究表明，两种原生CMS形式的核育性恢复基因，Rfn（针对nap CMS）和Rfp（pol CMS），代表单个核基因座的交替单倍型或等位基因。
精细遗传定位表明，Rfn确实定位于与Rfp相同的基因组区域。我们发现该区域富含RFL基因，其中三个基于其位置和表达情况，代表Rfn的潜在候选基因；这些基因中的一个，命名为PPR4，是首选候选基因，因为它在nap CMS系中不表达。对白菜、甘蓝、拟南芥和琴叶拟南芥基因组相应区域的比较，有助于深入了解这组RFL基因在不同进化谱系中的扩增情况。
与其他包含多个RFL基因的核育性恢复基因座不同，甘蓝型油菜Rf区域中的RFL基因并非串联排列，而是分散在基因组位置上。这些基因不共享相似的侧翼非编码区域，也不包含内含子，这表明它们主要通过逆转座介导的过程进行了复制。相比之下，片段重复导致了我们注释为RFL基因的10个序列在琴叶拟南芥基因组相应区域中的分布。我们的观察结果定义了芸苔属Rf基因座，并表明即使在密切相关的基因组中，不同的机制也可能导致RFL基因的增殖。
