Garcia Sònia, Wendel Jonathan F, Borowska-Zuchowska Natalia, Aïnouche Malika, Kuderova Alena, Kovarik Ales
Institut Botànic de Barcelona (IBB, CSIC - Ajuntament de Barcelona), Barcelona, Spain.
Department of Molecular Epigenetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia.
Front Plant Sci. 2020 Feb 10;11:41. doi: 10.3389/fpls.2020.00041. eCollection 2020.
Ribosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic origin of species. Data were obtained from more than 80 plant species, including several well-defined allopolyploids and homoploid hybrids of different evolutionary ages and from widely dispersed taxonomic groups.
(i) Diploids show simple circular-shaped graphs of their 5S rDNA clusters. In contrast, most allopolyploids and other interspecific hybrids exhibit more complex graphs composed of two or more interconnected loops representing intergenic spacers (IGS). (ii) There was a relationship between graph complexity and locus numbers. (iii) The sequences and lengths of the 5S rDNA units reconstituted from k-mers were congruent with those experimentally determined. (iv) Three-genomic comparative cluster analysis of reads from allopolyploids and progenitor diploids allowed identification of homoeologous 5S rRNA gene families even in relatively ancient (c. 1 Myr) and allopolyploids which already exhibit uniparental partial loss of rDNA repeats. (v) Finally, species harboring introgressed genomes exhibit exceptionally complex graph structures.
We found that the cluster graph shapes and graph parameters (k-mer coverage scores and connected component index) well-reflect the organization and intragenomic homogeneity of 5S rDNA repeats. We propose that the analysis of 5S rDNA cluster graphs computed by the RE pipeline together with the cytogenetic analysis might be a reliable approach for the determination of the hybrid or allopolyploid plant species parentage and may also be useful for detecting historical introgression events.
核糖体DNA（rDNA）位点已被广泛用于异源多倍体和杂种的鉴定，尽管这些研究中很少有使用高通量测序数据的。在此，我们使用RepeatExplorer（RE）管道中实现的图谱聚类方法，在基因组水平上分析同源5S rDNA阵列，以寻找物种的杂交起源。数据来自80多种植物，包括几个明确的异源多倍体和不同进化年龄的同倍体杂种，以及来自广泛分布的分类群。
（i）二倍体的5S rDNA簇呈现简单的圆形图谱。相比之下，大多数异源多倍体和其他种间杂种表现出更复杂的图谱，由两个或更多代表基因间隔区（IGS）的相互连接的环组成。（ii）图谱复杂性与位点数量之间存在关系。（iii）从k-mer重构的5S rDNA单元的序列和长度与实验确定的一致。（iv）对异源多倍体和祖本二倍体的reads进行三基因组比较聚类分析，即使在相对古老（约100万年）且已经表现出rDNA重复单亲部分缺失的异源多倍体中，也能鉴定出同源5S rRNA基因家族。（v）最后，含有渐渗基因组的物种表现出异常复杂的图谱结构。
我们发现聚类图谱形状和图谱参数（k-mer覆盖分数和连通分量指数）很好地反映了5S rDNA重复的组织和基因组内同质性。我们提出，通过RE管道计算的5S rDNA聚类图谱分析与细胞遗传学分析相结合，可能是确定杂交或异源多倍体植物物种亲本的可靠方法，也可能有助于检测历史渐渗事件。
