Data from: Asexual genome evolution in the apomictic Ranunculus auricomus complex: examining the effects of hybridization and mutation accumulation

Asexual lineages are thought to be prone to extinction because of deleterious mutation accumulation (Muller's ratchet). Here we analyze genomic effects of hybridity, polyploidy and allelic divergence in apomictic plants, and identify loci under divergent selection among sexual/apomictic lineages. RNAseq was used to sequence the flower-specific transcriptomes of 5 genotypes of the Ranunculus auricomus complex, representing 3 sexual and 2 apomictic reproductive biotypes. The 5 sequence libraries were pooled and de novo assembly performed, and the resultant assembly was used as a backbone for a subsequent alignment of each separate library. High quality single nucleotide (SNP) and insertion-deletion (indel) polymorphisms were mined from each library. Annotated genes for which open reading frames (ORF) could be determined were analyzed for signatures of divergent versus stabilizing selection. A comparison between all genotypes supports the hypothesis of Pleistocene hybrid origin of both apomictic genotypes from R. carpaticola and R. cassubicifolius, with subsequent allelic divergence of apomictic lineages (Meselson effect). Pairwise comparisons of non-synonymous (dN) to synonymous (dS) substitution rate ratios between apomictic and sexual genotypes for 1231 genes demonstrated similar distributions for all comparisons, although 324 genes demonstrated outlier (i.e. elevated) dN/dS ratios. Gene ontology analyses of these outliers revealed significant enrichment of genes associated with reproduction including meiosis and gametogenesis, following predictions of divergent selection between sexual and apomictic reproduction, although no significant signal of genome-wide mutation accumulation could be identified. The results suggest that gene function should be considered in order to understand effects of mutation accumulation in asexual lineages.

无性繁殖谱系因有害突变积累引发的穆勒棘轮效应（Muller's ratchet）而被认为极易走向灭绝。本研究分析了无融合生殖（apomictic）植物中杂交性、多倍性以及等位基因分化的基因组效应，并鉴定了有性/无性繁殖谱系间受歧化选择的基因座。本研究借助RNA测序（RNAseq）对毛茛（Ranunculus auricomus）复合群的5个基因型的花特异性转录组进行测序，这5个基因型分别代表3种有性生殖生物型与2种无融合生殖生物型。将5个测序文库混合后开展从头组装（de novo assembly），所得组装结果作为参考骨架用于后续各单独文库的序列比对。从每个文库中挖掘得到高质量的单核苷酸多态性（single nucleotide polymorphism, SNP）与插入缺失多态性（insertion-deletion polymorphism, indel）。对可确定开放阅读框（open reading frame, ORF）的注释基因开展分析，以检测歧化选择与稳定选择的特征信号。

所有基因型的比较分析支持如下假说：两种无融合生殖基因型均起源于更新世时期的卡帕多西亚毛茛（R. carpaticola）与卡西比弗利亚毛茛（R. cassubicifolius）的杂交事件，且无性繁殖谱系随后发生了等位基因分化（梅塞尔森效应，Meselson effect）。对1231个基因的无融合生殖与有性生殖基因型间的非同义替换率（non-synonymous substitution rate, dN）与同义替换率（synonymous substitution rate, dS）的比值开展两两比较，结果显示所有比较的分布模式均较为相似，但其中324个基因的dN/dS比值呈现异常升高的离群特征。对这些离群基因进行基因本体（Gene Ontology, GO）富集分析后发现，与繁殖相关的基因（包括减数分裂与配子发生相关基因）呈现显著富集，这与有性与无融合生殖间存在歧化选择的预测相符，但未检测到全基因组范围内突变积累的显著信号。

本研究结果表明，若要阐明无性繁殖谱系中突变积累的效应，需将基因功能纳入考量范畴。