<strong>Efficient hybrid strategies for assembling the plastome, mitochondriome, and large genome of diploid</strong> <em><strong>Ranunculus auricomus</strong></em>

Currently, it is still a challenge - in terms of laboratory effort and cost, as well as assembly quality - to unravel the sequence of large and complex genomes from non-model plants. This often hampers research on evolutionarily intricate species groups. The species-rich genus <i>Ranunculus</i> (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) or PacBio (HiFi) long-read, and hybrid-read assembly strategies. We used the diploid progenitor species <i>R. cassubicifolius</i><i> </i>(<i>R. auricomus</i><i> </i>complex), and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., <i>infA</i>, <i>ycf15</i>, or <i>rps</i>) with evolutionary implications. For the nuclear genome, we favored a PacBio-based assembly three-times polished with filtered reads and subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) as the representative sequence. We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35,482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.