Assembling genomes of non‐model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae)

作者：Kevin Karbstein, Nancy Choudhary, Ting Xie, Salvatore Tomasello, Natascha D. Wagner, Birthe H. Barke, Claudia Paetzold, John Paul Bradican, Michaela Preick, Axel Himmelbach, Nils Stein, Argyris Papantonis, Iker Irisarri, Jan de Vries, Boas Pucker, Elvira Hörandl · 发表于：The Plant Journal · 年份：2025 · DOI：10.1111/tpj.70390 · 被引用次数：3 · 研究领域：Plant Taxonomy and Phylogenetics、Genomics and Phylogenetic Studies、Chromosomal and Genetic Variations

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (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) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species 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., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequenc...