Karbstein Kevin, Choudhary Nancy, Xie Ting, Tomasello Salvatore, Wagner Natascha D, Barke Birthe H, Paetzold Claudia, Bradican John P, Preick Michaela, Himmelbach Axel, Stein Nils, Papantonis Argyris, Irisarri Iker, de Vries Jan, Pucker Boas, Hörandl Elvira
Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Göttingen, Göttingen, Germany.
Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, Jena, Germany.
Plant J. 2025 Sep;123(6):e70390. doi: 10.1111/tpj.70390.
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 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.
尽管基因组测序和组装技术在不断进步，但对于具有庞大复杂基因组的植物物种而言，成本仍然过高。因此，对维管植物生命之树中处于进化关键位置的某些分类群进行的基因组学研究受到了阻碍。物种丰富的毛茛属（毛茛科）是研究多倍体、无融合生殖和网状进化的重要被子植物类群。然而，目前既没有线粒体基因组序列，也没有高质量的核基因组序列。这限制了到目前为止的系统发育基因组学、功能和分类学分析。在此，我们测试了Illumina短读长、牛津纳米孔技术（ONT）和PacBio（HiFi）长读长以及混合读长组装策略。我们对二倍体祖先物种卡西毛茛（耳状毛茛物种复合体）进行了测序，并根据完整性、连续性和质量得分选择了最佳组装结果。我们首先分别使用Illumina和Illumina-PacBio混合策略组装了质体基因组（156 kbp，85个基因）和线粒体基因组（1.18 Mbp，40个基因）序列。我们还展示了更新后的毛茛科质体基因组和首个线粒体基因组系统发育树，包括对具有进化意义的基因丢失（如infA、ycf15或rps）的研究。对于核基因组序列，我们倾向于基于PacBio构建并经过滤后的短读长进行三次抛光的组装，随后通过染色质构象数据（Hi-C）将其构建成8条假染色体。我们获得了一个2.69 Gbp的单倍体基因组序列，发现94.1%的BUSCO基因完整，有35482个注释基因，并与现有的毛茛目基因组相比推断出了古老的基因重复事件。这里呈现的基因组信息将有助于对该物种复合体，以及毛茛属乃至毛茛科以外的类群进行深入的进化功能分析。
