Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada.
School of Biological Sciences, Monash University, Melbourne, Victoria, Australia.
Genome Biol Evol. 2023 Aug 1;15(8). doi: 10.1093/gbe/evad146.
White clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. Here, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively.
白车轴草（Trifolium repens L.；豆科）是世界农业牧场上一种重要的饲料和覆盖作物，越来越多地用于进化生态学和遗传学，以了解适应的遗传基础。历史上，由于缺乏该物种的高质量基因组资源，白车轴草的繁殖实践的改进和对自然遗传变异的评估受到了阻碍，部分原因是其高度杂合性和异源四倍体杂种起源。在这里，我们使用 PacBio HiFi 和染色体构象捕获（Omni-C）技术，为白车轴草生成了一个染色体水平的、单倍型解析的基因组组装，总长度为 9.98 兆碱基对（支架 N50 = 59.3 兆碱基对）和 10 亿碱基对（支架 N50 = 58.6 兆碱基对），分别用于单倍型 1 和 2，每个单倍型排列成 16 条染色体（每个亚基因组 8 条）。我们还提供了一个功能注释的单倍型映射组装（9.68 兆碱基对，支架 N50 = 59.9 兆碱基对），在连续性和组装准确性方面都大大优于现有参考组装。我们注释了 78,174 个蛋白编码基因，导致蛋白 BUSCO 完整性得分分别为 99.6%和 99.3%，针对 embryophyta_odb10 和 fabales_odb10 谱系数据集。
