油橄榄（Olea europaea L.）亚种油橄榄栽培品种佛朗托io和莱基诺的PacBio基因组组装

PacBio genome assembly of Olea europaea L. subsp. europaea cultivars Frantoio and Leccino.

作者信息

Sebastiani Luca, Sarfraz Iqra, Francini Alessandra, Celii Mirko, Wing Rod A, Zuccolo Andrea

机构信息

Institute of Crop Science, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy.

King Abdullah University of Science & Technology, Thuwal, Saudi Arabia.

出版信息

Sci Data. 2025 Jul 1;12(1):1095. doi: 10.1038/s41597-025-05363-4.

DOI:10.1038/s41597-025-05363-4

PMID:40593836

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12217686/

Abstract

We present two high-quality genome assemblies for Olea europaea L. cultivars 'Frantoio' and 'Leccino,' leveraging PacBio HiFi sequencing to achieve approximately 30 × genome coverage for each cultivar. The assemblies span 1.18 Gbp and 1.43 Gbp with contig N50 values of 1.78 Mbp and 45.88 Mbp for 'Frantoio' and 'Leccino,' respectively. BUSCO analysis revealed a great genome completeness (~97.9%), surpassing many of earlier Olea europaea assemblies and is in par with the most recent one. Repetitive content accounted for ~67.5% in 'Frantoio' and ~70.8% in 'Leccino,' with long terminal repeats (LTRs) dominating. Notably, a tandem repeat family, Satellite 1, represented ~16.9% and ~8.6% of the 'Leccino' and 'Frantoio' genomes, respectively. The structural variant (SV) analysis identified cultivar-specific genomic differences, emphasizing the diversity within domesticated olives. This comprehensive analysis provides valuable resources for studying olive genome evolution, domestication, and genetic improvement, underscoring the utility of long-read sequencing for resolving complex genomic features.

摘要

我们展示了油橄榄（Olea europaea L.）品种‘佛朗托io’和‘莱基诺’的两个高质量基因组组装结果，利用PacBio HiFi测序技术，每个品种实现了约30倍的基因组覆盖。‘佛朗托io’和‘莱基诺’的组装基因组分别跨越1.18 Gbp和1.43 Gbp，重叠群N50值分别为1.78 Mbp和45.88 Mbp。BUSCO分析显示基因组完整性很高（约97.9%），超过了许多早期的油橄榄基因组组装结果，与最新的组装结果相当。重复序列在‘佛朗托io’中占约67.5%，在‘莱基诺’中占约70.8%，其中长末端重复序列（LTRs）占主导。值得注意的是，一个串联重复序列家族，卫星1，分别占‘莱基诺’和‘佛朗托io’基因组的约16.9%和8.6%。结构变异（SV）分析确定了品种特异性的基因组差异，强调了驯化橄榄内部的多样性。这一全面分析为研究橄榄基因组进化、驯化和遗传改良提供了宝贵资源，突出了长读长测序在解析复杂基因组特征方面的实用性。