Olive (Olea europaea L.) is internationally renowned for its high-end product, extra virgin olive oil. An incomplete genome of O. europaea was previously obtained using shotgun sequencing in 2016. To further explore the genetic and breeding utilization of olive, an updated draft genome of olive was obtained using Oxford Nanopore third-generation sequencing and Hi-C technology. Seven different assembly strategies were used to assemble the final genome of 1.30 Gb, with contig and scaffold N50 sizes of 4.67 Mb and 42.60 Mb, respectively. This greatly increased the quality of the olive genome. We assembled 1.1 Gb of sequences of the total olive genome to 23 pseudochromosomes by Hi-C, and 53,518 protein-coding genes were predicted in the current assembly. Comparative genomics analyses, including gene family expansion and contraction, whole-genome replication, phylogenetic analysis, and positive selection, were performed. Based on the obtained high-quality olive genome, a total of nine gene families with 202 genes were identified in the oleuropein biosynthesis pathway, which is twice the number of genes identified from the previous data. This new accession of the olive genome is of sufficient quality for genome-wide studies on gene function in olive and has provided a foundation for the molecular breeding of olive species.

中文翻译：

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使用纳米孔测序从头组装新的油橄榄基因组

橄榄 （油橄榄L.) 以其高端产品特级初榨橄榄油而享誉国际。不完整的基因组欧罗巴之前是在 2016 年使用鸟枪测序获得的。为了进一步探索橄榄的遗传和育种利用，使用牛津纳米孔第三代测序和 Hi-C 技术获得了更新的橄榄基因组草图。七种不同的组装策略用于组装 1.30 Gb 的最终基因组，contig 和支架 N50 大小分别为 4.67 Mb 和 42.60 Mb。这大大提高了橄榄基因组的质量。我们通过 Hi-C 将 1.1 Gb 的总橄榄基因组序列组装成 23 条假染色体，在当前组装中预测了 53,518 个蛋白质编码基因。进行了比较基因组学分析，包括基因家族扩展和收缩、全基因组复制、系统发育分析和阳性选择。基于获得的优质橄榄基因组，在橄榄苦苷生物合成途径中，共鉴定出 9 个基因家族，共 202 个基因，是之前数据中鉴定出的基因数量的两倍。橄榄基因组的这一新加入对于橄榄基因功能的全基因组研究具有足够的质量，并为橄榄物种的分子育种提供了基础。