Browse Articles

Article|01 Apr 2021|OPEN
De novo assembly of a new Olea europaea genome accession using nanopore sequencing
Guodong Rao1,2,3,, Jianguo Zhang1,2,3,, Xiaoxia Liu3, Chunfu Lin4, Huaigen Xin5, Li Xue3 & Chenhe Wang3
1Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
2Key Laboratory of Tree Breeding and Cultivation, National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
3State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
4MIANNING Yuansheng Agricultural Science and Technology Co., Ltd., Liangshan Yi Autonomous Prefecture Mianning County, Sichuan 615600, China
5Biomarker Technologies Corporation, Beijing, 101300, China

Horticulture Research 8,
Article number: 64 (2021)
doi: 10.1038/hortres.2021.64
Views: 238

Received: 20 Aug 2020
Revised: 04 Jan 2021
Accepted: 11 Jan 2021
Published online: 01 Apr 2021

Abstract

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.