Prunus salicina Zhongli No. 6 Whole Genome v1.0 Assembly & Annotation

Publication

Huang Z, Shen F, Chen Y, Cao K, Wang L. Chromosome-scale Genome Assembly and Population Genomics Provide Insights into the Adaptation, Domestication, and Flavonoid Metabolism of Chinese Plum. Plant J. 2021 Sep 2. doi: 10.1111/tpj.15482.

Background

Plum is one of the most important horticultural crops worldwide, possessing extensive genetic diversity and high economic value and providing us vitamins, minerals, fiber, and antioxidant compounds for healthy diets. At present, the most commercially produced plums are the Chinese plum (Prunus salicina L., 2n = 2× = 16) and European plum (Prunus domestica L., 2n = 6× = 48). China is currently the largest plum (and sloes) producer, with an annual production of 6,801,187 metric tons in 2018, accounting for 53.9% of the world’s total. 

Genome facts and statistics

Chinese plum v1.0 was generated from DNA from a diploid Chinese cultivar 'Zhongli No. 6'. Chinese plum v1.0 currently consists of 8 pseudomolecules (scaffolds) representing the 8 chromosomes of plum. The genome sequencing consisted of approximately 117 fold whole genome shotgun sequencing employing Nanopore sequencing, and was assembled using CANU and SMARTdenvo. The assembled plum scaffolds cover nearly 99% of the genome. The high-quality genome assembly was comprised of 318.6 Mb (contig N50 length = 2.3 Mb) with 8 pseudomolecules. We identified 27481 high-confidence protein-coding genes. The annotated genes covered 95.9% of the complete BUSCO genes and ~92.28% of the annotated genes were expressed in at least one tissue or homologous to known proteins, which suggested that our genes annotation was very complete.
The genome sequencing and assembly was conducted by Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Science. 

Contacts: Zhenyu Huang (huangzhenyu@caas.cn) & Fei Shen (flynn123@cau.edu.cn)