A de novo assembly of the sweet cherry ( Prunus avium cv. Tieton) genome using linked-read sequencing technology

PeerJ

article

Jiawei Wang¹  Weizhen Liu²  Dongzi Zhu¹  Xiang Zhou³  Po Hong¹  Hongjun Zhao¹  Yue Tan¹  Xin Chen¹  Xiaojuan Zong¹  Li Xu¹  Lisi Zhang¹  Hairong Wei¹  Qingzhong Liu¹ 

[1] Scientific Observation and Experiment Station of Fruits in Huang-huai Area, Ministry of Agriculture, Shandong Institute of Pomology;School of Computer Science and Technology, Wuhan University of Technology;Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University

关键词: Sweet cherry;    Genome sequencing;    Genome assembly;    10× Genomics chromium;    Linked reads;   

DOI  :  10.7717/peerj.9114

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

【 授权许可】

CC BY