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

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...

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Bibliographic Details
Published in:PeerJ (San Francisco, CA) CA), 2020-06, Vol.8, p.e9114-e9114, Article e9114
Main Authors: Wang, Jiawei, Liu, Weizhen, Zhu, Dongzi, Zhou, Xiang, Hong, Po, Zhao, Hongjun, Tan, Yue, Chen, Xin, Zong, Xiaojuan, Xu, Li, Zhang, Lisi, Wei, Hairong, Liu, Qingzhong
Format: Article
Language:English
Subjects:
10× Genomics chromium
Agricultural Science
Bioinformatics
Chromosomes
Cultivars
Deoxyribonucleic acid
Diploids
DNA
Food quality
Genes
Genome assembly
Genome sequencing
Genomes
Genomics
Homology
Linked reads
Nucleotide sequence
Plant breeding
Plant Science
Proteins
Prunus avium
Ribonucleic acid
RNA
Species
Sweet cherry
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Summary: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 (2 n = 2 x = 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.
ISSN:2167-8359
2167-8359
DOI:10.7717/peerj.9114