期刊
PEERJ
卷 8, 期 -, 页码 -出版社
PEERJ INC
DOI: 10.7717/peerj.9114
关键词
Sweet cherry; Genome sequencing; Genome assembly; 10x Genomics chromium; Linked reads
资金
- Shandong Provincial Key Laboratory for Fruit Biotechnology Breeding
- Special Fund for Innovation Teams of Fruit Trees in Agricultural Technology System of Shandong Province [SDAIT-06-04]
- Agricultural scientific and technological innovation project of Shandong Academy of Agricultural Science [CXGC2018F03]
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.
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