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

文献类型： 外文期刊

作者： Wang, Jiawei 1 ; Liu, Weizhen 2 ; Zhu, Dongzi 1 ; Zhou, Xiang 3 ; Hong, Po 1 ; Zhao, Hongjun 1 ; Tan, Yue 1 ; Chen, Xin 1 ;

作者机构： 1.Shandong Inst Pomol, Minist Agr, Sci Observat & Expt Stn Fruits Huang Huai Area, Tai An, Shandong, Peoples R China

2.Wuhan Univ Technol, Sch Comp Sci & Technol, Wuhan, Hubei, Peoples R China

3.Huazhong Agr Univ, Coll Anim Sci & Technol, Minist Educ, Key Lab Agr Anim Genet Breeding & Reprod, Wuhan, Hubei, Peoples R China

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

期刊名称：PEERJ （ 影响因子：2.984； 五年影响因子：3.369 ）

ISSN： 2167-8359

年卷期： 2020 年 8 卷

页码：

收录情况： SCI

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.

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