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

被引:14
|
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 ]
Zong, Xiaojuan [1 ]
Xu, Li [1 ]
Zhang, Lisi [1 ]
Wei, Hairong [1 ]
Liu, Qingzhong [1 ]
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
来源
PEERJ | 2020年 / 8卷
关键词
Sweet cherry; Genome sequencing; Genome assembly; 10x Genomics chromium; Linked reads; RNA; ANNOTATION; ALIGNMENT; INFERENCE; PROGRAM; FAMILY; GENES;
D O I
10.7717/peerj.9114
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
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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页数:18
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