Cargando…
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 as...
Autores principales: | , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278891/ https://www.ncbi.nlm.nih.gov/pubmed/32547856 http://dx.doi.org/10.7717/peerj.9114 |
_version_ | 1783543436826116096 |
---|---|
author | 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 |
author_facet | 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 |
author_sort | Wang, Jiawei |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7278891 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-72788912020-06-15 A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology 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 PeerJ Agricultural Science 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. PeerJ Inc. 2020-06-05 /pmc/articles/PMC7278891/ /pubmed/32547856 http://dx.doi.org/10.7717/peerj.9114 Text en © 2020 Wang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Agricultural Science 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 A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title | A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title_full | A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title_fullStr | A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title_full_unstemmed | A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title_short | A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology |
title_sort | de novo assembly of the sweet cherry (prunus avium cv. tieton) genome using linked-read sequencing technology |
topic | Agricultural Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7278891/ https://www.ncbi.nlm.nih.gov/pubmed/32547856 http://dx.doi.org/10.7717/peerj.9114 |
work_keys_str_mv | AT wangjiawei adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT liuweizhen adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhudongzi adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhouxiang adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT hongpo adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhaohongjun adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT tanyue adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT chenxin adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zongxiaojuan adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT xuli adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhanglisi adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT weihairong adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT liuqingzhong adenovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT wangjiawei denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT liuweizhen denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhudongzi denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhouxiang denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT hongpo denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhaohongjun denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT tanyue denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT chenxin denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zongxiaojuan denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT xuli denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT zhanglisi denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT weihairong denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology AT liuqingzhong denovoassemblyofthesweetcherryprunusaviumcvtietongenomeusinglinkedreadsequencingtechnology |