Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing
Jiawei Wang,Weizhen Liu,Zhu Dongzi,Hong Po,Shizhong Zhang,Shijun Xiao,Tan Yue,Chen Xin,Xu Li,Zong Xiaojuan,Lisi Zhang,Hairong Wei,Yuan Xiaohui,Qingzhong Liu +13 more
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TLDR
The chromosome-scale assembly ofsweet cherry revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry.Abstract:
Sweet cherry (Prunus avium) is an economically significant fruit species in the genus Prunus. However, in contrast to other important fruit trees in this genus, only one draft genome assembly is available for sweet cherry, which was assembled using only Illumina short-read sequences. The incompleteness and low quality of the current sweet cherry draft genome limit its use in genetic and genomic studies. A high-quality chromosome-scale sweet cherry reference genome assembly is therefore needed. A total of 65.05 Gb of Oxford Nanopore long reads and 46.24 Gb of Illumina short reads were generated, representing ~190x and 136x coverage, respectively, of the sweet cherry genome. The final de novo assembly resulted in a phased haplotype assembly of 344.29 Mb with a contig N50 of 3.25 Mb. Hi-C scaffolding of the genome resulted in eight pseudochromosomes containing 99.59% of the bases in the assembled genome. Genome annotation revealed that more than half of the genome (59.40%) was composed of repetitive sequences, and 40,338 protein-coding genes were predicted, 75.40% of which were functionally annotated. With the chromosome-scale assembly, we revealed that gene duplication events contributed to the expansion of gene families for salicylic acid/jasmonic acid carboxyl methyltransferase and ankyrin repeat-containing proteins in the genome of sweet cherry. Four auxin-responsive genes (two GH3s and two SAURs) were induced in the late stage of fruit development, indicating that auxin is crucial for the sweet cherry ripening process. In addition, 772 resistance genes were identified and functionally predicted in the sweet cherry genome. The high-quality genome assembly of sweet cherry obtained in this study will provide valuable genomic resources for sweet cherry improvement and molecular breeding.read more
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Chromosome-level draft genome of a diploid plum (Prunus salicina).
TL;DR: This work constructed the first high-quality chromosome-level plum genome using Pacific Biosciences, Illumina, and Hi-C technologies, which provides a valuable resource for facilitating plum breeding programs and studying the genetic diversity mechanisms of plums and Prunus species.
Journal ArticleDOI
Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees.
Xia Wang,Shengjun Liu,Hao Zuo,Weikang Zheng,Zhang Shanshan,Yue Huang,Gesang Pingcuo,Hong Ying,Zhao Fan,Li Yuanrong,Junwei Liu,Ting-Shuang Yi,Yanjun Zan,Robert M. Larkin,Xiuxin Deng,Zeng Xiuli,Qiang Xu +16 more
TL;DR: In this article, the authors collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492m in the Himalayas.
Journal ArticleDOI
MYB transcription factor family in sweet cherry (Prunus avium L.): genome-wide investigation, evolution, structure, characterization and expression patterns
I. A. Sabir,Muhammad Aamir Manzoor,Iftikhar Hussain Shah,Xunju Liu,M. S. Zahid,Songtao Jiu,Jiyuan J. Wang,Muhammad Abdullah,Caixi Zhang +8 more
TL;DR: In this article , a total of 69 MYB genes were investigated from the sweet cherry genome and classified into 28 subfamilies (C1-C28) based on phylogenetic and structural analysis.
Journal ArticleDOI
The draft chromosome-level genome assembly of tetraploid ground cherry (Prunus fruticosa Pall.) from long reads.
Thomas Wöhner,Ofere Francis Emeriewen,Alexander H. J. Wittenberg,Harrie Schneiders,Ilse Vrijenhoek,Júlia Halász,Károly Hrotkó,Katharina J. Hoff,Lars Gabriel,Janne Lempe,Jens Keilwagen,Thomas Berner,Mirko Schuster,Andreas Peil,Jens N. Wünsche,Stephan Kropop,Henryk Flachowsky +16 more
TL;DR: In this article, the authors used the PromethION platform and R10.3 pore type to sequence the genome of tetraploid ground cherry (Prunus fruticosa), and the final sequence was deposited at DDBJ/ENA/GenBank under the accession JAHHUK000000000.
References
More filters
Journal ArticleDOI
Circos: An information aesthetic for comparative genomics
Martin Krzywinski,Jacqueline E. Schein,Inanc Birol,Joseph M. Connors,Randy D. Gascoyne,Doug Horsman,Steven J.M. Jones,Marco A. Marra +7 more
TL;DR: Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements.
Journal ArticleDOI
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics
Brandi L. Cantarel,Pedro M. Coutinho,Corinne Rancurel,Thomas Bernard,Vincent Lombard,Bernard Henrissat +5 more
TL;DR: The Carbohydrate-Active Enzyme (CAZy) database is a knowledge-based resource specialized in the enzymes that build and breakdown complex carbohydrates and glycoconjugates and has been used to improve the quality of functional predictions of a number genome projects by providing expert annotation.
Journal ArticleDOI
InterProScan 5: genome-scale protein function classification
Philip Jones,David Binns,Hsin-Yu Chang,Matthew Fraser,Weizhong Li,Craig McAnulla,Hamish McWilliam,John Maslen,Alex L. Mitchell,Gift Nuka,Sebastien Pesseat,Antony F. Quinn,Amaia Sangrador-Vegas,Maxim Scheremetjew,Siew-Yit Yong,Rodrigo Lopez,Sarah Hunter +16 more
TL;DR: A new Java-based architecture for the widely used protein function prediction software package InterProScan is described, resulting in a flexible and stable system that is able to use both multiprocessor machines and/or conventional clusters to achieve scalable distributed data analysis.
Journal ArticleDOI
The carbohydrate-active enzymes database (CAZy) in 2013
TL;DR: The changes that have occurred in CAZy during the past 5 years are outlined and a novel effort to display the resolution and the carbohydrate ligands in crystallographic complexes of CAZymes is presented.
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