A haplotype-resolved genome assembly of Malus domestica ‘Red Fuji’

Haixu Peng; Yating Yi; Jinrong Li; You Qing; Xuyang Zhai; Yulin Deng; Ji Tian; Jie Zhang; Yujing Hu; Xiaoxiao Qin; Yanfen Lu; Yuncong Yao; Sen Wang; Yi Zheng

doi:10.1038/s41597-024-03401-1

Scientific Data (Jun 2024)

A haplotype-resolved genome assembly of Malus domestica ‘Red Fuji’

Haixu Peng,
Yating Yi,
Jinrong Li,
You Qing,
Xuyang Zhai,
Yulin Deng,
Ji Tian,
Jie Zhang,
Yujing Hu,
Xiaoxiao Qin,
Yanfen Lu,
Yuncong Yao,
Sen Wang,
Yi Zheng

Affiliations

Haixu Peng: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yating Yi: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Jinrong Li: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
You Qing: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Xuyang Zhai: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yulin Deng: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Ji Tian: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Jie Zhang: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yujing Hu: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Xiaoxiao Qin: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yanfen Lu: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yuncong Yao: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Sen Wang: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture
Yi Zheng: Beijing Key Laboratory for Agriculture Application and New Technique, Colege of Plant Science and Technology, Bejing University of Agriculture

DOI: https://doi.org/10.1038/s41597-024-03401-1
Journal volume & issue: Vol. 11, no. 1
pp. 1 – 9

Abstract

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Abstract The ‘Red Fuji’ apple (Malus domestica), is one of the most important and popular economic crops worldwide in the fruit industry. Using PacBio HiFi long reads and Hi-C reads, we assembled a high-quality haplotype-resolved genome of ‘Red Fuji’, with sizes of 668.7 and 668.8 Mb, and N50 sizes of 34.1 and 31.4 Mb. About 97.2% of sequences were anchored in 34 chromosomes. We annotated both haploid genomes, identifying a total of 95,439 protein-coding genes in the two haplotype genomes, with 98% functional annotation. The haplotype-resolved genome of ‘Red Fuji’ apple stands as a precise benchmark for an array of analyses, such as comparative genomics, transcriptomics, and allelic expression studies. This comprehensive resource is paramount in unraveling variations in allelic expression, advancing quality improvements, and refining breeding efforts.

Published in Scientific Data

ISSN: 2052-4463 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science
Website: https://www.nature.com/sdata/

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