Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

Yu Xing; Yang Liu; Qing Zhang; Xinghua Nie; Yamin Sun; Zhiyong Zhang; Huchen Li; Kefeng Fang; Guangpeng Wang; Hongwen Huang; Ton Bisseling; Qingqin Cao; Ling Qin

doi:10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

Gigascience. 2019 Sep 1;8(9):giz112. doi: 10.1093/gigascience/giz112.

Authors

Yu Xing^{1

2}, Yang Liu², Qing Zhang², Xinghua Nie², Yamin Sun³, Zhiyong Zhang^{1

2}, Huchen Li^{1

4}, Kefeng Fang⁵, Guangpeng Wang⁶, Hongwen Huang⁷, Ton Bisseling^{1

4}, Qingqin Cao^{1

2}, Ling Qin^{1

2}

Affiliations

¹ Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China.
² College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China.
³ Research Center for Functional Genomics and Biochip, 23 Hongda St., Tianjin 300457, China.
⁴ Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands.
⁵ College of Landscape Architecture, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China.
⁶ Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, 39 E Jieyangdajie, Changli 066600, China.
⁷ South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou 510650, China.

Abstract

Background: The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima.

Findings: We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago.

Conclusions: The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.

Keywords: Castanea mollissima; annotation; evolution; genome assembly.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Fagaceae / genetics*
Genome, Plant*
Phylogeny
Whole Genome Sequencing