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

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

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.

Original languageEnglish
Article numbergiz112
JournalGigaScience
Volume8
Issue number9
DOIs
Publication statusPublished - 1 Sep 2019

Fingerprint

Genes
Genome
Nuts
Breeding
Fagaceae
Quercus
Disease Resistance
Ecosystem
China
Ecosystems
Proteins
Molecules

Keywords

  • Castanea mollissima
  • annotation
  • evolution
  • genome assembly

Cite this

Xing, Y., Liu, Y., Zhang, Q., Nie, X., Sun, Y., Zhang, Z., ... Qin, L. (2019). Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). GigaScience, 8(9), [giz112]. https://doi.org/10.1093/gigascience/giz112
Xing, Yu ; Liu, Yang ; Zhang, Qing ; Nie, Xinghua ; Sun, Yamin ; Zhang, Zhiyong ; Li, Huchen ; Fang, Kefeng ; Wang, Guangpeng ; Huang, Hongwen ; Bisseling, Ton ; Cao, Qingqin ; Qin, Ling. / Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). In: GigaScience. 2019 ; Vol. 8, No. 9.
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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.",
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Xing, Y, Liu, Y, Zhang, Q, Nie, X, Sun, Y, Zhang, Z, Li, H, Fang, K, Wang, G, Huang, H, Bisseling, T, Cao, Q & Qin, L 2019, 'Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)', GigaScience, vol. 8, no. 9, giz112. https://doi.org/10.1093/gigascience/giz112

Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). / Xing, Yu; Liu, Yang; Zhang, Qing; Nie, Xinghua; Sun, Yamin; Zhang, Zhiyong; Li, Huchen; Fang, Kefeng; Wang, Guangpeng; Huang, Hongwen; Bisseling, Ton; Cao, Qingqin; Qin, Ling.

In: GigaScience, Vol. 8, No. 9, giz112, 01.09.2019.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima)

AU - Xing, Yu

AU - Liu, Yang

AU - Zhang, Qing

AU - Nie, Xinghua

AU - Sun, Yamin

AU - Zhang, Zhiyong

AU - Li, Huchen

AU - Fang, Kefeng

AU - Wang, Guangpeng

AU - Huang, Hongwen

AU - Bisseling, Ton

AU - Cao, Qingqin

AU - Qin, Ling

PY - 2019/9/1

Y1 - 2019/9/1

N2 - 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.

AB - 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.

KW - Castanea mollissima

KW - annotation

KW - evolution

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SN - 2047-217X

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