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05 09, 2023;10 (1): 259.

Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub.

Shi-Wei Zhao, Jing-Fang Guo, Lei Kong, Shuai Nie, Xue-Mei Yan, Tian-Le Shi, Xue-Chan Tian, Hai-Yao Ma, Yu-Tao Bao, Zhi-Chao Li, Zhao-Yang Chen, Ren-Gang Zhang, Yong-Peng Ma, Yousry A El-Kassaby, Ilga Porth, Wei Zhao, Jian-Feng Mao
Author Information
  1. Shi-Wei Zhao: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  2. Jing-Fang Guo: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  3. Lei Kong: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  4. Shuai Nie: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  5. Xue-Mei Yan: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  6. Tian-Le Shi: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  7. Xue-Chan Tian: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  8. Hai-Yao Ma: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  9. Yu-Tao Bao: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  10. Zhi-Chao Li: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  11. Zhao-Yang Chen: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
  12. Ren-Gang Zhang: Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. ORCID
  13. Yong-Peng Ma: Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China. ORCID
  14. Yousry A El-Kassaby: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. ORCID
  15. Ilga Porth: Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada. ORCID
  16. Wei Zhao: Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden. zhao.wei@umu.se.
  17. Jian-Feng Mao: National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China. jianfeng.mao@umu.se. ORCID
PMID: 37156769 DOI: 10.1038/s41597-023-02171-6

Abstract

Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.

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Grants

  1. 32171816/National Natural Science Foundation of China (National Science Foundation of China)

MeSH Term

Haplotypes
Magnoliopsida
Molecular Sequence Annotation
Phylogeny
Genome, Plant
Chromosomes, Plant
Dataset Journal Article
Article has an altmetric score of 1

Word Cloud

Created with Highcharts 10.0.0nepalensisCgenomeassemblyCoriarianitrogen-fixingshrubrootFrankiatanninresourcechromosome-scale99WallCoriariaceaeformsnodulesactinomyceteOilsextractsreportedbacteriostaticinsecticidalbarkprovidesvaluablecombiningPacBioHiFisequencingHi-Cscaffoldingtechniquesgeneratedhaplotype-resolvedapproximately620 MbsizecontigN5011 Mb9%totalassembledsequencesanchored40pseudochromosomespredicted60862protein-codinggenes5%annotateddatabasesidentified939tRNAs7297rRNAs982ncRNAsexpectedsignificantunderstandinggeneticbasisnodulationtoxicitybiosynthesisHaplotype-resolvednon-legume

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