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Nature communications
10 16, 2019;10 (1): 4702.

The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis.

Lisong Hu, Zhongping Xu, Maojun Wang, Rui Fan, Daojun Yuan, Baoduo Wu, Huasong Wu, Xiaowei Qin, Lin Yan, Lehe Tan, Soonliang Sim, Wen Li, Christopher A Saski, Henry Daniell, Jonathan F Wendel, Keith Lindsey, Xianlong Zhang, Chaoyun Hao, Shuangxia Jin
Author Information
  1. Lisong Hu: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  2. Zhongping Xu: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. ORCID
  3. Maojun Wang: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. ORCID
  4. Rui Fan: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  5. Daojun Yuan: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. ORCID
  6. Baoduo Wu: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  7. Huasong Wu: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  8. Xiaowei Qin: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  9. Lin Yan: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  10. Lehe Tan: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China.
  11. Soonliang Sim: Academy of Sciences Malaysia, Kuala Lumpur, 50480, Malaysia.
  12. Wen Li: Department of Plant & Environmental Science, Clemson University, Clemson, SC, 29631, USA.
  13. Christopher A Saski: Department of Plant & Environmental Science, Clemson University, Clemson, SC, 29631, USA.
  14. Henry Daniell: Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
  15. Jonathan F Wendel: Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA. ORCID
  16. Keith Lindsey: Department of Biosciences, Durham University, Durham, DH1 3LE, UK. ORCID
  17. Xianlong Zhang: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. ORCID
  18. Chaoyun Hao: Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan, 571533, China. cyhao_catas@163.com.
  19. Shuangxia Jin: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China. jsx@mail.hzau.edu.cn.
PMID: 31619678 DOI: 10.1038/s41467-019-12607-6

Abstract

Black pepper (Piper nigrum), dubbed the 'King of Spices' and 'Black Gold', is one of the most widely used spices. Here, we present its reference genome assembly by integrating PacBio, 10x Chromium, BioNano DLS optical mapping, and Hi-C mapping technologies. The 761.2 Mb sequences (45 scaffolds with an N50 of 29.8 Mb) are assembled into 26 pseudochromosomes. A phylogenomic analysis of representative plant genomes places magnoliids as sister to the monocots-eudicots clade and indicates that black pepper has diverged from the shared Laurales-Magnoliales lineage approximately 180 million years ago. Comparative genomic analyses reveal specific gene expansions in the glycosyltransferase, cytochrome P450, shikimate hydroxycinnamoyl transferase, lysine decarboxylase, and acyltransferase gene families. Comparative transcriptomic analyses disclose berry-specific upregulated expression in representative genes in each of these gene families. These data provide an evolutionary perspective and shed light on the metabolic processes relevant to the molecular basis of species-specific piperine biosynthesis.

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MeSH Term

Acyltransferases
Alkaloids
Benzodioxoles
Carboxy-Lyases
Chromosome Mapping
Chromosomes
Cytochrome P-450 Enzyme System
Gene Expression Profiling
Genome, Plant
Genomics
Glycosyltransferases
Phylogeny
Piper nigrum
Piperidines
Polyunsaturated Alkamides

Chemicals

Alkaloids
Benzodioxoles
Piperidines
Polyunsaturated Alkamides
Cytochrome P-450 Enzyme System
Acyltransferases
Glycosyltransferases
Carboxy-Lyases
lysine decarboxylase
piperine
Journal Article Research Support, Non-U.S. Gov't

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