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05 01, 2017;6 (5): 1-14.

Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics.

Yuling Lin, Jiumeng Min, Ruilian Lai, Zhangyan Wu, Yukun Chen, Lili Yu, Chunzhen Cheng, Yuanchun Jin, Qilin Tian, Qingfeng Liu, Weihua Liu, Chengguang Zhang, Lixia Lin, Dongmin Zhang, Minkyaw Thu, Zihao Zhang, Shengcai Liu, Chunshui Zhong, Xiaodong Fang, Jian Wang, Huanming Yang, Rajeev K Varshney, Ye Yin, Zhongxiong Lai
Author Information
  1. Yuling Lin: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  2. Jiumeng Min: BGI-Shenzhen, Shenzhen 518083, China.
  3. Ruilian Lai: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  4. Zhangyan Wu: BGI-Shenzhen, Shenzhen 518083, China.
  5. Yukun Chen: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  6. Lili Yu: BGI-Shenzhen, Shenzhen 518083, China.
  7. Chunzhen Cheng: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  8. Yuanchun Jin: BGI-Shenzhen, Shenzhen 518083, China.
  9. Qilin Tian: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  10. Qingfeng Liu: BGI-Shenzhen, Shenzhen 518083, China.
  11. Weihua Liu: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  12. Chengguang Zhang: BGI-Shenzhen, Shenzhen 518083, China.
  13. Lixia Lin: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  14. Dongmin Zhang: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  15. Minkyaw Thu: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  16. Zihao Zhang: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  17. Shengcai Liu: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  18. Chunshui Zhong: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
  19. Xiaodong Fang: BGI-Shenzhen, Shenzhen 518083, China.
  20. Jian Wang: BGI-Shenzhen, Shenzhen 518083, China.
  21. Huanming Yang: BGI-Shenzhen, Shenzhen 518083, China.
  22. Rajeev K Varshney: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
  23. Ye Yin: BGI-Shenzhen, Shenzhen 518083, China.
  24. Zhongxiong Lai: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
PMID: 28368449 DOI: 10.1093/gigascience/gix023

Abstract

Longan (Dimocarpus longan Lour.), an important subtropical fruit in the family Sapindaceae, is grown in more than 10 countries. Longan is an edible drupe fruit and a source of traditional medicine with polyphenol-rich traits. Tree size, alternate bearing, and witches' broom disease still pose serious problems. To gain insights into the genomic basis of longan traits, a draft genome sequence was assembled. The draft genome (about 471.88 Mb) of a Chinese longan cultivar, "Honghezi," was estimated to contain 31 007 genes and 261.88 Mb of repetitive sequences. No recent whole-genome-wide duplication event was detected in the genome. Whole-genome resequencing and analysis of 13 cultivated D. longan accessions revealed the extent of genetic diversity. Comparative transcriptome studies combined with genome-wide analysis revealed polyphenol-rich and pathogen resistance characteristics. Genes involved in secondary metabolism, especially those from significantly expanded (DHS, SDH, F3΄H, ANR, and UFGT) and contracted (PAL, CHS, and F3΄5΄H) gene families with tissue-specific expression, may be important contributors to the high accumulation levels of polyphenolic compounds observed in longan fruit. The high number of genes encoding nucleotide-binding site leucine-rich repeat (NBS-LRR) and leucine-rich repeat receptor-like kinase proteins, as well as the recent expansion and contraction of the NBS-LRR family, suggested a genomic basis for resistance to insects, fungus, and bacteria in this fruit tree. These data provide insights into the evolution and diversity of the longan genome. The comparative genomic and transcriptome analyses provided information about longan-specific traits, particularly genes involved in its polyphenol-rich and pathogen resistance characteristics.

Keywords

Longan genome genetic diversity pathogen resistance polyphenols biosynthesis

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MeSH Term

Alternative Splicing
Evolution, Molecular
Fruit
Gene Expression Regulation, Plant
Genome, Plant
Phylogeny
Polymorphism, Single Nucleotide
Polyphenols
Sapindaceae
Sequence Analysis, RNA

Chemicals

Polyphenols
Journal Article Research Support, Non-U.S. Gov't

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