title: Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics.
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.
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Yuling
authors.initials: Y
authors.lastname: Lin
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Jiumeng
authors.initials: J
authors.lastname: Min
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Ruilian
authors.initials: R
authors.lastname: Lai
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Zhangyan
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Yukun
authors.initials: Y
authors.lastname: Chen
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Lili
authors.initials: L
authors.lastname: Yu
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Chunzhen
authors.initials: C
authors.lastname: Cheng
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Yuanchun
authors.initials: Y
authors.lastname: Jin
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Qilin
authors.initials: Q
authors.lastname: Tian
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Qingfeng
authors.initials: Q
authors.lastname: Liu
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Weihua
authors.initials: W
authors.lastname: Liu
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Chengguang
authors.initials: C
authors.lastname: Zhang
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Lixia
authors.initials: L
authors.lastname: Lin
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Dongmin
authors.initials: D
authors.lastname: Zhang
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Minkyaw
authors.initials: M
authors.lastname: Thu
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Zihao
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Shengcai
authors.initials: S
authors.lastname: Liu
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Chunshui
authors.initials: C
authors.lastname: Zhong
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Fang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.|James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.
authors.forename: Huanming
authors.initials: H
authors.lastname: Yang
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.|School of Plant Biology, The University of Western Australia, Crawley, Perth, Australia.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: BGI-Shenzhen, Shenzhen 518083, China.
authors.forename: Ye
authors.initials: Y
authors.lastname: Yin
authors.affiliation: Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
authors.forename: Zhongxiong
authors.initials: Z
authors.lastname: Lai
mesh_terms: D017398:Alternative Splicing; D019143:Evolution, Molecular; D005638:Fruit / Q000235:genetics*; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D059808:Polyphenols / Q000096:biosynthesis; D029631:Sapindaceae / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D059808:Polyphenols
keywords: Longan genome; genetic diversity; pathogen resistance; polyphenols biosynthesis