Lin Yuling, Min Jiumeng, Lai Ruilian, Wu Zhangyan, Chen Yukun, Yu Lili, Cheng Chunzhen, Jin Yuanchun, Tian Qilin, Liu Qingfeng, Liu Weihua, Zhang Chengguang, Lin Lixia, Zhang Dongmin, Thu Minkyaw, Zhang Zihao, Liu Shengcai, Zhong Chunshui, Fang Xiaodong, Wang Jian, Yang Huanming, Varshney Rajeev K, Yin Ye, Lai Zhongxiong
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
BGI-Shenzhen, Shenzhen 518083, China.
Gigascience. 2017 May 1;6(5):1-14. doi: 10.1093/gigascience/gix023.
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.
龙眼（Dimocarpus longan Lour.）是无患子科一种重要的亚热带水果，在10多个国家均有种植。龙眼是一种可食用的核果类水果，也是一种具有富含多酚特性的传统药材来源。树体大小、隔年结果和丛枝病仍然是严重问题。为深入了解龙眼性状的基因组基础，组装了一个基因组草图序列。估计中国龙眼品种“红核子”的基因组草图（约471.88 Mb）包含31007个基因和261.88 Mb的重复序列。在该基因组中未检测到近期的全基因组范围复制事件。对13个栽培龙眼品种进行全基因组重测序和分析揭示了遗传多样性程度。比较转录组研究结合全基因组分析揭示了富含多酚和抗病特性。参与次生代谢的基因，特别是那些来自具有组织特异性表达的显著扩增（DHS、SDH、F3΄H、ANR和UFGT）和收缩（PAL、CHS和F3΄5΄H）基因家族的基因，可能是龙眼果实中观察到的多酚类化合物高积累水平的重要贡献者。编码核苷酸结合位点富含亮氨酸重复序列（NBS-LRR）和富含亮氨酸重复序列类受体激酶蛋白的基因数量众多，以及NBS-LRR家族近期的扩增和收缩，表明该果树对昆虫、真菌和细菌具有抗性的基因组基础。这些数据为龙眼基因组的进化和多样性提供了见解。比较基因组和转录组分析提供了有关龙眼特异性状的信息，特别是涉及其富含多酚和抗病特性的基因。
