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

Longan (Dimocarpus longan), an important subtropical fruit, is grown in more than 10 countries of the world. Longan is an edible drupe fruit and source of traditional medicine with polyphenol-rich traits, while 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 China longan cultivar Honghezi was estimated to contain 31,007 high- quality 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, F3H, ANR, and UFGT) and contracted (PAL, CHS, and F35H) 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, and 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）是一类重要的亚热带果树，全球已有超过10个国家开展商业化种植。龙眼属于可食用核果类水果，同时也是富含多酚的传统药用原料，但树体大小、隔年结果以及丛枝病仍对其产业发展造成严重制约。为解析龙眼性状的基因组学基础，本研究组装获得了其全基因组草图序列。
以中国龙眼品种‘红核子’（Honghezi）为材料，组装得到的基因组草图大小约为471.88 Mb，经注释包含31007个高质量蛋白编码基因与261.88 Mb的重复序列，且未检测到近期发生的全基因组复制事件。对13份栽培龙眼（D. longan）种质资源开展全基因组重测序与分析，明确了其遗传多样性水平。结合全基因组分析的比较转录组研究，揭示了龙眼富含多酚与抗病性的性状特征。次生代谢相关基因，尤其是具有组织特异性表达的显著扩张基因家族（如DHS、SDH、F3H、ANR与UFGT）以及收缩基因家族（如PAL、CHS与F35H）的成员，可能是龙眼果实中多酚类物质高水平积累的关键贡献因子。编码核苷酸结合位点亮氨酸富集重复序列（nucleotide-binding site leucine-rich repeat, NBS-LRR）与亮氨酸重复序列受体激酶的基因数量较多，且NBS-LRR家族近期发生了扩张与收缩事件，这为该果树的抗虫、抗真菌与抗细菌能力提供了基因组学基础。
本研究获得的基因组数据为解析龙眼基因组的演化与多样性提供了重要线索。比较基因组学与转录组学分析揭示了龙眼的特异性状，尤其是与其富含多酚与抗病性相关的基因调控机制。