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.
Highlights
Dimocarpus longan Lour. (D. longan) originated from South China or Southeast Asia and is commonly called longan or “dragon eye” in Asia
The estimated 0.88% heterozygosity rate in the whole genome of the longan “HHZ” cultivar is reported here for the first time. This heterozygosity rate is higher than the rates reported for kiwifruit (0.536%) [16], plum (0.03%) [12,22], and poplar [23], and lower than the rates for pear (1–2% sequence divergence) [15] and pineapple (1.89% in F153, 1.98% in MD2, 2.93% in CB5) [17]. These results imply that the idea that fruit trees always have high heterozygosity, which may be due to artificial grafting and/or asexual reproduction
We identified a total of 1 255 816 single nucleotide polymorphisms (SNPs) and 34 390 indels across the nine longan tissues and found that the highest number of SNPs and indels were detected in young fruit (161 897) and leaf (4673), respectively, suggesting that the expressed transcripts may be more diverse in these two tissues
Summary
Dimocarpus longan Lour. (D. longan) originated from South China or Southeast Asia and is commonly called longan or “dragon eye” in Asia. (D. longan) originated from South China or Southeast Asia and is commonly called longan or “dragon eye” in Asia. It is an important tropical/subtropical evergreen fruit tree that has a diploid genome (2n = 2x = 30) and belongs to the family Sapindaceae. Longan is widely cultivated in Southeast Asia, South Asia, Australia, and Hawaii [1]. As an edible drupe fruit and source of traditional medicine, longan is grown in most areas of Southern China, including Guangdong, Guangxi, Fujian, Sichuan, Yunnan, and Hainan [3]. In China, there are more than 300 longan varieties; most are landraces and farm varieties, a few wild populations exist in Hainan, Guangdong, Guangxi, and Yunnan provinces [7,8]. To identify cultivars and improve longan breeding, knowledge of the longan genetic background is required
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