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.

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

“…These genes included 58 DlWRKYs , which were also found by Lin et al [37], and one gene Dlo_ 022548.1 ( DlWRKY 36) found in our study. Finally, after the WRKY domain scanning and sequence alignment, 55 DlWRKY genes were determined in the longan genome (Table 1).…”

“…Recently, the successful genome sequencing of longan makes it possible to analyze WRKY TFs at the whole-genome level [37]. The present study is the first to identify and characterize WRKY proteins from whole-genome sequences of longan.…”

“…Longan whole-genome sequences, transcript data, and proteins were downloaded from the NCBI Sequence Read Archive (SRA315202) or [37]. The HMM profile of the WRKY DNA binding domain (PF03106) which was extracted from the Pfam database () was used to obtain the potential members of the longan WRKY genes [59] and used to search the putative WRKY genes from the longan genome with HMMER 3.0 () with the default parameters and 0.01 as the cutoff value.…”

Exploration of the effect of blue light on microRNAs involved in the accumulation of functional metabolites of longan embryonic calli through RNA‐sequencing

“…Clean reads were mapped to the longan reference genome using the Bowtie2 method . The expression level of genes and transcripts was calculated using RNA‐Seq by Expectation–Maximization (RSEM) software .…”

“…Moreover, the high‐throughput sequencing of agarwood showed that genes associated with secondary metabolism were regulated under red light/far‐red conditions linked to the regulation of miRNAs . However, many studies on plant RNA‐seq revealed that the related miRNAs of light regulated metabolism were different in different species . It is therefore also necessary to investigate how the miRNAs respond to light in longan ECs by RNA‐seq.…”