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

Lin, Y; Min, J; Lai, R; Wu, Z; Chen, Y; Yu, L; Cheng, C; Jin, Y; Tian, Q; Liu, Q; Liu, W; Zhang, C; Lin, L; Hu, Y; Zhang, D; Thu, M; Zhang, Z; Liu, S; Zhong, C; Fang, X; Wang, J; Yang, H; Varshney, R, K; Yin, Y; Lai, Z (2017): GigaScience Database. http://dx.doi.org/10.5524/100276

Summary:
--------
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, 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, 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.


Files:
------
all.gene.FPKM.9sample.txt - Gene expression levels (fpkm values tables)
BUSCO_genome.full_table_genome - BUSCO assessments of genome assembly (table)
BUSCO_genome.short_summary_genome - BUSCO assessments of genome assembly (summary)
BUSCO_protein.full_table_protein - BUSCO assessments of protein (table)
BUSCO_protein.short_summary_protein - BUSCO assessments of protein (summary)
BUSCO_Transcriptome.full_table_transcriptome - BUSCO assessments of transcriptome (table)
BUSCO_Transcriptome.short_summary_transcriptome - BUSCO assessments of transcriptome (summary)
category.txt - Species name and short name
longan.gff.gz - gff Annotation
longan.iprscan.gene.GO.gz - iprscan.gene.GO Annotation
longan.iprscan.gene.ipr.gz - iprscan.gene.ipr Annotation
longan.iprscan.gene.wego.gz - iprscan.gene.wego Annotation
longan.iprscan.gz - iprscan Annotation
longan.iprscan.ipr.gene.gz - iprscan.ipr.gene Annotation
longan.KEGG.blast.gz - KEGG.blast Annotation
longan.KEGG.blast.ko.class.gz - KEGG.blast.ko.class Annotation
longan.KEGG.blast.map.fig.tar.gz - KEGG.blast.map.fig.tar Annotation
longan.KEGG.blast.map.gene.gz - KEGG.blast.map.gene Annotation
longan.cds.gz - coding sequence
longan.pep.gz - pep sequence
longan.scaffold.fa.gz - scaffold.fa sequence
longan.snp.genotype - Genotype information
longan.SwissProt.gz - SwissProt Annotation
longan.TrEMBL.gz - TrEMBL Annotation
phylogenetic_tree.newick - Phylogenetic tree files
single-copy_gene_multi_alignment.phy - Single copy genes multi-alignment files
DB.SNP.vcf - Sequence variants
FY.SNP.vcf - Sequence variants
HHZ.SNP.vcf - Sequence variants
JHLY.SNP.vcf - Sequence variants
JYW.SNP.vcf - Sequence variants
LDB.SNP.vcf - Sequence variants
LL.SNP.vcf - Sequence variants	
MQ.SNP.vcf - Sequence variants
SEY.SNP.vcf - Sequence variants
SJM.SNP.vcf - Sequence variants
SL1H.SNP.vcf - Sequence variants
SX.SNP.vcf - Sequence variants
WIL.SNP.vcf - Sequence variants
YTB.SNP.vcf - Sequence variants