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Data released on March 22, 2017

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): Supporting data for "Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics" GigaScience Database. http://dx.doi.org/10.5524/100276 RIS BibTeX Text

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.

Contact Submitter

Related manuscripts:

doi:10.1093/gigascience/gix023

Accessions (data included in GigaDB):

BioProject: PRJNA305337
BioProject: PRJNA326792

Genomic

http://gigadb.org/images/data/cropped/100276.jpg

Funding:

  • Funding body - Chinese Ministry of Education
  • Award ID - 20093515110005
  • Comment - The Doctoral Program of Higher Education of the Chinese Ministry of Education
  • Funding body - Chinese Ministry of Education
  • Award ID - 20123515120008
  • Comment - The Doctoral Program of Higher Education of the Chinese Ministry of Education
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31572088
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31272149
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31201614
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31078717
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31672127
  • Funding body - Fujian Provincial Department of Science & Technology
  • Award ID - 2015NZ0002-1
  • Comment - Science and Technology Plan Major Projects of Fujian Province
  • Funding body - Fujian Provincial Department of Science & Technology
  • Award ID - 2015J06004
  • Comment - Natural Science Funds for Distinguished Young Scholar in Fujian Province
  • Funding body - Fujian Provincial Department of Education
  • Award ID - 20151104
  • Comment - The program for New Century Excellent Talents in Fujian Province
  • Funding body - Fujian Provincial Department of Education
  • Award ID - JA14099
  • Comment - The Education Department of Fujian Province Science and Technology Project
  • Funding body - Fujian Agriculture and Forestry University
  • Award ID - 612014028
  • Comment - The Program for High-level University Construction of the Fujian Agriculture and Forestry University
  • Funding body - Fujian Agriculture and Forestry University
  • Award ID - xjq201405
  • Comment - Natural Science Funds for Distinguished Young Scholar of the Fujian Agriculture and Forestry University

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
GSM2236758128017longan Dimocarpus longan Description:Total RNAs were isolated from root tis...
Alternative names: 'sijimi' -R
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
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GSM2236759128017longan Dimocarpus longan Description:Total RNAs were isolated from stem tis...
Alternative names: 'sijimi' -S
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
GSM2236760128017longan Dimocarpus longan Description:Total RNAs were isolated from leaf tis...
Alternative names: 'sijimi' -L
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
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GSM2236761128017longan Dimocarpus longan Description:Total RNAs were isolated from flowerbu...
Alternative names: 'sijimi' -FB
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
GSM2236762128017longan Dimocarpus longan Description:Total RNAs were isolated from flower t...
Alternative names: 'sijimi' -F
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
GSM2236763128017longan Dimocarpus longan Description:Total RNAs were isolated from youngfru...
Alternative names: 'sijimi' -YF
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
GSM2236764128017longan Dimocarpus longan Description:Total RNAs were isolated from pericarp...
Alternative names: 'sijimi' -P1
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
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GSM2236765128017longan Dimocarpus longan Description:Total RNAs were isolated from pulp tis...
Alternative names: 'sijimi' -P2
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
GSM2236766128017longan Dimocarpus longan Description:Total RNAs were isolated from seed tis...
Alternative names: 'sijimi' -S
Sample relationship:isSameSpecimenAs:GSM2236758-GS...
...
+
SAMN04320697128017longan Dimocarpus longan Description:DNA extracted from the leaf of a 80-10...
Alternative names:ancient longan tree No.1
Sample relationship:isSameSpecimenAs:SAMN04451654-...
...
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Displaying 1-10 of 14 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
File Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDFile TypeFile FormatSizeRelease Date 
Sequence variantsVCF13.49 MB2017-03-16
Sequence variantsVCF25.19 MB2017-03-16
Sequence variantsVCF17.48 MB2017-03-16
Sequence variantsVCF11.33 MB2017-03-16
Sequence variantsVCF9.21 MB2017-03-16
Coding sequenceFASTA12.98 MB2017-03-16
AnnotationGFF2.21 MB2017-03-16
AnnotationIPR234.31 KB2017-03-16
AnnotationIPR443.61 KB2017-03-16
AnnotationWEGO111.89 KB2017-03-16
Displaying 11-20 of 42 File(s).

History:

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