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Data released on June 06, 2018

Supporting data for "Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly"

Yin, D; Ji, C; Ma, X; Li, H; Zhang, W; Li, S; liu, F; Zhao, K; Li, F; Li, K; Ning, L; He, J; Wang, Y; Zhao, F; Xie, Y; Zheng, H; Zhang, X; Zhang, Y; Zhang, J (2018): Supporting data for "Genome of an allotetraploid wild peanut Arachis monticola: a de novo assembly" GigaScience Database. http://dx.doi.org/10.5524/100453 RIS BibTeX Text

Arachis monticola (2n = 4x = 40) is the only allotetraploid wild peanut within section Arachis, with an AABB-type genome of about ~2.7 Gb. The AA-type subgenome is derived from diploid wild peanut Arachis duranensis, and the BB-type subgenome is derived from diploid wild peanut Arachis ipaensis. A. monticola is regarded either as the direct progenitor of the cultivated peanut or as an introgressive derivative between the cultivated peanut and wild species. The large polyploidy genome structure and enormous nearly identical regions of the genome make the assembly of chromosomal pseudomolecules very challenging. Here we report the first reference quality assembly of the A. monticola genome, using a series of advanced technologies. The final whole genome of A. monticola is ~2.62 Gb, and has a contig N50 and scaffold N50 of 106.66 Kb and 124.92 Mb, respectively. The vast majority (91.83%) of the assembled sequence was anchored onto the 20 pseudo-chromosomes and 96.07% of assemblies were accurately separated into AA- and BB- subgenomes. We demonstrated efficiency of the current state of the strategy for de novo assembly of the highly complex allotetraploid species, wild peanut (A. monticola), based on whole-genome shotgun sequencing, single molecule real-time (SMRT) sequencing, high-throughput chromosome conformation capture (Hi-C) technology and BioNano optical genome map. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within Arachis genus and among legume crops.

Contact Submitter

Accessions (data included in GigaDB):

BioProject: PRJNA430760

Keywords:

peanut genome arachis monticola de novo assembly hi-c smrt 

Genomic, Transcriptomic

http://gigadb.org/images/data/cropped/100453.png

Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 31471525
  • Awardee - D Yin
  • Funding body - NSFC-Henan United Fund
  • Award ID - U1704232
  • Comment - Key program
  • Awardee - D Yin
  • Funding body - Henan Province
  • Award ID - 161100111000
  • Comment - key scientific and technological project
  • Awardee - D Yin
  • Funding body - Henan Province
  • Award ID - S2012-05-G03
  • Comment - Henan modern agriculture industry technology system
  • Awardee - D Yin
  • Funding body - Henan Province
  • Award ID - 2018JR0001
  • Comment - Innovation Scientists and Technicians Troop Construction Projects of Henan Province
  • Awardee - D Yin

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Yin_lab_Peanut_DNA227691  Arachis monticola Description:DNA extracted from the leaf of the pea...
Molecular data type:DNA
Isolate:PI 263393
...
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Yin_lab_Peanut_RNA227691  Arachis monticola Description:RNA extracted from the leaf of the pea...
Molecular data type:RNA
Isolate:PI 263393
...
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Displaying 1-2 of 2 Sample(s).

Files: (FTP site) Table Settings

Columns:

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

File NameSample IDData TypeFile FormatSizeRelease Date 
annotationGFF59.16 MB2018-05-23
annotationGFF593.09 MB2018-05-23
BLASTUNKNOWN476.84 MB2018-05-23
Coding SequenceFASTA72.9 MB2018-05-23
Genome sequenceFASTA2.27 GB2018-05-23
Genome sequenceFASTA2.46 GB2018-05-23
Optical mapUNKNOWN16.99 MB2018-05-23
Optical mapUNKNOWN1.38 GB2018-05-23
otherTSV0.21 KB2018-05-23
otherTSV0.19 KB2018-05-23
Displaying 1-10 of 14 File(s).

History:

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