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Data released on June 08, 2018

Supporting data for "Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub"

Gao, F; Wang, X; Li, X; Xu, M; Li, H; Abla, M; Sun, H; Wei, S; Feng, J; Zhou, Y (2018): Supporting data for "Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub" GigaScience Database. http://dx.doi.org/10.5524/100466 RIS BibTeX Text

Ammopiptanthus nanus is a rare broad-leaved shrub in the desert and arid regions of Central Asia. This plant species exhibits extremely high tolerance to drought and freezing and has been used in abiotic tolerance research in plants. As a relic of the Tertiary period, A. nanus is of great significance to plant biogeographic research in the ancient Mediterranean region. Here we report a draft genome assembly using the PacBio platform and gene annotation for A. nanus.
A total of 64.72 gigabases (Gb) of raw PacBio Sequel reads were generated from four 20 kb libraries. After filtering, 64.53 Gb of clean reads were obtained, giving 72.59 × coverage depth. Assembly using Canu gave an assembly length of 823.74 Mb, with a contig N50 of 2.76 Mb. The final size of the assembled A. nanus genome was close to the 889 Mb estimated by k-mer analysis. The gene annotation completeness was evaluated by BUSCO, and 1,327 out of the 1,440 conserved genes (92.15%) could be found in the A. nanus assembly. Genome annotation revealed that 74.08% of the A. nanus genome is composed of repetitive elements, and 53.44% of long terminal repeat elements (LTRs). We predicted 37,188 protein-coding genes, of which 96.53% were functionally annotated.
The genomic sequences of A. nanus could be a valuable source for comparative genomic analysis in the legume family, and will be useful for understanding the phylogenetic relationships of the Thermopsideae and the evolutionary response of plant species to the Qinghai Tibetan Plateau uplift.

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Accessions (data included in GigaDB):

BioProject: PRJNA413722

Keywords:

ammopiptanthus nanus pacbio sequencing genome assembly genome annotation 

Genomic

http://gigadb.org/images/data/cropped/100466.png

Funding:

  • Funding body - National Natural Science Foundation of China
  • Award ID - 31670335
  • Awardee - F Gao
  • Funding body - National Natural Science Foundation of China
  • Award ID - 31770363
  • Awardee - Y Zhou
  • Funding body - Chinese Ministry of Education
  • Award ID - B08044
  • Comment - 111 projects
  • Awardee - Y Zhou
  • Funding body - Chinese Ministry of Education
  • Award ID - YLDXXK201819
  • Comment - 985 projects
  • Awardee - Y Zhou

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN07764301111851  Ammopiptanthus nanus Description:DNA isolated from leaf of Ammopiptanth...
Alternative accession-BioProject:PRJNA413722
Analyte type:DNA
...
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Displaying 1-1 of 1 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 
protein sequenceFASTA14.19 MB2018-06-05
Coding SequenceFASTA41.23 MB2018-06-05
annotationGFF144.87 KB2018-06-05
mixed archivearchive57.82 KB2018-06-05
annotationGFF162.09 KB2018-06-05
annotationGFF12.23 KB2018-06-05
annotationGFF134.71 KB2018-06-05
Sequence assemblyFASTA795.41 MB2018-06-05
annotationGFF10.59 KB2018-06-05
annotationUNKNOWN1 MB2018-06-05
Displaying 1-10 of 13 File(s).

History:

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