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

Dataset type: Genomic
Data released on June 08, 2018

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.


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.

Additional details

Read the peer-reviewed publication(s):

Gao, F., Wang, X., Li, X., Xu, M., Li, H., Abla, M., … Zhou, Y. (2018). Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. GigaScience. doi:10.1093/gigascience/giy074

Accessions (data included in GigaDB):

BioProject: PRJNA413722

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN07764301111851  Ammopiptanthus nanus Description:DNA isolated from leaf of Ammopiptanth...
Alternative accession-BioProject:PRJNA413722
Analyte type:DNA
Displaying 1-1 of 1 Sample(s).

File NameSample IDData TypeFile FormatSizeRelease Date 
mixed archivearchive57.82 KB2018-06-05
Coding SequenceUNKNOWN41.92 MB2018-06-05
Coding SequenceFASTA41.23 MB2018-06-05
protein sequenceFASTA14.19 MB2018-06-05
Sequence assemblyFASTA795.41 MB2018-06-05
Repeat sequenceGFF204.41 MB2018-06-05
annotationGFF10.59 KB2018-06-05
annotationUNKNOWN1 MB2018-06-05
ReadmeTEXT2.59 KB2018-06-05
annotationGFF144.87 KB2018-06-05
Displaying 1-10 of 13 File(s).
Funding body Awardee Award ID Comments
National Natural Science Foundation of China F Gao 31670335
National Natural Science Foundation of China Y Zhou 31770363
Chinese Ministry of Education Y Zhou B08044 111 projects
Chinese Ministry of Education Y Zhou YLDXXK201819 985 projects
Date Action
June 8, 2018 Dataset publish
June 15, 2018 readme.txt: additional file attribute added
June 15, 2018 File readme.txt updated
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy074