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
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.
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):
|Sample ID||Taxonomic ID||Common Name||Genbank Name||Scientific Name||Sample Attributes|
|SAMN07764301||111851||Ammopiptanthus nanus|| Description:DNA isolated from leaf of Ammopiptanth...|
... Description:DNA isolated from leaf of Ammopiptanthus nanus
Geographic location (country and/or sea,region):China:Xinjiang Autonomous Region:Wuqia county:Kangsu town
Collected by:M Abla; X Wang; S Wei
Environment (biome):desert [ENVO_01001357]