Supporting data for "The draft genome sequence of a desert tree Populus pruinosa"

Dataset type: Genomic
Data released on July 18, 2017

Liu J; Ma J; Ma T; Wang K; Yang W; Zhang J (2017): Supporting data for "The draft genome sequence of a desert tree Populus pruinosa" GigaScience Database. http://dx.doi.org/10.5524/100319

DOI10.5524/100319

Populus pruinosa is a large tree that grows in deserts and shows distinct differences in both morphology and adaptation from those of its sister species, P. euphratica. Here we present a draft genome sequence for P. pruinosa and examine genomic variations between the two species.
A total of 60 Gb of clean reads from whole-genome sequencing of a P. pruinosa individual were generated using the Illumina HiSeq2000 platform. The assembled genome is 479.3 Mb in length, with an N50 contig size of 14.0 kb and a scaffold size of 698.5 kb. 45.47% of the genome is composed of repetitive elements. We predicted 35,131 protein-coding genes, of which 88.06% were functionally annotated. Gene family clustering revealed 224 unique and 640 expanded gene families in the P. pruinosa genome. Further evolutionary analysis identified numerous genes with elevated values for pairwise genetic differentiation between P. pruinosa and P.euphratica.
We provide the genome sequence and gene annotation for P. pruinosa. A large number of genetic variations were recovered by comparison of the genomes between P. pruinosa and P. euphratica. These variations will provide a valuable resource for studying the genetic bases for the phenotypic and adaptive divergence of the two sister species.

Additional details

Read the peer-reviewed publication(s):

Yang, W., Wang, K., Zhang, J., Ma, J., Liu, J., & Ma, T. (2017). The draft genome sequence of a desert tree Populus pruinosa. GigaScience, 6(9), 1–7. doi:10.1093/gigascience/gix075

Accessions (data included in GigaDB):

BioProject: PRJNA353148
BioProject: PRJNA354971





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Populus leaf RNA492479  Populus pruinosa Description:RNA extracted from the leaf tissues of...
Tissue:Leaf
Analyte type:RNA
...
+
Populus phloem RNA492479  Populus pruinosa Description:RNA extracted from the phloem tissues ...
Tissue:phloem
Analyte type:RNA
...
+
Populus xylem RNA492479  Populus pruinosa Description:RNA extracted from the xylem tissues o...
Tissue:xylem
Analyte type:RNA
...
+
SAMN06011208492479  Populus pruinosa Description:genomic DNA extracted from the leaf ti...
Tissue:leaf
Analyte type:DNA
...
+
Displaying 1-4 of 4 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
alignmentBAM3.45 GB2017-07-03
alignmentBAM9.18 GB2017-07-03
alignmentBAM19.88 GB2017-07-03
alignmentBAM32.06 GB2017-07-03
AlignmentsFASTA9.45 MB2017-07-03
annotationGFF36.34 MB2017-07-03
annotationGFF39.37 MB2017-07-03
annotationGFF54.18 MB2017-07-03
annotationGFF81.2 MB2017-07-03
annotationGFF27.58 MB2017-07-03
Displaying 1-10 of 193 File(s).
Funding body Awardee Award ID Comments
National Key Technology R&D Program of China Tao Ma 2016YFD0600101
National Key Project for Basic Research Jianquan Liu 2012CB114504
National Natural Science Foundation of China Jianquan Liu 31561123001
National Natural Science Foundation of China Tao Ma 31500502

Protocols.io:

Date Action
July 18, 2017 Dataset publish
October 2, 2017 Manuscript Link added : 10.1093/gigascience/gix075