Supporting data for "High quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant"

Dataset type: Genomic
Data released on June 19, 2018

Dong AX; Xin HB; Li ZJ; Liu H; Sun YQ; Nie S; Zhao ZN; Cui RF; Zhang RG; Yun QZ; Wang XN; Maghuly F; Porth I; Cong RC; Mao JF (2018): Supporting data for "High quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant" GigaScience Database. http://dx.doi.org/10.5524/100463

DOI10.5524/100463

Salvia splendens Ker-Gawler, scarlet or tropical sage, is a tender herbaceous perennial widely introduced and seen in public gardens all over the world. With few molecular resources, breeding is still restricted to traditional phenotypic selection, and the genetic mechanisms underlying phenotypic variation still remain unknown. Hence, a high quality reference genome will be very valuable for marker assisted breeding, genome editing or molecular genetics. We generated 66 gigabases (Gb) and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using PacBio Single-Molecule Real-Time (SMRT) and Illumina HiSeq sequencing platforms. PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 megabases (Mb), and a total length of 808 Mb. The repetitive sequences identified accounted for 57.52% of the genome sequence and 54,008 protein-coding genes were predicted collectively with ab initio and homology-based gene prediction from the masked genome. The divergence time between S. splendens and S. miltiorrhiza was estimated with 28.21 million years ago (Mya). Moreover, 3,797 species-specific genes and 1,187 expanded gene families were identified for the scarlet sage genome. We provide the first genome sequence and gene annotation for the scarlet sage. The availability of these resources will be of great importance for further breeding strategies, genome editing and also for comparative genomics among related species.

Additional details

Read the peer-reviewed publication(s):

Dong, A.-X., Xin, H.-B., Li, Z.-J., Liu, H., Sun, Y.-Q., Nie, S., … Mao, J.-F. (2018). High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. GigaScience, 7(7). doi:10.1093/gigascience/giy068

Accessions (data included in GigaDB):

BioProject: PRJNA422035





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN08162997180675bonfire salvia Salvia splendens Description:Genomic DNA extracted from leaves of s...
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08162997
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SAMN08162998180675bonfire salvia Salvia splendens Description:Genomic DNA extracted from leaves of s...
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08162998
...
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SAMN08162999180675bonfire salvia Salvia splendens Description:RNA extracted from root of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08162999
...
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SAMN08163000180675bonfire salvia Salvia splendens Description:RNA extracted from root of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163000
...
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SAMN08163001180675bonfire salvia Salvia splendens Description:RNA extracted from root of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163001
...
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SAMN08163002180675bonfire salvia Salvia splendens Description:RNA extracted from stem of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163002
...
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SAMN08163003180675bonfire salvia Salvia splendens Description:RNA extracted from stem of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163003
...
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SAMN08163004180675bonfire salvia Salvia splendens Description:RNA extracted from stem of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163004
...
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SAMN08163005180675bonfire salvia Salvia splendens Description:RNA extracted from leaf of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163005
...
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SAMN08163006180675bonfire salvia Salvia splendens Description:RNA extracted from leaf of red flower
Alternative names:scarlet sage
Alternative accession-BioSample:SAMN08163006
...
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Displaying 1-10 of 32 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
otherUNKNOWN88.27 MB2018-05-30
otherUNKNOWN40.37 MB2018-05-30
Sequence assemblyFASTA781.34 MB2018-05-30
scriptPython0.88 KB2018-05-30
Coding SequenceFASTA78.42 MB2018-05-30
annotationGFF85.3 MB2018-05-30
protein sequenceFASTA36.58 MB2018-05-30
transcriptome sequenceFASTA99.12 MB2018-05-30
ReadmeTEXT3.23 KB2018-05-30
Repeat sequenceGFF100.95 MB2018-05-30
Displaying 1-10 of 14 File(s).
Funding body Awardee Award ID Comments
Fundamental Research Funds for the Central Universities Jian-Feng Mao YX2013-41 Genetics of adaptative variation in conifer trees
Beijing Key Laboratory of Greening Plants Breeding Hai-Bo Xin Z201605 Genome sequencing of scalar sage
Date Action
June 19, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy068