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High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

ABSTRACT: Background: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 remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics. Findings:We generated 66 Gb and 37 Gb of raw DNA sequences, respectively, from whole-genome sequencing of a largely homozygous scarlet sage inbred line using Pacific Biosciences (PacBio) single-molecule real-time and Illumina HiSeq sequencing platforms. The PacBio de novo assembly yielded a final genome with a scaffold N50 size of 3.12 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 Salvia miltiorrhiza was estimated at 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. Conclusions: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 comparative genomics among related species.

SUBMITTER: Dong AX

PROVIDER: S-EPMC6030905 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

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High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Dong Ai-Xiang AX Xin Hai-Bo HB Li Zi-Jing ZJ Liu Hui H Sun Yan-Qiang YQ Nie Shuai S Zhao Zheng-Nan ZN Cui Rong-Feng RF Zhang Ren-Gang RG Yun Quan-Zheng QZ Wang Xin-Ning XN Maghuly Fatemeh F Porth Ilga I Cong Ri-Chen RC Mao Jian-Feng JF

GigaScience 20180701 7

<h4>Background</h4>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 remain unknown. Hence, a high-quality reference genome will be very valuable for marker-assisted breeding, genome editing, and molecular genetics.<h4>Findings</h4>We generat ...[more]

PMID: 29931210

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Project description:BackgroundAs an important perennial herbaceous flower, Salvia splendens possesses high ornamental value. Understanding its branching processes may help scientists select the best plant type. Although Salvia splendens is a frequently-used horticultural flower, only limited transcriptomic or genomic research is available in public databases. In the present study, we, for the first time, constructed a comprehensive dataset for Salvia splendens through de novo high-throughput transcriptome sequencing.Methodology/principal findingsWe performed de novo transcriptome sequencing on two different branching type plants (Strain 35 and Cailinghong) using the Illumina paired-end sequencing technology. For Strain 35, a total of 16,488,829 reads were generated and assembled into 38,498 unigenes, with a mean length of approximately 779 bp. For Cailinghong, 16,464,713 reads were generated and assembled into 34,302 unigenes, with a mean length of approximately 812 bp. Moreover, a total of 49,310 unigenes for Salvia splendens were identified, among them 33,925 (68.80%) were annotated in the non-redundant NCBI database, 25,371 (51.45%) were annotated in the Swiss-Prot database, while 24,888 (50.47%) and 9,896 (20.07%) unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. Using the Kyoto Encyclopedia of Genes and Genomes pathway database, we identified 134 differently expressed unigenes between Strain 35 and Cailinghong, and then these unigenes were mapped to 79 pathways. In addition, we detected 2,453 simple sequence repeats (SSRs).ConclusionsWe obtained a comprehensive transcriptomic information from this work and provided a valuable resource of transcript sequences of Salvia splendens in public databases. Moreover, some candidate genes potentially involved in branching were identified. Furthermore, numerous obtained SSRs might contribute to marker-assisted selection. These data could be further utilized in functional genomics studies on Salvia splendens.

Dataset Information

High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Publications

High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant.

Similar Datasets

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