Characterizing the Leaf Transcriptome of Chrysanthemum rhombifolium (Ling et C. Shih), a Drought Resistant, Endemic Plant From China

Abstract

Chrysanthemum rhombifolium (Ling et C. Shih), an endemic plant that is extremely well-adapted to harsh environments. However, little is known about its molecular biology of the plant's resistant traits against stress, or even its molecular biology of overall plant. To investigate the molecular biology of C. rhombifolium and mechanism of stress adaptation, we performed transcriptome sequencing of its leaves using an Illumina platform. A total of 130,891 unigenes were obtained, and 97,496 (~74.5%) unigenes were annotated in the public protein database. The similarity search indicated that 40,878 and 74,084 unigenes showed significant similarities to known proteins from NCBI non-redundant and Swissprot protein databases, respectively. Of these, 56,213 and 42,005 unigenes were assigned to the Gene Ontology (GO) database and Cluster of Orthologous Groups (COG), respectively, and 38,918 unigenes were mapped into five main categories, including 18 KEGG pathways. Metabolism was the largest category (23,128, 59.4%) among the main KEGG categories, suggesting active metabolic processes in C. rhombifolium. About 2,459 unigenes were annotated to have a role in defense mechanism or stress tolerance. Transcriptome analysis of C. rhombifolium revealed the presence of 12,925 microsatellites in 10,524 unigenes and mono, trip, and dinucleotides having higher polymorphism rates. The phylogenetic analysis based on GME gene among related species confirmed the reliability of the transcriptomic data. This work is the first genetic study of C. rhombifolium as a new plant resource of stress-tolerant genes. This large number of transcriptome sequences enabled us to comprehensively understand the basic genetics of C. rhombifolium and discover novel genes that will be helpful in the molecular improvement of chrysanthemums.

The genus Chrysanthemum: Phylogeny, biodiversity, phytometabolites, and chemodiversity

“…The geographic/ecological conditions, hybridization and polyploidy play important roles in the divergence and speciation of Chrysanthemum . The comparative transcriptome analysis of CM and diploid C. boreale revealed whole-genome duplication (WGD) and gene selection patterns in these taxa ( Won et al, 2017 ); the transcriptomes of C. rhombifolium and C. dichrum were also preliminarily characterized ( Liu et al, 2021a ; Zhang et al, 2021a ), but the phylotranscriptomic analysis covering more Chrysanthemum species has not been reported.…”

Transcriptome Approach Reveals the Response Mechanism of Heimia myrtifolia (Lythraceae, Myrtales) to Drought Stress

“…From the transcriptional level, it can be revealed that differential gene expression in plant signal transduction, endogenous hormones, photosynthesis, and other pathways under drought stress will deepen the comprehensive understanding of the mechanism of drought stress resistance (Sprenger et al, 2016). In recent years, an increasing number of studies have used sequencing technology to explore the molecular mechanisms of garden plants under drought stress, such as Salix babylonica and Chrysanthemum rhombifolium, and these results have greatly promoted drought resistance research on garden plants (Xu et al, 2021;Zhang et al, 2021). In research on Pinus massoniana, several transcription factor genes associated with the circadian rhythm (HY5 and LHY), signal transduction (ERF), and defense responses (WRKY) have been identified as playing a key role in adapting to drought stress (Du et al, 2018).…”

De Novo Transcriptome Assembly, Functional Annotation and SSR Marker Discovery of Qinling Takin (Budorcas taxicolor bedfordi)

“…Because of the deep coverage and single base-pair resolution, RNA sequencing (RNA-Seq) is an efficient method to analyze large-scale transcriptome sequence investigations and obtain molecular markers, even in species lacking a reference genome [ 13 , 14 ]. This next-generation sequencing (NGS)-based technique has recently been widely used for d e novo transcriptome sequencing assembly, novel gene and molecular marker discovery, and investigating gene expression in various species [ 15 , 16 , 17 , 18 , 19 ]. Therefore, this study used RNA-Seq and de novo assembly to characterize and annotate the transcriptome of takin muscle, and several unigenes and microsatellite markers were identified.…”