ArticlePloS one2013
Next-generation sequencing of the Chrysanthemum nankingense (Asteraceae) transcriptome permits large-scale unigene assembly and SSR marker discovery.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers.
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59 citing papers in PubMed, 121 citations in OpenAlex.
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- De novo transcriptome assembly of Dalbergia sissoo Roxb. (Fabaceae) under Botryodiplodia theobromae-induced dieback disease.Scientific reports · 2023Article
- Assessment of the chemical and genetic variability among accessions ofFrontiers in plant science · 2023Article
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- Development and validation of SSR markers related to flower color based on full-length transcriptome sequencing in Chrysanthemum.Scientific reports · 2022Article
- The Complete Chloroplast Genome Sequence ofGenes · 2022Article
- Characterization of thePlants (Basel, Switzerland) · 2022Article
- Senescence in dahlia flowers is regulated by a complex interplay between flower age and floret position.Frontiers in plant science · 2022Article
- Expression Analysis ofFrontiers in plant science · 2022Article
- Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium.BMC genomic data · 2021Article
- Transcriptome and Metabolome Analyses of the Flowers and Leaves ofFrontiers in genetics · 2021Article
- Characterizing the Leaf Transcriptome ofFrontiers in genetics · 2021Article
- Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists.Scientific reports · 2020Article
- Article
- Genetic Divergence and Relationship AmongFrontiers in genetics · 2020Article
- The Heterologous Expression of a Chrysanthemum nankingense TCP Transcription Factor Blocks Cell Division in Yeast and Arabidopsis thaliana.International journal of molecular sciences · 2019Article
- Article
- Transcriptome sequencing of Pinus kesiya var. langbianensis and comparative analysis in the Pinus phylogeny.BMC genomics · 2018Article
- SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis.BMC genomics · 2018Article
- Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSimple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Chrysanthemum is one of the largest genera in the Asteraceae family. Only few Chrysanthemum expressed sequence tag (EST) sequences have been acquired to date, so the number of available EST-SSR markers is very low. METHODOLOGY/PRINCIPAL
findingsIllumina paired-end sequencing technology produced over 53 million sequencing reads from C. nankingense mRNA. The subsequent de novo assembly yielded 70,895 unigenes, of which 45,789 (64.59%) unigenes showed similarity to the sequences in NCBI database. Out of 45,789 sequences, 107 have hits to the Chrysanthemum Nr protein database; 679 and 277 sequences have hits to the database of Helianthus and Lactuca species, respectively. MISA software identified a large number of putative EST-SSRs, allowing 1,788 primer pairs to be designed from the de novo transcriptome sequence and a further 363 from archival EST sequence. Among 100 primer pairs randomly chosen, 81 markers have amplicons and 20 are polymorphic for genotypes analysis in Chrysanthemum. The results showed that most (but not all) of the assays were transferable across species and that they exposed a significant amount of allelic diversity. CONCLUSIONS/SIGNIFICANCE: SSR markers acquired by transcriptome sequencing are potentially useful for marker-assisted breeding and genetic analysis in the genus Chrysanthemum and its related genera.
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