ArticleBMC genomics2016
De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 32 citations in OpenAlex.
- Article
- Orthogroup and phylotranscriptomic analyses identify transcription factors involved in the plant cold response: A case study of Arabidopsis BBX29.Plant communications · 2023Article
- A phylotranscriptomic dataset of angiosperm species under cold stress.Scientific data · 2023Article
- Improved chilling tolerance in glasshouse-grown potted sweet basil by end-of-production, short-duration supplementary far red light.Frontiers in plant science · 2023Article
- Preharvest and postharvest techniques that optimize the shelf life of fresh basil (Frontiers in plant science · 2023Review
- De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development.BMC plant biology · 2022Article
- A glance at the chemodiversity ofPhytochemistry reviews : proceedings of the Phytochemical Society of Europe · 2022Review
- Transcriptome sequencing and gene expression profiling ofBreeding science · 2021Article
- Comparative physiological and proteomic analyses of mangrove plant Kandelia obovata under cold stress.Ecotoxicology (London, England) · 2021Article
- The genome sequence of tetraploid sweet basil, Ocimum basilicum L., provides tools for advanced genome editing and molecular breeding.DNA research : an international journal for rapid publication of reports on genes and genomes · 2020Article
- Responses of Manila Grass (Zoysia matrella) to chilling stress: From transcriptomics to physiology.PloS one · 2020Article
- Ocimum metabolomics in response to abiotic stresses: Cold, flood, drought and salinity.PloS one · 2019Article
- Starch content differences between two sweet potato accessions are associated with specific changes in gene expression.Functional & integrative genomics · 2018Article
- Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response.Genes & genomics · 2018Article
- Selection and evaluation of reference genes for qRT-PCR analysis inPlant methods · 2018Article
- Plant Glycine-Rich Proteins in Stress Response: An Emerging, Still Prospective Story.Frontiers in plant science · 2018Review
- Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China.Molecules (Basel, Switzerland) · 2017Article
- De novo assembly and analysis of the transcriptome of Rumex patientia L. during cold stress.PloS one · 2017Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
backgroundOcimum americanum var. pilosum is a chilling-sensitive, widely distributed plant that is consumed as a vegetable in central and southern China. To increase our understanding of cold stress responses in this species, we performed de novo transcriptome assembly for O. americanum var. pilosum and compared the transcriptomes of plants grown under normal and low temperatures.
resultsA total of 115,022,842 high quality, clean reads were obtained from four libraries (two replicates of control samples and two replicates of chilling-treated samples) and were used to perform de novo transcriptome assembly. After isoforms were considered, 42,816 unigenes were generated, 30,748 of which were similar to known proteins as determined by a BLASTx search (E-value < =1.0E-05) against NCBI non-redundant, Swiss-Prot, Gene Ontology, KEGG, and Cluster of COG databases. Comparative analysis of transcriptomes revealed that 5179 unigenes were differentially expressed (with at least 2-fold changes, FDR < 0.01) in chilling-treated samples, and that 2344 and 2835 unigenes were up- and down-regulated by chilling stress, respectively. Expression of the 10 most up-regulated and the five most down-regulated unigenes was validated by qRT-PCR. To increase our understanding of these differentially expressed unigenes, we performed Gene ontology and KEGG pathway enrichment analyses. The CBF-mediated transcriptional cascade, a well-known cold tolerance pathway, was reconstructed using our de novo assembled transcriptome.
conclusionOur study has generated a genome-wide transcript profile of O. americanum var. pilosum and a de novo assembled transcriptome, which can be used to characterize genes related to diverse biological processes. This is the first study to assess the cold-responsive transcriptome in an Ocimum species. Our results suggest that cold temperature significantly affects genes related to protein translation and cellular metabolism in this chilling sensitive species. Although most of the CBF pathway genes have orthologs in O. americanum var. pilosum, none of the identified cold responsive (COR) gene orthologs was induced by cold, which is consistent with the lack of cold tolerance in this plant.
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