Long noncoding RNAs in Brassica rapa L. following vernalization

@article{Shea2019LongNR,
  title={Long noncoding RNAs in Brassica rapa L. following vernalization},
  author={Daniel John Shea and Namiko Nishida and Satoko Takada and Etsuko Itabashi and Satoshi Takahashi and Ayasha Akter and Naomi Miyaji and Kenji Osabe and Hasan Mehraj and Motoki Shimizu and Motoaki Seki and Tomohiro Kakizaki and Keiichi Okazaki and Elizabeth S. Dennis and Ryo Fujimoto},
  journal={Scientific Reports},
  year={2019},
  volume={9}
}
Brassica rapa L. is an important agricultural crop that requires a period of prolonged cold for flowering. This process is known as vernalization. Studies have shown that long noncoding RNAs (lncRNAs) play important roles in abiotic stress responses and several cold-responsive noncoding RNAs have been suggested to be involved in vernalization. We examined the transcriptome of the Chinese cabbage inbred line (B. rapa L. var. pekinensis) RJKB-T24, and identified 1,444 long intergenic noncoding… 
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Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis)
TLDR
The results reveal the potential mRNA and non-coding RNAs involved in vernalization, providing a foundation for further studies on the molecular mechanisms underlying vernAlization in Chinese cabbage.
Global identification of long non-coding RNAs involved in the induction of spinach flowering
TLDR
This study is the first report on identifying bolting and flowering-related lncRNAs based on transcriptome sequencing in spinach, which provides a useful resource for future functional genomics studies, genes expression researches, evaluating genes regulatory networks and molecular breeding programs in the regulation of the genetic mechanisms related to bolting in spinach.
Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L.
TLDR
Results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc, and long intergenic noncoding RNAs are enriched in the chromatin regions encoding lncRNAs.
Genome-wide identification of cold responsive transcription factors in Brassica napus L
TLDR
The results revealed the alteration of gene expression in cold stressed semi-winter and winter ecotype B. napus lines and provided a valuable collection of candidate key regulators involved in B. Napus response to cold stress, which could expand the understanding of plant stress response and benefit the future improvement of the breed of rapeseeds.
Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering
TLDR
Comparison of changes in the transcriptome between Q2 and Qinyou8 responding drought stress and rehydration treatment at the seedling stage increased the understanding of expression characterization of rapeseed lncRNAs in response to drought Stress and re-watering.
Improved reference genome annotation of Brassica rapa by PacBio RNA sequencing
TLDR
The Pacific Biosciences single-molecular long-read technology was used to improve gene models and produced the annotated genome version 3.5.1, which produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.
Nitrogen Signaling Genes and SOC1 Determine the Flowering Time in a Reciprocal Negative Feedback Loop in Chinese Cabbage (Brassica rapa L.) Based on CRISPR/Cas9-Mediated Mutagenesis of Multiple BrSOC1 Homologs
TLDR
Two flowering mechanisms in Chinese cabbage are identified: a reciprocal negative feedback loop between nitrogen signaling genes (BrNIA1 and BrNIR1) and BrS OC1s to control flowering time and positive feedback control of the expression of BrSOC1s.
Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing
TLDR
This work used the Pacific Biosciences single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5.1, a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.
Genome-wide analysis of long noncoding RNAs, 24-nt siRNAs, DNA methylation and H3K27me3 marks in Brassica rapa
TLDR
A suite of candidate lncRNAs that may be epigenetically regulated in the Brassica genus are identified and identified in relation to genome-wide 24-nt small interfering RNAs, DNA methylation, and histone H3 lysine 27 trimethylation marks.
Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation
TLDR
The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lnc RNAs as potential biomarkers for tailoring abiotics stress-tolerant plants in the future.
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