Differential expression of microRNAs may regulate pollen development in Brassica oleracea

Song, Jinhui; Yang, Jian; Pan, Feng; Jin, Baozhe

doi:10.4238/2015.november.24.10

Cited by 13 publications

(8 citation statements)

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“…These miRNA families are highly conserved in Brassicaceae species, where they are expressed in leaves, siliques, and flowers. These miRNAs are reported to function in regulation of genes related to growth (miR157/171/824) [ 59 ], Brassica -specific stomatal organization (miR824), pollen development (miR824) [ 60 ], abiotic stress tolerance, and plant–pathogen interactions (miR398) [ 61 ].…”

Section: Discussionmentioning

confidence: 99%

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

et al. 2017

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BackgroundThe cyclic nucleotide-gated ion channel (CNGC) family affects the uptake of cations, growth, pathogen defence, and thermotolerance in plants. However, the systematic identification, origin and function of this gene family has not been performed in Brassica oleracea, an important vegetable crop and genomic model organism.ResultsIn present study, we identified 26 CNGC genes in B. oleracea genome, which are non-randomly localized on eight chromosomes, and classified into four major (I-IV) and two sub-groups (i.e., IV-a and IV-b). The BoCNGC family is asymmetrically fractioned into the following three sub-genomes: least fractionated (14 genes), most fractionated-I (10), and most fractionated-II (2). The syntenic map of BoCNGC genes exhibited strong relationships with the model Arabidopsis thaliana and B. rapa CNGC genes and provided markers for defining the regions of conserved synteny among the three genomes. Both whole-genome triplication along with segmental and tandem duplications contributed to the expansion of this gene family. We predicted the characteristics of BoCNGCs regarding exon-intron organisations, motif compositions and post-translational modifications, which diversified their structures and functions. Using orthologous Arabidopsis CNGCs as a reference, we found that most CNGCs were associated with various protein–protein interaction networks involving CNGCs and other signalling and stress related proteins. We revealed that five microRNAs (i.e., bol-miR5021, bol-miR838d, bol-miR414b, bol-miR4234, and bol-miR_new2) have target sites in nine BoCNGC genes. The BoCNGC genes were differentially expressed in seven B. oleracea tissues including leaf, stem, callus, silique, bud, root and flower. The transcript abundance levels quantified by qRT-PCR assays revealed that BoCNGC genes from phylogenetic Groups I and IV were particularly sensitive to cold stress and infections with bacterial pathogen Xanthomonas campestris pv. campestris, suggesting their importance in abiotic and biotic stress responses.ConclusionOur comprehensive genome-wide analysis represents a rich data resource for studying new plant gene families. Our data may also be useful for breeding new B. oleracea cultivars with improved productivity, quality, and stress resistance.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4244-y) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

et al. 2017

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“…For example, a study in B. napus has shown that the genes regulating pollen development by nuclear-mitochondrial interaction might be inhibited by energy deficits caused by orf224 / atp6 [5]. Meanwhile, increasing evidence has demonstrated that microRNAs (miRNAs) could act as important regulators of CMS systems in plants [7,8,9,10]. For example, some miRNAs and their targets, which may regulate flower bud development such as gma-miR156b/ GmSPL9a and gma-miR4413b/ GmPPR , were found in soybean lines, and a miRNA-mediated regulatory network was established [7].…”

Section: Introductionmentioning

confidence: 99%

CircRNA Expression Pattern and ceRNA and miRNA–mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris

Liang

Zhang

et al. 2019

IJMS

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Male-sterile plants provide an important breeding tool for the heterosis of hybrid crops, such as Brassicaceae. In the last decade, circular RNAs (circRNAs), as a novel class of covalently closed and single-stranded endogenous non-coding RNAs (ncRNAs), have received much attention because of their functions as “microRNA (miRNA) sponges” and “competing endogenous RNAs” (ceRNAs). However, the information about circRNAs in the regulation of male-sterility and anther development is limited. In this study, we established the Polima cytoplasm male sterility (CMS) line “Bcpol97-05A”, and the fertile line, “Bcajh97-01B”, in Brassica campestris L. ssp. chinensis Makino, syn. B. rapa ssp. chinensis, and performed RNA expression profiling comparisons between the flower buds of the sterile line and fertile line by whole-transcriptome sequencing. A total of 31 differentially expressed (DE) circRNAs, 47 DE miRNAs, and 4779 DE mRNAs were identified. By using Cytoscape, the miRNA-mediated regulatory network and ceRNA network were constructed, and the circRNA A02:23507399|23531438 was hypothesized to be an important circRNA regulating anther development at the post-transcriptional level. The gene ontology (GO) analysis demonstrated that miRNAs and circRNAs could regulate the orderly secretion and deposition of cellulose, sporopollenin, pectin, and tryphine; the timely degradation of lipids; and the programmed cell death (PCD) of tapetum cells, which play key roles in anther development. Our study revealed a new circRNA–miRNA–mRNA network, which is involved in the anther development of B. campestris, which enriched the understanding of CMS in flowering plants, and laid a foundation for further study on the functions of circRNAs and miRNAs during anther development.

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“…Increasingly, miRNAs have been identified and characterized in some important medicinal herbs ( Song et al, 2009 ; Wu et al, 2012b ) and different tissues of medicinal plants ( Xu et al, 2014 ; Khaldun et al, 2015 ). Further, the prediction of phenylpropanoid and terpenoid biosynthetic pathway genes targeting miRNAs in various plant species ( Shi et al, 2010 ; Mathiyalagan et al, 2013 ), as well as evidence of flower development ( Song et al, 2015 ; Niu et al, 2016 ) and stress resistance ( Navarro et al, 2006 ; Lu et al, 2008 ; Zhang Y. et al, 2016 ), miRNAs produce insight into the study of miRNAs in different tissues and varieties of L. japonica .…”

Section: Discussionmentioning

confidence: 99%

Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica

et al. 2016

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MicroRNAs (miRNAs), which play crucial regulatory roles in plant secondary metabolism and responses to the environment, could be developed as promising biomarkers for different varieties and production areas of herbal medicines. However, limited information is available for miRNAs from Lonicera japonica, which is widely used in East Asian countries owing to various pharmaceutically active secondary metabolites. Selection of suitable reference genes for quantification of target miRNA expression through quantitative real-time (qRT)-PCR is important for elucidating the molecular mechanisms of secondary metabolic regulation in different tissues and varieties of L. japonica. For precise normalization of gene expression data in L. japonica, 16 candidate miRNAs were examined in three tissues, as well as 21 cultivated varieties collected from 16 production areas, using GeNorm, NormFinder, and RefFinder algorithms. Our results revealed combination of u534122 and u3868172 as the best reference genes across all samples. Their specificity was confirmed by detecting the cycling threshold (Ct) value ranges in different varieties of L. japonica collected from diverse production areas, suggesting the use of these two reference miRNAs is sufficient for accurate transcript normalization with different tissues, varieties, and production areas. To our knowledge, this is the first report on validation of reference miRNAs in honeysuckle (Lonicera spp.). Restuls from this study can further facilitate discovery of functional regulatory miRNAs in different varieties of L. japonica.

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Differential expression of microRNAs may regulate pollen development in Brassica oleracea

Cited by 13 publications

References 40 publications

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles

CircRNA Expression Pattern and ceRNA and miRNA–mRNA Networks Involved in Anther Development in the CMS Line of Brassica campestris

Validation of Suitable Reference Genes for Assessing Gene Expression of MicroRNAs in Lonicera japonica

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