scholarly journals Conserved and non-conserved triggers of 24-nt reproductive phasiRNAs in eudicots

2021 ◽  
Author(s):  
Suresh Pokhrel ◽  
Kun Huang ◽  
Blake C. Meyers
Keyword(s):  
Small Rnas ◽  
Reproductive Organs ◽  
Flowering Plant ◽  
Small Interfering Rnas ◽  
Expression Of Genes ◽  
Tapetal Cells ◽  
Wild Strawberry ◽  
Flowering Plant Species ◽  
Mother Cells ◽  
And Function

AbstractPlant small RNAs (sRNAs) play important roles in plant growth and development by modulating expression of genes and transposons. In many flowering plant species, male reproductive organs, the anthers, produce abundant phased small interfering RNAs (phasiRNAs). Two classes of reproductive phasiRNAs are generally known, mostly from monocots: pre-meiotic 21-nt phasiRNAs triggered by miR2118, and meiotic 24-nt phasiRNAs triggered by miR2275. Here, we describe conserved and non-conserved triggers of 24-nt phasiRNAs in several eudicots. We found that the abundant 24-nt phasiRNAs in the basal eudicot columbine are produced by the canonical trigger, miR2275, as well as by other non-conserved triggers, miR482/2118 and aco_cand81. These triggering miRNAs are localized in microspore mother cells (MMC) and tapetal cells of meiotic and post-meiotic stage anthers. Furthermore, we identified a new trigger (miR11308) of 24-nt phasiRNAs and an expanded number of 24-PHAS loci in wild strawberry. We validated the presence of miR2275-derived 24-nt phasiRNAs pathway in rose. Finally, we evaluated all the eudicots that have been validated for the presence of 24-nt phasiRNAs as models to study biogenesis and function of 24-nt phasiRNAs and conclude that columbine would be an excellent model because of its extensive number of 24-PHAS loci and its diversity of trigger miRNAs.

scholarly journals Pre-meiotic, 21-nucleotide Reproductive PhasiRNAs Emerged in Seed Plants and Diversified in Flowering Plants

2020 ◽  
Author(s):  
Suresh Pokhrel ◽  
Kun Huang ◽  
Sébastien Bélanger ◽  
Jeffrey L. Caplan ◽  
Elena M. Kramer ◽  
...  
Keyword(s):  
Small Rnas ◽  
Reproductive Development ◽  
Regulatory Elements ◽  
Reproductive Organs ◽  
Anther Development ◽  
Genome Integrity ◽  
Seed Plants ◽  
Small Interfering Rnas ◽  
Wild Strawberry ◽  
Fine Tune

AbstractPlant small RNAs (sRNAs) are important regulatory elements that fine-tune gene expression and maintain genome integrity by silencing transposons. They have critical roles in most pathways involved in plant growth and reproductive development. Reproductive organs of monocots produce abundant phased, small interfering RNAs (phasiRNAs). The 21-nt reproductive phasiRNAs triggered by miR2118 are highly enriched in pre-meiotic anthers, and have not been described in eudicots. The 24-nt reproductive phasiRNAs are triggered by miR2275, and are highly enriched during meiosis in many angiosperms. Here, we describe additional variants of 21-nt reproductive phasiRNAs, including those triggered by miR11308 in wild strawberry, a eudicot, and we validate the presence of this pathway in rose. We report the widespread presence of the 21-nt reproductive phasiRNA pathway in eudicots, with novel biogenesis triggers in the basal eudicot columbine and the rosid flax. In eudicots, these 21-nt phasiRNAs are enriched in pre-meiotic stages, a spatiotemporal distribution consistent with that of monocots and suggesting a role in anther development. Although this pathway is apparently absent in well-studied eudicot families including the Brassicaceae, Solanaceae and Fabaceae, our work in eudicots supports a singular finding in spruce, indicating that the pathway of 21-nt reproductive phasiRNAs emerged in seed plants and was lost in some lineages.

Advances in understanding plant root hairs in relation to nutrient acquisition and crop root function

2021 ◽  
pp. 127-162
Author(s):  
Timothy S. George ◽  
◽  
Lawrie K. Brown ◽  
A. Glyn Bengough ◽  
◽  
...  
Keyword(s):  
Plant Root ◽  
Root Hairs ◽  
Microbial Interactions ◽  
Flowering Plant ◽  
Agricultural Sustainability ◽  
Root Tip ◽  
Pattern Length ◽  
Crop Root ◽  
Flowering Plant Species ◽  
And Function

Root hairs are found on most terrestrial flowering plant species. They form from epidermal cells at a predetermined distance behind the growing root tip in three main patterns. Their presence, pattern, length, density and function are genetically controlled and numerous genes are expressed solely in root hairs. Their growth and proliferation are attenuated by the environment and root hairs growing in soil are generally shorter and less dense than those in laboratory studies. Root hairs have a number of functions including anchorage, root soil contact and bracing to enable roots to penetrate hard soils. However, their primary function is acquisition of nutrients and water, in particular phosphate. They are the site of transporters, exudation of active compounds and infection point of symbiotic microbial interactions. They have a profound effect on rhizosphere characteristics and are a potentially useful target for breeding crops for future agricultural sustainability.

scholarly journals Widespread imprinting of transposable elements and variable genes in the maize endosperm

PLoS Genetics ◽  
2021 ◽  
Vol 17 (4) ◽  
pp. e1009491
Author(s):  
Sarah N. Anderson ◽  
Peng Zhou ◽  
Kaitlin Higgins ◽  
Yaniv Brandvain ◽  
Nathan M. Springer
Keyword(s):  
Transposable Elements ◽  
Critical Time ◽  
Flowering Plant ◽  
Nucleotide Polymorphisms ◽  
Maternal Expression ◽  
Expression Of Genes ◽  
Using Data ◽  
Plant Life Cycle ◽  
Flowering Plant Species ◽  
Genome Assemblies

Fertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding how imprinted expression arises has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene, and read alignments over maternal TE-gene pairs indicate that these are fused rather than independent transcripts.

scholarly journals Widespread imprinting of transposable elements and young genes in the maize endosperm

2020 ◽  
Author(s):  
Sarah N Anderson ◽  
Peng Zhou ◽  
Kaitlin Higgins ◽  
Yaniv Brandvain ◽  
Nathan M Springer
Keyword(s):  
Transposable Elements ◽  
Critical Time ◽  
Flowering Plant ◽  
Nucleotide Polymorphisms ◽  
Maternal Expression ◽  
Expression Of Genes ◽  
Using Data ◽  
Plant Life Cycle ◽  
Flowering Plant Species ◽  
Genome Assemblies

AbstractFertilization and seed development is a critical time in the plant life cycle, and coordinated development of the embryo and endosperm are required to produce a viable seed. In the endosperm, some genes show imprinted expression where transcripts are derived primarily from one parental genome. Imprinted gene expression has been observed across many flowering plant species, though only a small proportion of genes are imprinted. Understanding the rate of turnover for gain or loss of imprinted expression has been complicated by the reliance on single nucleotide polymorphisms between alleles to enable testing for imprinting. Here, we develop a method to use whole genome assemblies of multiple genotypes to assess for imprinting of both shared and variable portions of the genome using data from reciprocal crosses. This reveals widespread maternal expression of genes and transposable elements with presence-absence variation within maize and across species. Most maternally expressed features are expressed primarily in the endosperm, suggesting that maternal de-repression in the central cell facilitates expression. Furthermore, maternally expressed TEs are enriched for maternal expression of the nearest gene. Read alignments over maternal TE-gene pairs indicate fused transcripts, suggesting that variable TEs contribute imprinted expression of nearby genes.

scholarly journals A transcription factor DAF-5 functions in Haemonchus contortus development

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Wenda Di ◽  
Fangfang Li ◽  
Li He ◽  
Chunqun Wang ◽  
Caixian Zhou ◽  
...  
Keyword(s):  
Haemonchus Contortus ◽  
Developmental Stages ◽  
Reproductive Organs ◽  
Bimolecular Fluorescence Complementation ◽  
Parasitic Nematodes ◽  
Small Interfering Rnas ◽  
C Elegans ◽  
Dauer Formation ◽  
And Function

Abstract Background Abnormal dauer formation gene (daf-5), located downstream of the DAF-7 signalling pathway, mainly functions in dauer formation and reproductive processes in the free-living nematode Caenorhabditis elegans. Although the structure and function of daf-5 have been clarified in C. elegans, they still remain totally unknown in Haemonchus contortus, a socio-economically important parasitic nematode of gastric ruminants. Methods A homologue of daf-5, Hc-daf-5, and its inferred product (Hc-DAF-5) in H. contortus were identified and characterized in this study. Then the transcriptional profiles of Hc-daf-5 and the anatomical expression of Hc-DAF-5 in H. contortus were studied using an integrated molecular approach. RNA interference (RNAi) was performed to explore its function in transition from the exsheathed third-stage larvae (xL3s) to the fourth-stage larvae (L4s) in vitro. Finally, the interaction between Hc-DAF-5 and Hc-DAF-3 (a co-Smad) was detected by bimolecular fluorescence complementation (BiFc) in vitro. Results It was shown that Hc-DAF-5 was a member of the Sno/Ski superfamily. Hc-daf-5 was transcribed in all developmental stages of H. contortus, with significant upregulation in L3s. Native Hc-DAF-5 was localized in the reproductive organs, cuticle, and intestine via immunohistochemistry. RNAi revealed that specific small interfering RNAs (siRNAs) could retard xL3 development. In addition, the interaction between Hc-DAF-5 and Hc-DAF-3 indicated that the SDS box of Hc-DAF-5 was dispensable for the binding of Hc-DAF-5 to Hc-DAF-3, and the MH2 domain was the binding region between Hc-DAF-3 and Hc-DAF-5. Conclusions In summary, these findings show that Hc-daf-5 functions in the developmental processes of H. contortus, and this study is the first attempt to characterize the daf-5 gene in parasitic nematodes. Graphical abstract

scholarly journals Dicer-like 5 deficiency confers temperature-sensitive male sterility in maize

2018 ◽  
Author(s):  
Chong Teng ◽  
Han Zhang ◽  
Reza Hammond ◽  
Kun Huang ◽  
Blake C. Meyers ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Plant Development ◽  
Small Rnas ◽  
Male Fertility ◽  
Flowering Plants ◽  
Genome Integrity ◽  
Temperature Sensitive ◽  
Small Interfering Rnas ◽  
Transcript Levels ◽  
Tapetal Cells

AbstractSmall RNAs play important roles during plant development by regulating transcript levels of target mRNAs, maintaining genome integrity, and reinforcing DNA methylation. Dicer-like 5 (Dcl5) is proposed to be responsible for precise slicing in many monocots to generate diverse 24-nt phased, secondary small interfering RNAs (phasiRNAs), which are exceptionally abundant in meiotic anthers of diverse flowering plants. The importance and functions of these phasiRNAs remain unclear. Here, we characterized several mutants of dcl5, including alleles generated by the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) Cas9 system and a transposon-disrupted allele. We report that dcl5 mutants have few or no 24-nt phasiRNAs, develop short anthers with defective tapetal cells, and exhibit temperature-sensitive male fertility. We propose that DCL5 and 24-nt phasiRNAs are critical for fertility under growth regimes for optimal yield.

scholarly journals Pre-meiotic 21-nucleotide reproductive phasiRNAs emerged in seed plants and diversified in flowering plants

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Suresh Pokhrel ◽  
Kun Huang ◽  
Sébastien Bélanger ◽  
Junpeng Zhan ◽  
Jeffrey L. Caplan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Small Rnas ◽  
Regulatory Elements ◽  
Reproductive Organs ◽  
Anther Development ◽  
Flowering Plants ◽  
Genome Integrity ◽  
Seed Plants ◽  
Small Interfering Rnas ◽  
Fine Tune

AbstractPlant small RNAs are important regulatory elements that fine-tune gene expression and maintain genome integrity by silencing transposons. Reproductive organs of monocots produce abundant phased, small interfering RNAs (phasiRNAs). The 21-nt reproductive phasiRNAs triggered by miR2118 are highly enriched in pre-meiotic anthers, and have been found in multiple eudicot species, in contrast with prior reports of monocot specificity. The 24-nt reproductive phasiRNAs are triggered by miR2275, and are highly enriched during meiosis in many angiosperms. Here, we report the widespread presence of the 21-nt reproductive phasiRNA pathway in eudicots including canonical and non-canonical microRNA (miRNA) triggers of this pathway. In eudicots, these 21-nt phasiRNAs are enriched in pre-meiotic stages, a spatiotemporal distribution consistent with that of monocots and suggesting a role in anther development. Although this pathway is apparently absent in well-studied eudicot families including the Brassicaceae, Solanaceae and Fabaceae, our work in eudicots supports an earlier singular finding in spruce, a gymnosperm, indicating that the pathway of 21-nt reproductive phasiRNAs emerged in seed plants and was lost in some lineages.

scholarly journals Gene Regulation Mediated by microRNA-Triggered Secondary Small RNAs in Plants

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 112 ◽  
Author(s):  
Felipe Fenselau de Felippes
Keyword(s):  
Gene Regulation ◽  
Small Rnas ◽  
Target Genes ◽  
Regulation Of Gene Expression ◽  
Small Interfering Rnas ◽  
Expression Of Genes ◽  
Secondary Sirnas ◽  
In Trans ◽  
Production Pattern ◽  
In Cis

In plants, proper development and response to abiotic and biotic stimuli requires an orchestrated regulation of gene expression. Small RNAs (sRNAs) are key molecules involved in this process, leading to downregulation of their target genes. Two main classes of sRNAs exist, the small interfering RNAs (siRNAs) and microRNAs (miRNAs). The role of the latter class in plant development and physiology is well known, with many examples of how miRNAs directly impact the expression of genes in cells where they are produced, with dramatic consequences to the life of the plant. However, there is an aspect of miRNA biology that is still poorly understood. In some cases, miRNA targeting can lead to the production of secondary siRNAs from its target. These siRNAs, which display a characteristic phased production pattern, can act in cis, reinforcing the initial silencing signal set by the triggering miRNA, or in trans, affecting genes that are unrelated to the initial target. In this review, the mechanisms and implications of this process in the gene regulation mediated by miRNAs will be discussed. This work will also explore techniques for gene silencing in plants that are based on this unique pathway.

scholarly journals tRNA-derived small RNAs target transposable element transcripts

2016 ◽  
Author(s):  
Sarah Choudury ◽  
R. Keith Slotkin ◽  
German Martinez
Keyword(s):  
Transposable Element ◽  
Small Rnas ◽  
Genome Stability ◽  
Degradation Products ◽  
Male Gamete ◽  
Flowering Plant ◽  
Wild Type Male ◽  
Rna Fragments ◽  
Bona Fide ◽  
Flowering Plant Species

ABSTRACTtRNA-derived RNA fragments (tRFs) are 18-26 nucleotide small RNAs that are not random degradation products, but are rather specifically cleaved from mature tRNA transcripts. Abundant in stressed or viral-infected cells, the function and potential targets of tRFs are not known. We identified that in the unstressed wild-type male gamete containing pollen of flowering plants, and analogous reproductive structure in non-flowering plant species, tRFs accumulate to high levels. In the reference plant Arabidopsis thaliana, tRFs are cleaved by Dicer-like 1 and incorporated into Argonaute1 (AGO1), akin to a microRNA. We utilized the fact that many plant small RNAs direct cleavage of their target transcripts to demonstrate that where the tRF-AGO1 complex acts to specifically target and cleave endogenous transposable element (TE) mRNAs produced from transcriptionally active TEs. The data presented here demonstrate that tRFs are bona-fide regulatory microRNA-like small RNAs involved in the regulation of genome stability through the targeting of TE transcripts.

scholarly journals A Novel DCL2-Dependent Micro-Like RNA Vm-PC-3p-92107_6 Affects Pathogenicity by Regulating the Expression of Vm-VPS10 in Valsa mali

2021 ◽  
Vol 12 ◽  
Author(s):  
Feiran Guo ◽  
Jiahao Liang ◽  
Ming Xu ◽  
Gao Zhang ◽  
Lili Huang ◽  
...  
Keyword(s):  
Small Rnas ◽  
Target Genes ◽  
Pathogenic Fungus ◽  
Small Interfering Rnas ◽  
Wild Type ◽  
Over Expression ◽  
In The Wild ◽  
Vacuolar Protein ◽  
And Function ◽  
Valsa Mali

Dicer proteins are mainly responsible for generating small RNAs (sRNAs), which are involved in gene silencing in most eukaryotes. In previous research, two DCL proteins in Valsa mali, the pathogenic fungus causing apple tree Valsa canker, were found associated with both the pathogenicity and generation of sRNAs. In this study, the differential expression of small interfering RNAs (siRNAs) and miRNA-like RNAs (milRNAs) was analyzed based on the deep sequencing of the wild type and Vm-DCL2 mutant, respectively. Overall, the generation of 40 siRNAs and 18 milRNAs was evidently associated with Vm-DCL2. The target genes of milRNAs were then identified using degradome sequencing; according to the prediction results, most candidate targets are related to pathogenicity. Further, expression of Vm-PC-3p-92107_6 was confirmed in the wild type but not in the Vm-DCL2 mutant. Moreover, the pathogenicity of Vm-PC-3p-92107_6 deletion mutants (ΔVm-PC-3p-92107_6) and the over-expression transformants (Vm-PC-3p-92107_6-OE) was significantly increased and decreased, respectively. Based on those degradome results, vacuolar protein sorting 10 (Vm-VPS10) was identified as the target of Vm-PC-3p-92107_6. Co-expression analysis in tobacco leaves further confirmed that Vm-PC-3p-92107_6 could suppress the expression of Vm-VPS10. Meanwhile, the expression levels of Vm-PC-3p-92107_6 and Vm-VPS10 displayed divergent trends in ΔVm-PC-3p-92107_6 and Vm-PC-3p-92107_6-OE, respectively. Perhaps most importantly, ΔVm-VPS10 featured a significant reduction in pathogenicity. Taken together, our results indicate that a DCL2-dependent milRNA Vm-PC-3p-92107_6 plays roles in pathogenicity by regulating the expression of Vm-VPS10. This study lays a foundation for the comprehensive analysis of pathogenic mechanisms of V. mali and deepens our understanding of the generation and function of fungal sRNA.

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