Noncoding RNAs, Emerging Regulators in Root Endosymbioses

Lelandais‐Brière, Christine; Moreau, J F; Hartmann, Caroline; Crespi, Martín

doi:10.1094/mpmi-10-15-0240-fi

Cited by 39 publications

(22 citation statements)

References 146 publications

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“…Conversely, DeSalvo et al ( ) speculated that host physiology may respond to different symbiont types, or that Symbiodinium may be able to explicitly influence host gene expression and physiology. Gene regulation following transfer of small RNAs between pathogen and host, or between mutualistic partners, has for instance been documented in plant–microbe interactions (Lelandais‐Brière, Moreau, Hartmann, & Crespi, ; Weiberg et al, ). Finally, the gene expression patterns observed here may also be a reflection of differences in host physiology associated with symbiont type.…”

Section: Discussionmentioning

confidence: 99%

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

Helmkampf

Bellinger

Frazier

et al. 2018

Ecology and Evolution

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Reef‐building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA‐seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai‘i Island with contrasting environmental conditions. We found that transcriptome‐wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site‐related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.

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Section: Discussionmentioning

confidence: 99%

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

Helmkampf

Bellinger

Frazier

et al. 2018

Ecology and Evolution

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“…An increasing number of sRNAs associated with the nodulation process have been identified at different stages of nodule development in several legume species, including M. truncatula, L. japonicus, and G. max (for review, see Bustos-Sanmamed et al, 2013;Lelandais-Brière et al, 2016). Targets of some of these miRNAs encode proteins involved in auxin signaling and response.…”

Section: Role Of Mirnas and Arfs In The Developmental Programs Of Detmentioning

confidence: 99%

The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth

et al. 2017

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Legume roots form two types of postembryonic organs, lateral roots and symbiotic nodules. Nodule formation is the result of the interaction of legumes with rhizobia and requires the mitotic activation and differentiation of root cells as well as an independent, but coordinated, program that allows infection by rhizobia. MicroRNA390 (miR390) is an evolutionarily conserved microRNA that targets the Trans-Acting Short Interference RNA3 (TAS3) transcript. Cleavage of TAS3 by ARGONAUTE7 results in the production of trans-acting small interference RNAs, which target mRNAs encoding AUXIN RESPONSE FACTOR2 (ARF2), ARF3, and ARF4. Here, we show that activation of the miR390/TAS3 regulatory module by overexpression of miR390 in Medicago truncatula promotes lateral root growth but prevents nodule organogenesis, rhizobial infection, and the induction of two key nodulation genes, Nodulation Signaling Pathway1 (NSP1) and NSP2. Accordingly, inactivation of the miR390/TAS3 module, either by expression of a miR390 target mimicry construct or mutations in ARGONAUTE7, enhances nodulation and rhizobial infection, alters the spatial distribution of the nodules, and increases the percentage of nodules with multiple meristems. Our results revealed a key role of the miR390/TAS3 pathway in legumes as a modulator of lateral root organs, playing opposite roles in lateral root and nodule development.

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“…The combinatorial complexity of the potential plant NF-Y complexes that could be formed from the three NF-Y subunits has obfuscated the role of each individual family member, although progress is being made. For example, NF-YA1 of alfalfa controls successful symbiosis between rhizobia and plant, and is required for the persistence of the nodule meristem [40,41].…”

Section: Resultsmentioning

confidence: 99%

`synder`: inferring genomic orthologs from synteny maps

Arendsee

Wilkey

Singh

et al. 2019

Preprint

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1Ortholog inference is a key step in understanding the evolution and function of a gene or 2 other genomic feature. Yet often no similar sequence can be identified, or the true ortholog 3 is hidden among false positives. A solution is to consider the sequence's genomic context. 4 We present the generic program, synder, for tracing features of interest between genomes 5 based on a synteny map. This approach narrows genomic search-space independently of 6 the sequence of the feature of interest. We illustrate the utility of synder by finding 7 orthologs for the Arabidopsis thaliana 13-member gene family of Nuclear Factor YC 8 transcription factor across the Brassicaceae clade. 9 1 Introduction 10 A powerful first step in understanding the evolution and function of a genomic feature is 11 resolving its genomic context, that is, comparing the feature to orthologous features in 12 other species. Comparing multiple orthologous features across species allows evolutionary 13 patterns to be uncovered. These patterns may include evidence of purifying selection, which 14 implies the feature is important to the survival of the species; positive selection, implying 15 the feature is rapidly evolving along one lineage; and functional dependencies between sites 16 (for example, amino acids in an enzyme reaction site) [1]. These evolutionary trends have 17 direct application in fields such as rational protein design [2]. Distinguishing between 18 orthologs (homologous features arising through speciation) and paralogs (homologous 19 features arising through gene duplication) is foundational to understanding the history of a 20 feature. Genomic context is also critical for discerning the origins of the often large 21 numbers of species-specific "orphan" genes that are found in most genome projects [3][4][5][6]. 22Identifying orthologs is not easy. A simple sequence similarity search of a query feature 23 (e.g., a gene, transposon, miRNA, or any sequence interval) against a genome or proteome 24 of a target species may obtain thousands of hits in a swooping continuum; these could 25 include: the true ortholog, related family members (paralogs), and non-specific hits. 26Therefore, methods for winnowing the search results have been developed to identify the 27 true orthologs. A straightforward approach to identify orthologs of protein-coding genes is 28 reciprocal best hits [7]. In this technique, a protein encoded by a gene from the focal species 29 is searched (e.g. with BLAST) against the target proteome. The highest scoring gene is 30 then searched back against the proteome of the focal species. If the top scoring hit of the 31 second search is the original query gene, then the two genes are accepted as orthologs. 32There are also methods that build on reciprocal best hits, such as the reciprocal smallest 33 distance method that considers evolutionary distance in addition to similarity score [8]. 34Little or no significant sequence similarity is expected across species for some classes of 35 2 features. A lack of significan...

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Noncoding RNAs, Emerging Regulators in Root Endosymbioses

Cited by 39 publications

References 146 publications

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth

`synder`: inferring genomic orthologs from synteny maps

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Noncoding RNAs, Emerging Regulators in Root Endosymbioses

Cited by 39 publications

References 146 publications

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

Symbiont type and environmental factors affect transcriptome‐wide gene expression in the coral Montipora capitata

The MicroRNA390/TAS3 Pathway Mediates Symbiotic Nodulation and Lateral Root Growth

synder: inferring genomic orthologs from synteny maps

Contact Info

Product

Resources

About

`synder`: inferring genomic orthologs from synteny maps