Despacito: the slow evolutionary changes in plant microRNAs

Baldrich, Patricia; Beric, Aleksandra; Meyers, Blake C.

doi:10.1016/j.pbi.2018.01.007

Cited by 44 publications

(45 citation statements)

References 51 publications

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“…Often, the functional diversification of miRNA gene duplicates occurs over time through a series of modifications to archetype miRNAs, such as nucleotide polymorphisms, resulting in the specialization of miRNA gene function in a particular tissue (Ameres and Zamore, 2013). This typically involves changes in complementary pairing with target genes that drive the expression dynamics in relevant pathways (Baldrich et al, 2018). In animals, the seed region is considered as the basic determinant of miRNA specificity (Chandradoss et al, 2015).…”

Section: Gd Events Have Effects On Evolutionary Dynamics Of Maize Mirmentioning

confidence: 99%

“…Post-duplication, many genes have been retained in the genome as paralogous pairs, and individual genes comprising the pair have been either sub-functionalized (partitioning and sharing the original gene function) and/or neo-functionalized (gaining novel functions) via sequence and/ or expression divergence (Freeling, 2009). Studies in different species have revealed that ancient miRNA gene families have evolved via several of GD events (Baldrich et al, 2018). For example, the miR166 family contains seven members in Arabidopsis.…”

Section: Introductionmentioning

confidence: 99%

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Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)

Zhang

et al. 2020

Front. Genet.

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The evolutionary dynamics and tissue specificity of protein-coding genes are well documented in plants. However, the evolutionary consequences of small RNAs (sRNAs) on tissue-specific functions remain poorly understood. Here, we performed integrated analysis of 195 deeply sequenced sRNA libraries of maize B73, representing more than 10 tissues, and identified a comprehensive list of 419 maize microRNA (miRNA) genes, 271 of which were newly discovered in this study. We further characterized the evolutionary dynamics and tissue specificity of miRNA genes and corresponding miRNA isoforms (isomiRs). Our analysis revealed that tissue specificity of isomiR events tends to be associated with miRNA gene abundance and suggested that the frequencies of isomiR types are affected by the local genomic regions. Moreover, genome duplication (GD) events have dramatic effect on evolutionary dynamics of maize miRNA genes, and the abundance divergence for tissue-specific miRNA genes is associated with GD events. Further study indicated that duplicate miRNA genes with tissue-specific expression patterns, such as miR2275a, a phased siRNA (phasiRNA) trigger, contribute to phenotypic traits in maize. Additionally, our study revealed the expression preference of 21-and 24-nt phasiRNAs in relation to tissue specificity. This large-scale sRNAomic study depicted evolutionary implications of tissue-specific maize sRNAs, which coordinate genome duplication, isomiR modification, phenotypic traits and phasiRNAs differentiation.

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Section: Gd Events Have Effects On Evolutionary Dynamics Of Maize Mirmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)

Zhang

et al. 2020

Front. Genet.

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“…Diverse roles and functions of miRNAs have been well described previously and miRNAs interactions with the canonical target site in the mRNAs have been a subject of wide explorations. Recently, it has been shown that the miRNAs not only show lineage specific conserved functions but also diverge functions also, which increase the target repertoire of the plant miRNAs (Baldrich et al, 2018) It is noteworthy to highlight that these interactions have not only shown at the miRNAs level but also the level of siRNAs, which have alternative biogenesis pathway through the RdDM pathway. Irrespective of the biogenesis pathway, post-transcriptional regulatory role of miRNAs has been widely demonstrated ranging from the developmental to the functional landscape of plant abiotic and biotic stress.…”

Section: Resultsmentioning

confidence: 99%

“…For each isomiR, a cross-species conservation based on sequence conservation and also the concurrent read depth are provided. Recent studies have shown that genic miRNAs have different rates of evolutions such as the family targeting the chalcone 4 -O-glucosyltransferase (4 CGT) (Baldrich et al, 2018) and also the family specific miRNAs such as os-miR7695 in O. sativa (Baldrich et al, 2018) and miR-1510 in legumes (Baldrich et al, 2018). As the relationship between the canonical miRNAs and potential targets unravel with more diverse species, it is understandable that the corresponding isomiR diversity and their targets will eventually lead to better understanding of miRNAome.…”

Section: Resultsmentioning

confidence: 99%

Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants

Yang

Wen

Mudunuri³

et al. 2019

Front. Plant Sci.

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microRNAs (miRNAs) play an important role as key regulators controlling the post-transcriptional events in plants across development, abiotic and biotic stress, tissue polarity and also in defining the evolutionary basis of the origin of the post-transcriptional machinery. Identifying patterns of regulated and co-regulated small RNAs, in particular miRNAs and their sequence variants with the availability of next generation sequencing approaches has widely demonstrated the role of miRNAs and their temporal regulation in maintaining plant development and their response to stress conditions. Although the role of canonical miRNAs has been widely explored and functional diversity is revealed, those works for isomiRs are still limited and urgent to be carried out across plants. This relative lack of information with respect to isomiRs might be attributed to the non-availability of large-scale detection of isomiRs across wide plant species. In the present research, we addressed this by developing Plant isomiR Atlas, which provides large-scale detection of isomiRs across 23 plant species utilizing 677 smallRNAs datasets and reveals a total of 98,374 templated and non-templated isomiRs from 6,167 precursors. Plant isomiR Atlas provides several visualization features such as species specific isomiRs, isomiRs and canonical miRNAs overlap, terminal modification classifications, target identification using psRNATarget and TargetFinder and also canonical miRNAs:target interactions. Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate to understand the functional role of isomiRs. Plant isomiR Atlas is available at www.mcr.org.in/isomir.One Sentence Summary Plant isomiR Atlas will play a key role in understanding the regulatory nature of miRNAome and will accelerate the understanding and diversity of functional targets of plants isomiRs.

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“…Evolution of MIR genes by inverted duplication of their target genes has been hypothesized for a number of young, i.e. species-, genus-or family-specific plant miRNAs (Allen et al, 2004;Fahlgren et al, 2007;Baldrich et al, 2018).…”

Section: Evolution Of Mir444 and Mir824 Genes By Partial Inverted Dupmentioning

confidence: 99%

Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense‐transcribed sequences

et al. 2019

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Some microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKC C -group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that, in both cases, the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.

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Despacito: the slow evolutionary changes in plant microRNAs

Cited by 44 publications

References 51 publications

Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)

Integrated Analysis of Large-Scale Omics Data Revealed Relationship Between Tissue Specificity and Evolutionary Dynamics of Small RNAs in Maize (Zea mays)

Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants

Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense‐transcribed sequences

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