scholarly journals The Streptochaeta Genome and the Evolution of the Grasses

2021 ◽  
Vol 12 ◽  
Author(s):  
Arun S. Seetharam ◽  
Yunqing Yu ◽  
Sébastien Bélanger ◽  
Lynn G. Clark ◽  
Blake C. Meyers ◽  
...  
Keyword(s):  
Small Rnas ◽  
Rice Genome ◽  
Gene Trees ◽  
Floral Structure ◽  
Final Assembly ◽  
Gene Space ◽  
Secondary Sirnas ◽  
Large Families ◽  
The Common ◽  
Post Transcriptional Regulation

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size. We find good collinearity with the rice genome and have captured most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

scholarly journals The Streptochaeta genome and the evolution of the grasses

2021 ◽  
Author(s):  
Arun S Seetharam ◽  
Yunqing Yu ◽  
Sebastien Belanger ◽  
Lynn G. Clark ◽  
Blake C. Meyers ◽  
...  
Keyword(s):  
Small Rnas ◽  
Common Ancestor ◽  
Gene Trees ◽  
Floral Structure ◽  
Final Assembly ◽  
Gene Space ◽  
Secondary Sirnas ◽  
Large Families ◽  
The Common ◽  
Post Transcriptional Regulation

In this work, we sequenced and annotated the genome of Streptochaeta angustifolia, one of two genera in the grass subfamily Anomochlooideae, a lineage sister to all other grasses. The final assembly size is over 99% of the estimated genome size, capturing most of the gene space. Streptochaeta is similar to other grasses in the structure of its fruit (a caryopsis or grain) but has peculiar flowers and inflorescences that are distinct from those in the outgroups and in other grasses. To provide tools for investigations of floral structure, we analyzed two large families of transcription factors, AP2-like and R2R3 MYBs, that are known to control floral and spikelet development in rice and maize among other grasses. Many of these are also regulated by small RNAs. Structure of the gene trees showed that the well documented whole genome duplication at the origin of the grasses (ρ) occurred before the divergence of the Anomochlooideae lineage from the lineage leading to the rest of the grasses (the spikelet clade) and thus that the common ancestor of all grasses probably had two copies of the developmental genes. However, Streptochaeta (and by inference other members of Anomochlooideae) has lost one copy of many genes. The peculiar floral morphology of Streptochaeta may thus have derived from an ancestral plant that was morphologically similar to the spikelet-bearing grasses. We further identify 114 loci producing microRNAs and 89 loci generating phased, secondary siRNAs, classes of small RNAs known to be influential in transcriptional and post-transcriptional regulation of several plant functions.

scholarly journals Metazoan tsRNAs: Biogenesis, Evolution and Regulatory Functions

2019 ◽  
Vol 5 (1) ◽  
pp. 18 ◽  
Author(s):  
Shengqian Dou ◽  
Yirong Wang ◽  
Jian Lu
Keyword(s):  
Small Rnas ◽  
Mrna Translation ◽  
Evolutionary Genomics ◽  
Biological Processes ◽  
Domains Of Life ◽  
Conservation Patterns ◽  
Fundamental Biology ◽  
Non Coding Rnas ◽  
Regulatory Functions ◽  
Post Transcriptional Regulation

Transfer RNA-derived small RNAs (tsRNAs) are an emerging class of regulatory non-coding RNAs that play important roles in post-transcriptional regulation across a variety of biological processes. Here, we review the recent advances in tsRNA biogenesis and regulatory functions from the perspectives of functional and evolutionary genomics, with a focus on the tsRNA biology of Drosophila. We first summarize our current understanding of the biogenesis mechanisms of different categories of tsRNAs that are generated under physiological or stressed conditions. Next, we review the conservation patterns of tsRNAs in all domains of life, with an emphasis on the conservation of tsRNAs between two Drosophila species. Then, we elaborate the currently known regulatory functions of tsRNAs in mRNA translation that are independent of, or dependent on, Argonaute (AGO) proteins. We also highlight some issues related to the fundamental biology of tsRNAs that deserve further study.

Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans

Science ◽  
2006 ◽  
Vol 315 (5809) ◽  
pp. 241-244 ◽  
Author(s):  
Julia Pak ◽  
Andrew Fire
Keyword(s):  
Rna Interference ◽  
Small Rnas ◽  
De Novo ◽  
Messenger Rnas ◽  
Cellular Regulation ◽  
Rdrp Activity ◽  
Antisense Transcripts ◽  
Double Stranded Rna ◽  
C Elegans ◽  
Secondary Sirnas

RNA interference (RNAi) is a phylogenetically widespread gene-silencing process triggered by double-stranded RNA. In plants and Caenorhabditis elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: “Primary siRNAs” (derived from DICER nuclease-mediated cleavage of the original trigger) and “secondary siRNAs” [additional small RNAs whose synthesis requires an RNA-directed RNA polymerase (RdRP)]. Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found that secondary siRNAs constitute the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode whereby each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular messenger RNAs by RdRP activity may have key roles in cellular regulation.

scholarly journals Postcards from the Rice Genome: Massive Analysis of Small RNAs in Response to Environmental Stress

2011 ◽  
Vol 23 (12) ◽  
pp. 4165-4165
Author(s):  
Nancy A. Eckardt
Keyword(s):  
Environmental Stress ◽  
Small Rnas ◽  
Rice Genome

scholarly journals Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Sibo Wang ◽  
Hongping Liang ◽  
Yan Xu ◽  
Linzhou Li ◽  
Hongli Wang ◽  
...  
Keyword(s):  
Small Rna ◽  
Stress Responses ◽  
Small Rnas ◽  
Common Ancestor ◽  
Regulation Of Gene Expression ◽  
Mirna Biogenesis ◽  
Last Common Ancestor ◽  
Evolutionary Transitions ◽  
Genome Wide ◽  
Post Transcriptional Regulation

AbstractSmall RNAs play a major role in the post-transcriptional regulation of gene expression in eukaryotes. Despite the evolutionary importance of streptophyte algae, knowledge on small RNAs in this group of green algae is almost non-existent. We used genome and transcriptome data of 34 algal and plant species, and performed genome-wide analyses of small RNA (miRNA & siRNA) biosynthetic and degradation pathways. The results suggest that Viridiplantae started to evolve plant-like miRNA biogenesis and degradation after the divergence of the Mesostigmatophyceae in the streptophyte algae. We identified two major evolutionary transitions in small RNA metabolism in streptophyte algae; during the first transition, the origin of DCL-New, DCL1, AGO1/5/10 and AGO4/6/9 in the last common ancestor of Klebsormidiophyceae and all other streptophytes could be linked to abiotic stress responses and evolution of multicellularity in streptophytes. During the second transition, the evolution of DCL 2,3,4, and AGO 2,3,7 as well as DRB1 in the last common ancestor of Zygnematophyceae and embryophytes, suggests their possible contribution to pathogen defense and antibacterial immunity. Overall, the origin and diversification of DICER and AGO along with several other small RNA pathway-related genes among streptophyte algae suggested progressive adaptations of streptophyte algae during evolution to a subaerial environment.

scholarly journals Functional specialization of monocot DCL3 and DCL5 proteins through the evolution of the PAZ domain

2021 ◽  
Author(s):  
Shirui Chen ◽  
Wei Liu ◽  
Masahiro Naganuma ◽  
Yukihide Tomari ◽  
Hiro-oki Iwakawa
Keyword(s):  
Small Rnas ◽  
Rna Silencing ◽  
Functional Differentiation ◽  
Small Interfering Rnas ◽  
Double Stranded Rna ◽  
Secondary Sirnas ◽  
Fixed End ◽  
Paz Domain ◽  
Reproductive Processes

Monocot DICER-LIKE3 (DCL3) and DCL5 produce distinct 24-nt heterochromatic small interfering RNAs (hc-siRNAs) and phased secondary siRNAs (phasiRNAs). The former small RNAs are linked to plant heterochromatin, and the latter to reproductive processes. It is assumed that these DCLs evolved from an ancient "eudicot-type" DCL3 ancestor, which may have produced both types of siRNAs. However, how functional differentiation was achieved after gene duplication remains elusive. Here, we find that monocot DCL3 and DCL5 exhibit biochemically distinct preferences for 3′ overhangs and 5′ phosphates, consistent with the structural properties of their in vivo double-stranded RNA substrates. Importantly, these distinct substrate specificities are determined by the PAZ domains of DCL3 and DCL5 which have accumulated mutations during the course of evolution. These data explain the mechanism by which these DCLs cleave their cognate substrates from a fixed end, ensuring the production of functional siRNAs. Our study also indicates how plants have diversified and optimized RNA silencing mechanisms during evolution.

scholarly journals Secondary siRNAs in Plants: Biosynthesis, Various Functions, and Applications in Virology

2021 ◽  
Vol 12 ◽  
Author(s):  
Neeti Sanan-Mishra ◽  
A. Abdul Kader Jailani ◽  
Bikash Mandal ◽  
Sunil K. Mukherjee
Keyword(s):  
Gene Silencing ◽  
Small Rnas ◽  
Rna Silencing ◽  
Viral Infections ◽  
Natural Resistance ◽  
Virus Induced Gene Silencing ◽  
Systemic Spread ◽  
Secondary Sirnas ◽  
Silencing Pathways ◽  
Virus Interactions

The major components of RNA silencing include both transitive and systemic small RNAs, which are technically called secondary sRNAs. Double-stranded RNAs trigger systemic silencing pathways to negatively regulate gene expression. The secondary siRNAs generated as a result of transitive silencing also play a substantial role in gene silencing especially in antiviral defense. In this review, we first describe the discovery and pathways of transitivity with emphasis on RNA-dependent RNA polymerases followed by description on the short range and systemic spread of silencing. We also provide an in-depth view on the various size classes of secondary siRNAs and their different roles in RNA silencing including their categorization based on their biogenesis. The other regulatory roles of secondary siRNAs in transgene silencing, virus-induced gene silencing, transitivity, and trans-species transfer have also been detailed. The possible implications and applications of systemic silencing and the different gene silencing tools developed are also described. The details on mobility and roles of secondary siRNAs derived from viral genome in plant defense against the respective viruses are presented. This entails the description of other compatible plant–virus interactions and the corresponding small RNAs that determine recovery from disease symptoms, exclusion of viruses from shoot meristems, and natural resistance. The last section presents an overview on the usefulness of RNA silencing for management of viral infections in crop plants.

scholarly journals Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation

2018 ◽  
Author(s):  
Qili Fei ◽  
Yu Yu ◽  
Li Liu ◽  
Yu Zhang ◽  
Patricia Baldrich ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Small Rnas ◽  
Post Processing ◽  
Young Plant ◽  
Precursor Processing ◽  
Mature Form ◽  
Plant Mirna ◽  
Secondary Sirnas ◽  
Precursor Structure ◽  
Mirna Duplex

ABSTRACTPhased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous NB-LRRs, previously described as 21 nt in its mature form, primarily accumulates as a 22 nt isoform via monouridylation. We demonstrate that in Arabidopsis, this uridylation is performed by HESO1. Biochemical experiments showed that the 3’ terminus of miR1510 is only partially 2’-O-methylated, because of the terminal mispairing in the miR1510/miR1510* duplex that inhibits HEN1 activity in soybean. miR1510 emerged in the Phaseoleae ~41 to 42 MYA with a conserved precursor structure yielding a 22 nt monouridylated form, yet a variant in mung bean is processed directly in a 22 nt mature form. This analysis of miR1510 yields two observations: (1) plants can utilize post-processing modification to generate abundant 22 nt miRNA isoforms to more efficiently regulate target mRNA abundances; (2) comparative analysis demonstrates an example of selective optimization of precursor processing of a young plant miRNA.

scholarly journals Evolution of plasticity in production and transgenerational inheritance of small RNAs under dynamic environmental conditions

2019 ◽  
Author(s):  
Willian T.A.F. Silva ◽  
Sarah P. Otto ◽  
Simone Immler
Keyword(s):  
Phenotypic Plasticity ◽  
Environmental Conditions ◽  
Small Rnas ◽  
Regulation Of Gene Expression ◽  
Selective Advantage ◽  
Regulatory Elements ◽  
Optimal Level ◽  
Transgenerational Inheritance ◽  
Dual Nature ◽  
Post Transcriptional Regulation

AbstractIn a changing environment, small RNAs (sRNAs) play an important role in the post-transcriptional regulation of gene expression and can vary in abundance depending on the conditions experienced by an individual (phenotypic plasticity) and its parents (non-genetic inheritance). Many sRNAs are unusual in that they can be produced in two ways, either using genomic DNA as the template (primary sRNAs) or existing sRNAs as the template (secondary sRNAs). Thus, organisms can evolve rapid plastic responses to their current environment by adjusting the amplification rate of sRNA templates. sRNA levels can also be transmitted transgenerationally by the direct transfer of either sRNAs or the proteins involved in amplification. Theory is needed to describe the selective forces acting on sRNA levels, accounting for the dual nature of sRNAs as regulatory elements and templates for amplification and for the potential to transmit sRNAs and their amplification agents to offspring. Here, we develop a model to study the dynamics of sRNA production and inheritance in a fluctuating environment. We tested the selective advantage of mutants capable of sRNA-mediated phenotypic plasticity within resident populations with fixed levels of sRNA transcription. Even when the resident was allowed to evolve an optimal constant rate of sRNA production, plastic amplification rates capable of responding to environmental conditions were favored. By contrast, mechanisms allowing sRNA transcripts or amplification agents to be inherited were favored primarily when parents and offspring face similar environments and when selection acts before the optimal level of sRNA can be reached within the organism. Our study provides a clear set of testable predictions for the evolution of sRNA-related mechanisms of phenotypic plasticity and transgenerational inheritance.

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