scholarly journals Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci

2018 ◽  
Author(s):  
Seth Polydore ◽  
Alice Lunardon ◽  
Michael J. Axtell
Keyword(s):  
Arabidopsis Thaliana ◽  
Small Rnas ◽  
Cleavage Site ◽  
Common Ancestor ◽  
Land Plants ◽  
Last Common Ancestor ◽  
Repetitive Region ◽  
Pol Ii ◽  
Starting Point ◽  
Rna Transcript

AbstractSmall RNAs regulate key physiological functions in land plants. Small RNAs can be divided into two categories: microRNAs (miRNAs) and short interfering RNAs (siRNAs); siRNAs are further sub-divided into transposon/repetitive region-localized heterochromatic siRNAs and phased siRNAs (phasiRNAs). PhasiRNAs are produced from the miRNA-mediated cleavage of a Pol II RNA transcript; the miRNA cleavage site provides a defined starting point from which phasiRNAs are produced in a distinctly phased pattern. 21-22 nucleotide (nt)-dominated phasiRNA-producing loci (PHAS) are well represented in all land plants to date. In contrast, 24 nt-dominated PHAS loci are known to be encoded only in monocots and are generally restricted to male reproductive tissues. Currently, only one miRNA (miR2275) is known to trigger the production of these 24 nt-dominated PHAS loci. In this study, we use stringent methodologies in order to examine whether or not 24 nt-dominated PHAS loci also exist in Arabidopsis thaliana. We find that highly expressed heterochromatic siRNAs were consistently mis-identified as 24 nt-dominated PHAS loci using multiple PHAS-detecting algorithms. We also find that MIR2275 is not found in A. thaliana, and it seems to have been lost in the last common ancestor of Brassicales. Altogether, our research highlights the potential issues with widely used PHAS-detecting algorithms which may lead to false positives when trying to annotate new PHAS, especially 24 nt-dominated loci.

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 TAS3 miR390-dependent loci in non-vascular land plants: Towards a comprehensive reconstruction of the gene evolutionary history

2018 ◽  
Author(s):  
Sergey Y. Morozov ◽  
Irina A. Milyutina ◽  
Tatiana N. Erokhina ◽  
Liudmila V. Ozerova ◽  
Alexey V. Troitsky ◽  
...  
Keyword(s):  
Small Rnas ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Land Plants ◽  
Specific Class ◽  
Small Interfering Rnas ◽  
Evolutionary Transition ◽  
Evolutionary Pathway ◽  
Regulate Gene Expression ◽  
Genomic Dnas

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified SGS3-coding sequences in charophytes and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants.

scholarly journals Transcriptional responses to arbuscular mycorrhizal symbiosis development are conserved in the early divergent Marchantia paleacea

2020 ◽  
Author(s):  
Mara Sgroi ◽  
Uta Paszkowski
Keyword(s):  
Common Ancestor ◽  
Arbuscular Mycorrhizal ◽  
Land Plants ◽  
Arbuscular Mycorrhizal Symbiosis ◽  
Mycorrhizal Symbiosis ◽  
Plant Colonization ◽  
Last Common Ancestor ◽  
Transcriptional Responses ◽  
Evolutionarily Conserved ◽  
Marchantia Paleacea

AbstractArbuscular mycorrhizal symbiosis (AMS) arose in land plants more than 400 million years ago, perhaps acting as a major contributor to plant terrestrialization. The ability to engage in AMS is evolutionarily conserved across most clades of extant land plants, including early diverging bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components that underpin AMS in early diverging land plants as the mechanisms regulating the symbiosis were primarily characterized in angiosperms. Several AMS associated genes were recently shown to be conserved in liverworts and hornworts, but evidence of them being associated with symbiosis in bryophytes is scarce. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across progressive stages of symbiosis development. Gene orthology inference and comparative analysis of the M. paleacea transcriptional profile with a well characterised legume model -Medicago truncatula - revealed a deep conservation of transcriptional responses to AMS across distantly related species. We identified evolutionarily conserved patterns of expression of genes required for pre-symbiotic signalling, intracellular colonization and symbiotic nutrient exchange. Our study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across distantly related land plants. If bryophytes are confirmed to be monophyletic, our analysis provides novel insights on the first molecular pathways associated with symbiosis at the dawn of plant colonization of land.Significance StatementArbuscular mycorrhizal symbiosis (AMS) between plants and soil fungi was proposed as one of the key adaptations enabling land colonization by plants. The symbiosis is widespread across most extant plant clades, including early-diverging bryophytes, suggesting that it evolved before the last common ancestor of land plants. Recent phylogenetic analyses uncovered that genes regulating AMS in angiosperms are present in the genomes of bryophytes. Our work shows that a set of these genes are transcriptionally induced during AMS in liverworts. Based on the conservation of their transcriptional profiles across land plants, we propose that these genes acquired an AMS-associated function before the last common ancestor of land plants.

scholarly journals TAS3 miR390-dependent loci in non-vascular land plants: Towards a comprehensive reconstruction of the gene evolutionary history

2018 ◽  
Author(s):  
Sergey Y. Morozov ◽  
Irina A. Milyutina ◽  
Tatiana N. Erokhina ◽  
Liudmila V. Ozerova ◽  
Alexey V. Troitsky ◽  
...  
Keyword(s):  
Small Rnas ◽  
Evolutionary History ◽  
Common Ancestor ◽  
Land Plants ◽  
Specific Class ◽  
Small Interfering Rnas ◽  
Evolutionary Transition ◽  
Evolutionary Pathway ◽  
Regulate Gene Expression ◽  
Genomic Dnas

Trans-acting small interfering RNAs (ta-siRNAs) are transcribed from protein non-coding genomic loci and belong to a plant-specific class of endogenous small RNAs. These siRNAs have been found to regulate gene expression in most taxa including seed plants, gymnosperms, ferns and mosses. In this study, bioinformatic and experimental PCR-based approaches were used as tools to analyze TAS3 and TAS6 loci in transcriptomes and genomic DNAs from representatives of evolutionary distant Bryophyta, Marchantiophyta and Anthocerotophyta. We revealed previously undiscovered TAS3 loci in classes Sphagnopsida and Anthocerotopsida, as well as TAS6 loci in Bryophyta classes Tetraphidiopsida, Polytrichopsida, Andreaeopsida and Takakiopsida. These data further unveil the evolutionary pathway of the miR390-dependent TAS3 loci in land plants. We also identified SGS3-coding sequences in charophytes and hypothesized that the appearance of TAS3-related sequences could take place at a very early step in evolutionary transition from charophyte algae to an earliest common ancestor of land plants.

scholarly journals Experimental evidence for yawn contagion in orangutans (Pongo pygmaeus)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Evy van Berlo ◽  
Alejandra P. Díaz-Loyo ◽  
Oscar E. Juárez-Mora ◽  
Mariska E. Kret ◽  
Jorg J. M. Massen
Keyword(s):  
Experimental Evidence ◽  
Common Ancestor ◽  
Great Apes ◽  
Pongo Pygmaeus ◽  
Last Common Ancestor ◽  
Contagious Yawning ◽  
Proximate Mechanism ◽  
Social Species ◽  
Ultimate Causation

AbstractYawning is highly contagious, yet both its proximate mechanism(s) and its ultimate causation remain poorly understood. Scholars have suggested a link between contagious yawning (CY) and sociality due to its appearance in mostly social species. Nevertheless, as findings are inconsistent, CY’s function and evolution remains heavily debated. One way to understand the evolution of CY is by studying it in hominids. Although CY has been found in chimpanzees and bonobos, but is absent in gorillas, data on orangutans are missing despite them being the least social hominid. Orangutans are thus interesting for understanding CY’s phylogeny. Here, we experimentally tested whether orangutans yawn contagiously in response to videos of conspecifics yawning. Furthermore, we investigated whether CY was affected by familiarity with the yawning individual (i.e. a familiar or unfamiliar conspecific and a 3D orangutan avatar). In 700 trials across 8 individuals, we found that orangutans are more likely to yawn in response to yawn videos compared to control videos of conspecifics, but not to yawn videos of the avatar. Interestingly, CY occurred regardless of whether a conspecific was familiar or unfamiliar. We conclude that CY was likely already present in the last common ancestor of humans and great apes, though more converging evidence is needed.

scholarly journals Recombinant transfer in the basic genome ofEscherichia coli

2015 ◽  
Vol 112 (29) ◽  
pp. 9070-9075 ◽  
Author(s):  
Purushottam D. Dixit ◽  
Tin Yau Pang ◽  
F. William Studier ◽  
Sergei Maslov
Keyword(s):  
Common Ancestor ◽  
Recipient Cell ◽  
Gene Clusters ◽  
Selective Advantage ◽  
Last Common Ancestor ◽  
Genome Sequences ◽  
Bacterial Genomes ◽  
Basic Genome ◽  
Single Base Pair ◽  
Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

Improved resolution of recalcitrant nodes in the animal phylogeny through the analysis of genome gene content and morphology

2021 ◽  
Author(s):  
Ksenia Juravel ◽  
Luis Porras ◽  
Sebastian Hoehna ◽  
Davide Pisani ◽  
Gert Wörheide
Keyword(s):  
Common Ancestor ◽  
Sister Group ◽  
The Other ◽  
Gene Content ◽  
Statistical Hypothesis ◽  
Phylogenetic Position ◽  
Last Common Ancestor ◽  
Statistical Hypothesis Testing ◽  
Animal Phylogeny ◽  
Phylogenetic Hypotheses

An accurate phylogeny of animals is needed to clarify their evolution, ecology, and impact on shaping the biosphere. Although multi-gene alignments of up to several hundred thousand amino acids are nowadays routinely used to test hypotheses of animal relationships, some nodes towards the root of the animal phylogeny are proving hard to resolve. While the relationships of the non-bilaterian lineages, primarily sponges (Porifera) and comb jellies (Ctenophora), have received much attention since more than a decade, controversies about the phylogenetic position of the worm-like bilaterian lineage Xenacoelomorpha and the monophyly of the "Superphylum" Deuterostomia have more recently emerged. Here we independently analyse novel genome gene content and morphological datasets to assess patterns of phylogenetic congruence with previous amino-acid derived phylogenetic hypotheses. Using statistical hypothesis testing, we show that both our datasets very strongly support sponges as the sister group of all the other animals, Xenoacoelomorpha as the sister group of the other Bilateria, and largely support monophyletic Deuterostomia. Based on these results, we conclude that the last common animal ancestor may have been a simple, filter-feeding organism without a nervous system and muscles, while the last common ancestor of Bilateria might have been a small, acoelomate-like worm without a through gut.

Inductive patterning of the embryonic brain in Drosophila

Development ◽  
2002 ◽  
Vol 129 (9) ◽  
pp. 2121-2128
Author(s):  
Damon T. Page
Keyword(s):  
Brain Development ◽  
Common Ancestor ◽  
Last Common Ancestor ◽  
Embryonic Brain ◽  
Germ Layers ◽  
Brain Anomaly ◽  
Prechordal Plate ◽  
Foregut Endoderm ◽  
The Brain ◽  
Brain Patterning

In vertebrates (deuterostomes), brain patterning depends on signals from adjacent tissues. For example, holoprosencephaly, the most common brain anomaly in humans, results from defects in signaling between the embryonic prechordal plate (consisting of the dorsal foregut endoderm and mesoderm) and the brain. I have examined whether a similar mechanism of brain development occurs in the protostome Drosophila, and find that the foregut and mesoderm act to pattern the fly embryonic brain. When the foregut and mesoderm of Drosophila are ablated, brain patterning is disrupted. The loss of Hedgehog expressed in the foregut appears to mediate this effect, as it does in vertebrates. One mechanism whereby these defects occur is a disruption of normal apoptosis in the brain. These data argue that the last common ancestor of protostomes and deuterostomes had a prototype of the brains present in modern animals, and also suggest that the foregut and mesoderm contributed to the patterning of this ‘proto-brain’. They also argue that the foreguts of protostomes and deuterostomes, which have traditionally been assigned to different germ layers, are actually homologous.

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