scholarly journals Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Guillaume Wos ◽  
Rimjhim Roy Choudhury ◽  
Filip Kolář ◽  
Christian Parisod
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Common Garden ◽  
Elevational Gradient ◽  
Mountain Regions ◽  
Transcriptomic Response ◽  
Genetic Lineages ◽  
Two Factors ◽  
Arabidopsis Arenosa ◽  
Expression Response

Abstract Background Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing to genome dynamics. Although some elements were reported to be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity and diversity of TEs. Here, we combined common garden experiment with short-read sequencing to investigate genomic abundance and expression of 2245 consensus TE sequences (containing retrotransposons and DNA transposons) in an alpine environment in Arabidopsis arenosa. To disentangle general trends from local differentiation, we leveraged four foothill-alpine population pairs from different mountain regions. Seeds of each of the eight populations were raised under four treatments that differed in temperature and irradiance, two factors varying with elevation. RNA-seq analysis was performed on leaves of young plants to test for the effect of elevation and subsequently of temperature and irradiance on expression of TE sequences. Results Genomic abundance of the 2245 consensus TE sequences varied greatly between the mountain regions in line with neutral divergence among the regions, representing distinct genetic lineages of A. arenosa. Accounting for intraspecific variation in abundance, we found consistent transcriptomic response for some TE sequences across the different pairs of foothill-alpine populations suggesting parallelism in TE expression. In particular expression of retrotransposon LTR Copia (e.g. Ivana and Ale clades) and LTR Gypsy (e.g. Athila and CRM clades) but also non-LTR LINE or DNA transposon TIR MuDR consistently varied with elevation of origin. TE sequences responding specifically to temperature and irradiance belonged to the same classes as well as additional TE clades containing potentially stress-responsive elements (e.g. LTR Copia Sire and Tar, LTR Gypsy Reina). Conclusions Our study demonstrated that the A. arenosa genome harbours a considerable diversity of TE sequences whose abundance and expression response varies across its native range. Some TE clades may contain transcriptionally active elements responding to a natural environmental gradient. This may further contribute to genetic variation between populations and may ultimately provide new regulatory mechanisms to face environmental challenges.

scholarly journals Transposable Elements and Teleost Migratory Behaviour

2021 ◽  
Vol 22 (2) ◽  
pp. 602
Author(s):  
Elisa Carotti ◽  
Federica Carducci ◽  
Adriana Canapa ◽  
Marco Barucca ◽  
Samuele Greco ◽  
...  
Keyword(s):  
Transposable Elements ◽  
Environmental Changes ◽  
Chromosomal Rearrangements ◽  
Quantitative Difference ◽  
Regulatory Elements ◽  
Phylogenetic Position ◽  
Migratory Behaviour ◽  
Relative Contribution ◽  
Migratory Routes ◽  
Eukaryotic Genomes

Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.

scholarly journals Use of Citizen Science Data for Characterizing Patterns and Drivers of Avian Altitudinal Migration

2019 ◽  
Vol 3 ◽  
Author(s):  
Pei-Yu Tsai ◽  
Chie-Jen Ko ◽  
Ya-Jung Lu ◽  
Chia Hsieh ◽  
Mao-Ning Tuanmu
Keyword(s):  
Citizen Science ◽  
Environmental Changes ◽  
Global Analysis ◽  
Research Question ◽  
Bird Species ◽  
Migration Behavior ◽  
Mountain Regions ◽  
Science Data ◽  
Essential Information ◽  
Altitudinal Migration

Altitudinal migration, the seasonal and repeateing movement of animal individuals between breeding and non-breeding areas at different elevations, is a common and important but understudied behavior in birds. Difficulty in characterizing avian altitudinal migration has prevented a comprehensive understanding of both patterns and drivers of this behavior. To fill this knowledge gap, we investigated altitudinal migration patterns and underlying mechanisms for a major proportion (~70%) of an entire resident bird community on a subtropical island with an almost 4000-m elevational gradient. We quantified migration tendency of individual bird species based on the seasonal shift in the elevational distribution of their occurrence records in the eBird database. We then built phylogeny-controlled regression models to examine the associations between the birds’ migration tendencies and their functional traits to test major hypotheses on the mechanisms of altitudinal migration. The results showed a common but variable altitudinal migration behavior among the 118 species examined, with 40 and 11 species conducting post-breeding downhill and uphill migration, respectively. The species that have a narrower thermal tolerance range, can tolerate lower temperatures, have a smaller body size, have a more diverse or invertebrate-rich diet, or use an open nest had a higher downhill migration tendency. In contrast, no traits examined showed consistent associations with the uphill migration tendency. This suggests that post-breeding downhill and uphill migrations are driven by different processes and current hypotheses can only explain the former, but not the latter. This relatively comprehensive study demonstrated the power of citizen science data to provide new insights into an old research question from a novel perspective. Using the same approach, we are investigating the behavior in mountain regions around the world. With the global analysis, we will be able to understand the general patterns and mechanisms of avian altitudinal migration and also investigate their variation among mountain regions in different climate zones. In the face of rapid environmental changes in mountain ecosystems, the approach used in this study may also provide essential information for the conservation of mountainous biodiversity.

scholarly journals “What You Need, Baby, I Got It”: Transposable Elements as Suppliers of Cis-Operating Sequences in Drosophila

Biology ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 25 ◽  
Author(s):  
Roberta Moschetti ◽  
Antonio Palazzo ◽  
Patrizio Lorusso ◽  
Luigi Viggiano ◽  
René Massimiliano Marsano
Keyword(s):  
Transposable Elements ◽  
Transcriptional Control ◽  
Environmental Changes ◽  
Model Organism ◽  
Model Organisms ◽  
Regulatory Sequences ◽  
Transcriptional Pattern ◽  
Constitutive Components ◽  
Host Genes

Transposable elements (TEs) are constitutive components of both eukaryotic and prokaryotic genomes. The role of TEs in the evolution of genes and genomes has been widely assessed over the past years in a variety of model and non-model organisms. Drosophila is undoubtedly among the most powerful model organisms used for the purpose of studying the role of transposons and their effects on the stability and evolution of genes and genomes. Besides their most intuitive role as insertional mutagens, TEs can modify the transcriptional pattern of host genes by juxtaposing new cis-regulatory sequences. A key element of TE biology is that they carry transcriptional control elements that fine-tune the transcription of their own genes, but that can also perturb the transcriptional activity of neighboring host genes. From this perspective, the transposition-mediated modulation of gene expression is an important issue for the short-term adaptation of physiological functions to the environmental changes, and for long-term evolutionary changes. Here, we review the current literature concerning the regulatory and structural elements operating in cis provided by TEs in Drosophila. Furthermore, we highlight that, besides their influence on both TEs and host genes expression, they can affect the chromatin structure and epigenetic status as well as both the chromosome’s structure and stability. It emerges that Drosophila is a good model organism to study the effect of TE-linked regulatory sequences, and it could help future studies on TE–host interactions in any complex eukaryotic genome.

scholarly journals Provenance Geographical and Climatic Characteristics Influence Budburst Phenology of Southwestern Ponderosa Pine Seedlings

Forests ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1067
Author(s):  
Aalap Dixit ◽  
Thomas Kolb ◽  
Owen Burney
Keyword(s):  
Pinus Ponderosa ◽  
Ponderosa Pine ◽  
Common Garden ◽  
Elevational Gradient ◽  
High Elevation ◽  
Mean Annual Precipitation ◽  
Positive Trend ◽  
Provenance Variation ◽  
Pine Seedlings ◽  
Budburst Phenology

Ponderosa pine (Pinus ponderosa Lawson & C. Lawson var. scopulorum Engelm.) forests of the southwestern US are threatened by climate change and deforestation. Information about geographic patterns of provenance variation in budburst phenology is needed to make decisions about selecting seed sources for future planting. In this study, provenance variation in the budburst phenology of ponderosa pine seedlings was examined using common garden studies. Seedlings from 21 provenances, representing an elevational gradient in Arizona and New Mexico, were planted in July 2018 at a ponderosa pine-dominated field site in northern Arizona. Field budburst was monitored weekly on all seedlings in the spring of 2019. Field budburst was compared with budburst timing of the same provenances measured under greenhouse conditions. The hypotheses for this study were that (1) budburst varies among provenances, with earlier budburst in low-elevation provenances, and (2) differences in budburst timing among provenances are consistent for seedlings grown in greenhouse and field environments. Field results show that provenances vary in budburst date and that low- and middle-elevation provenances break bud sooner than high-elevation provenances. Field budburst date had a moderate, positive correlation with provenance mean annual precipitation (r = 0.522) and a moderate, negative trend with latitude (r = −0.413). Budburst date of provenances in the greenhouse had a moderate, positive trend with budburst date in the field (r = 0.554), suggesting application of greenhouse results to field plantings. Such information about provenance variation and environmental and geographic trends in budburst timing will be useful for developing species-specific seed transfer guidelines and effective assisted migration strategies in a changing climate.

scholarly journals Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica)

2020 ◽  
Vol 131 (2) ◽  
pp. 356-368
Author(s):  
Elodie Chapuis ◽  
Nadeen Ali ◽  
Camille Noûs ◽  
Guillaume Besnard
Keyword(s):  
Adaptive Response ◽  
Common Garden ◽  
Meloidogyne Javanica ◽  
Cultivated Plants ◽  
Asexual Parasite ◽  
Soil Nematode ◽  
Root Knot Nematode ◽  
Genetic Lineages ◽  
Morphological Differences ◽  
Wild Progenitors

Abstract Cultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.

Ubiquitin gene expression: response to environmental changes

1991 ◽  
Vol 20 (1-2) ◽  
pp. 17-23 ◽  
Author(s):  
Judith Fraser ◽  
Hue Anh Luu ◽  
Jeana Neculcea ◽  
David Y. Thomas ◽  
Reginald K. Storms
Keyword(s):  
Gene Expression ◽  
Environmental Changes ◽  
Gene Expression Response ◽  
Expression Response

Simulation of Mediterranean forest carbon pools under expected environmental scenarios

2010 ◽  
Vol 40 (5) ◽  
pp. 850-860 ◽  
Author(s):  
M. Chiesi ◽  
M. Moriondo ◽  
F. Maselli ◽  
L. Gardin ◽  
L. Fibbi ◽  
...  
Keyword(s):  
Primary Production ◽  
Environmental Changes ◽  
Net Primary Production ◽  
Gross Primary Production ◽  
Central Italy ◽  
Forest Carbon ◽  
Simulation Approach ◽  
Two Factors ◽  
Vegetation Carbon ◽  
The Impact

Simulating the effects of possible environmental changes on the forest carbon budget requires the use of calibrated and tested models of ecosystem processes. A recently proposed simulation approach based on the use of the BIOME-BGC model was applied to yield estimates of present carbon fluxes and pools in Tuscany forests (central Italy). After the validation of these estimates against existing ground data, the simulation approach was used to assess the impact of plausible climate changes (+2 °C and increased CO2 concentration) on forest carbon dynamics (gross primary production (GPP), net primary production (NPP), and relevant allocations). The results indicate that the temperature change tends to inhibit all production and allocation processes, which are instead enhanced by the CO2 concentration rise. The combination of the two factors leads to a general increase in both GPP and NPP that is higher for deciduous oaks and chestnut (+30% and 24% for GPP and +42% and 31% for NPP, respectively). Additionally, vegetation carbon is slightly increased, while total soil carbon remains almost unchanged with respect to the present conditions. These findings are analyzed with reference to the Tuscany forest situation and previous studies on the subject.

scholarly journals Differential requirement of MED14 and UVH6 for heterochromatin transcription upon destabilization of silencing

2018 ◽  
Author(s):  
Pierre Bourguet ◽  
Stève de Bossoreille ◽  
Leticia López-González ◽  
Marie-Noëlle Pouch-Pélissier ◽  
Ángeles Gómez-Zambrano ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Heat Stress ◽  
Environmental Changes ◽  
Constitutive Heterochromatin ◽  
Epigenetic Marks ◽  
Two Factors ◽  
Silencing Pathways ◽  
Heterochromatin Silencing ◽  
Insight Into ◽  
Chromatin Patterns

AbstractConstitutive heterochromatin is commonly associated with high levels of repressive epigenetic marks and is stably maintained transcriptionally silent by the concerted action of different, yet convergent, silencing pathways. Reactivation of heterochromatin transcription is generally associated with alterations in levels of these epigenetic marks. However, in mutants for particular epigenetic regulators, or upon particular environmental changes such as heat stress, heterochromatin-associated silencing is destabilized without noticeable changes in epigenetic marks. This suggests that transcription can occur in a non-permissive chromatin context, yet the factors involved remain poorly known. Here, we show that heat stress-induced transcription of heterochromatin depends on the TFIIH component UVH6 and the Mediator subunit MED14. Mutants for these two factors exhibit hypersensitivity to heat stress, and under these conditions, UVH6 and MED14 are required for transcription of a high number of loci. We further show that MED14, but not UVH6, is required for transcription when heterochromatin silencing is destabilized in the absence of stress. In this case, MED14 requires proper chromatin patterns of repressive epigenetic marks for its function. We also uncover that MED14 regulates non-CG DNA methylation at a subset of RNA-directed DNA methylation target loci. These findings provide insight into the control of heterochromatin transcription upon silencing destabilization and identify MED14 as a regulator of DNA methylation.

scholarly journals Comparative Gene Expression Analysis Reveals Mechanism of Pinus contorta Response to the Fungal Pathogen Dothistroma septosporum

2020 ◽  
Author(s):  
Mengmeng Lu ◽  
Nicolas Feau ◽  
Dragana Obreht Vidakovic ◽  
Nicholas Ukrainetz ◽  
Barbara Wong ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fungal Pathogen ◽  
Pinus Contorta ◽  
Lodgepole Pine ◽  
Selective Constraint ◽  
Transcriptomic Response ◽  
Gene Expression Response ◽  
Gene Modules ◽  
Expression Response ◽  
Dothistroma Septosporum

Many conifers have distributions that span wide ranges in both biotic and abiotic conditions, but the basis of response to biotic stress has received much less attention than response to abiotic stress. In this study, we investigated the gene expression response of lodgepole pine (Pinus contorta) to attack by the fungal pathogen Dothistroma septosporum, which causes Dothistroma needle blight (DNB), a disease that has caused severe climate-related outbreaks in northwestern British Columbia. We inoculated tolerant and susceptible pines with two D. septosporum isolates and analyzed the differentially expressed genes, differential exon usage, and co-expressed gene modules using RNA-seq data. We found a rapid and strong transcriptomic response in tolerant lodgepole pine samples inoculated with one D. septosporum isolate, and a late and weak response in susceptible samples inoculated with another isolate. We mapped 43 of the DEG- or gene-module-identified genes to the reference plant-pathogen interaction pathway deposited in KEGG database. These genes are present in PAMP-triggered and effector-triggered immunity pathways. Genes comprising pathways and gene modules had signatures of strong selective constraint, while the highly expressed genes in tolerant samples appear to have been favored by selection to counterattack the pathogen. We identified candidate resistance genes that may respond to D. septosporum effectors. Taken together, our results show that gene expression response to D. septosporum infection in lodgepole pine varies both among tree genotypes and pathogen strains, and involves both known candidate genes and a number of genes with previously unknown functions.

Sign in / Sign up

Export Citation Format

Share Document