scholarly journals Weak Effect of Gypsy Retrotransposon Bursts on Sonneratia alba Salt Stress Gene Expression

2022 ◽  
Vol 12 ◽  
Author(s):  
Yushuai Wang ◽  
Aimei Dai ◽  
Tian Tang
Keyword(s):  
Abscisic Acid ◽  
Salt Stress ◽  
Evolutionary Dynamics ◽  
Removal Rate ◽  
Age Distribution ◽  
Purifying Selection ◽  
Small Rna Sequencing ◽  
Ltr Retrotransposons ◽  
Mangrove Species ◽  
Sonneratia Alba

Transposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question. We compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments. S. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3′-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8'-hydroxylase 3 functioning in abscisic acid catabolism. This study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.

scholarly journals Weak effect of Gypsy retrotransposon bursts on Sonneratia alba salt stress gene expression

2021 ◽  
Author(s):  
Yushuai Wang ◽  
Aimei Dai ◽  
Tian Tang
Keyword(s):  
Abscisic Acid ◽  
Salt Stress ◽  
Evolutionary Dynamics ◽  
Removal Rate ◽  
Age Distribution ◽  
Purifying Selection ◽  
Small Rna Sequencing ◽  
Ltr Retrotransposons ◽  
Mangrove Species ◽  
Sonneratia Alba

AbstractBackground and AimsTransposable elements (TEs) are an important source of genetic diversity and can be co-opted for the regulation of host genes. However, to what extent the pervasive TE colonization of plant genomes has contributed to stress adaptation remains controversial. Plants inhabiting harsh environments in nature provide a unique opportunity to answer this question.MethodsWe compared TE compositions and their evolutionary dynamics in the genomes of two mangrove species: the pioneer Sonneratia alba and its less salt-tolerant relative S. caseolaris. Age distribution, strength of purifying selection and the removal rate of LTR (long terminal repeat) retrotransposons were estimated. Phylogenetic analysis of LTR retrotransposons and their distribution in the genome of S. alba were surveyed. Small RNA sequencing and whole-genome bisulfite sequencing was conducted using leaves of S. alba. Expression pattern of LTR retrotransposons and their nearby genes were examined using RNA-seq data of S. alba under different salt treatments.Key ResultsS. alba possesses more TEs than S. caseolaris. Particularly, many more young Gypsy LTR retrotransposons have accumulated in S. alba than in S. caseolaris despite an increase in purifying selection against TE insertions. The top two most abundant Gypsy families in S. alba preferentially insert in gene-poor regions. They are under relaxed epigenetic repression, probably due to the presence of CHROMO domains in their 3’-ends. Although a considerable number of TEs in S. alba showed differential expression under salt stress, only four copies were significantly correlated with their nearby genes in expression levels. One such TE-gene pair involves Abscisic acid 8’-hydroxylase 3 functioning in abscisic acid catabolism.ConclusionsThis study sheds light on the evolutionary dynamics and potential function of TEs in an extremophile. Our results suggest that the conclusion on co-option of TEs should be cautious even though activation of TEs by stress might be prevalent.

scholarly journals Constant conflict betweenGypsyLTR retrotransposons and CHH methylation within a stress-adapted mangrove genome

2018 ◽  
Author(s):  
Yushuai Wang ◽  
Weiqi Liang ◽  
Tian Tang
Keyword(s):  
Evolutionary Dynamics ◽  
Purifying Selection ◽  
Stress Adaptation ◽  
List Type ◽  
Ltr Retrotransposons ◽  
Evolutionary Potential ◽  
Neighboring Gene ◽  
Rhizophora Apiculata ◽  
As Stress ◽  
Interfering Rna

SummaryEvolutionary dynamics of the conflict between transposable elements (TEs) and their host genome remain elusive. This conflict would be intense in stress-adapted plants as stress can often reactivate TEs. Mangroves reduce TE load convergently in their adaptation to intertidal environments and thus provide a unique opportunity to address the host-TE conflict and its interaction with stress adaptation.Using the mangroveRhizophora apiculataas a model, we investigated methylation and short interfering RNA (siRNA) targeting patterns in relation to the abundance and age of long terminal repeat (LTR) retrotransposons. We also examined LTR retrotransposons’ distance to genes, impact on neighboring gene expression, and population frequencies.We found differential accumulation among classes of LTR retrotransposons despite high overall methylation levels. This can be attributed to 24-nt siRNA-mediated CHH methylation preferentially targetingGypsyelements, particularly in their LTR regions. OldGypsyelements possess unusually abundant siRNAs which show cross-mapping to young copies.Gypsyelements appear to be closer to genes and under stronger purifying selection than other classes.Our results suggest a continuous host-TE battle masked by the TE load reduction inR. apiculata. This conflict may enable mangroves likeR. apiculatato maintain genetic diversity and thus evolutionary potential during stress adaptation.

scholarly journals A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Shan-Shan Zhou ◽  
Xue-Mei Yan ◽  
Kai-Fu Zhang ◽  
Hui Liu ◽  
Jie Xu ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Age Determination ◽  
Genome Plasticity ◽  
Ltr Retrotransposons ◽  
Functional Variation ◽  
Plant Genomes ◽  
Sequencing Technologies ◽  
Plant Groups ◽  
Functional Implications ◽  
Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

scholarly journals Under salt stress guard cells rewire ion transport and abscisic acid (ABA) signaling

2021 ◽  
Author(s):  
Sohail M. Karimi ◽  
Matthias Freund ◽  
Brittney M. Wager ◽  
Michael Knoblauch ◽  
Jörg Fromm ◽  
...  
Keyword(s):  
Abscisic Acid ◽  
Salt Stress ◽  
Ion Transport ◽  
Guard Cells ◽  
Aba Signaling

Tomato Asr1 mRNA and protein are transiently expressed following salt stress, osmotic stress and treatment with abscisic acid

Plant Science ◽  
1995 ◽  
Vol 110 (2) ◽  
pp. 205-213 ◽  
Author(s):  
Hagit Amitai-Zeigerson ◽  
Pablo A. Scolnik ◽  
Dudy Bar-Zvi
Keyword(s):  
Abscisic Acid ◽  
Salt Stress ◽  
Osmotic Stress

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

scholarly journals Struktur Komunitas, Cadangan Karbon, dan Estimasi Nilai Ekonomi Mangrove di Muara Sungai Musi

2021 ◽  
Vol 26 (2) ◽  
pp. 228-234
Author(s):  
Harum Farahisah ◽  
Fredinan Yulianda ◽  
Hefni Effendi
Keyword(s):  
Ecosystem Services ◽  
Carbon Storage ◽  
Free Market ◽  
Economic Value ◽  
River Estuary ◽  
Carbon Dioxide Absorption ◽  
Mangrove Species ◽  
Nypa Fruticans ◽  
Sonneratia Alba ◽  
Musi River

Mangrove ecosystem services, aside for the fisheries sector, also have ecosystem services in mitigating climate change as carbon sinks and storage. Musi river estuary located in Banyuasin Regency, South Sumatra has the potential of mangrove forests as carbon reserves. The purpose of the study is to analyze the community structure, potential carbon stocks, and economic value of mangroves in the Musi River Estuary. Data were collected at five stations using the 100 m quadratic transect method vertically to the coastline. Data analysis was conducted based on the allometric equation for biomass information, carbon storage, and the economic value of carbon stores. Mangrove ecosystems in the Musi River estuary are Sonneratia alba, Nypa fruticans, Sonneratia casiolaris, and Rhizopora apiculata. Mangrove species that have important roles in the sustainability of ecosystems are Nypa fruticans and Sonneratia alba each with IVI of 145.6 and 101.28, respectively. Carbon storage of mangrove in the Musi river estuary is 107.34 tonC / ha and carbon dioxide absorption is 393.59 tCO2 / ha with a mangrove area of ± 5276 ha. The total estimated economic value of carbon generated from mangrove are Rp174.441.016.895 (free market) and Rp455.872.524.151 (CDM). Keywords: carbon, mangrove, Musi river estuary

scholarly journals Potential Regeneration of Mangrove Coastal of Payum Beach Merauke District

2019 ◽  
pp. 11-23
Author(s):  
Stenly M.B.S Wairara ◽  
Reny Sianturi
Keyword(s):  
Tree Level ◽  
Sampling Location ◽  
Mangrove Species ◽  
Transect Line ◽  
Rhizophora Apiculata ◽  
Sonneratia Alba ◽  
Avicennia Alba ◽  
Data Collection Technique ◽  
Aegialitis Annulata ◽  
Important Value Index

The purpose of this study was to analyze the regeneration potential of mangroves found on the coast of Payum, Merauke Regency, Papua Province. This research was conducted in August-October 2018. The data collection technique was purposive sampling using Transect Line Plots. The sampling location was chosen based on the representation of the presence of mangroves in three locations, namely zones A, B and C. The results of this study explained that there were three tree-level mangrove species, namely Avicennia alba, Rhizophora apiculata and Sonneratia alba. Type A. alba dominates in zone A with an important value index (INP) of 205.76%, zone B does not have a certain type that dominates, while Rhizophora apiculata dominates in zone C with INP 185.35%. The potential of the three mangrove species in zones A, B and C is good. Aegialitis annulata species are only found in sapling and seedling levels. In zones A and B are classified as new while in zone C is classified as bad. This study concluded that Avicennia alba, Rhizophora apiculata and Sonneratia alba had the potential to regenerate in all three locations (Zones A, B and C) compared to Aegialitis annulata.

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