Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia

Genes, Journal Year: 2018, Volume and Issue: 9(6), P. 311 - 311

Published: June 20, 2018

Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes plants. However, identification of lncRNAs Pyrus betulifolia is limited compared with studies functional gene expression. Using high-throughput sequencing technology, the transcriptome P. under drought stress was analyzed to identify lncRNAs. A total 14,478 were identified, which 251 found be drought-responsive. The putative target genes these differentially expressed significantly enriched metabolic processes, organic substance macromolecule heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested results RNA data analysis reliable. This study will provide genetic resources for pear breeding reference pomological studies.

Language: Английский

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TOA: A software package for automated functional annotation in non‐model plant species

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(2), P. 621 - 636

Published: Oct. 18, 2020

Abstract The increase of sequencing capacity provided by high‐throughput platforms has made it possible to routinely obtain large sets genomic and transcriptomic sequences from model non‐model organisms. Subsequent analysis gene discovery in next‐generation experiments are, however, bottlenecked functional annotation. One common way perform annotation obtained experiments, is searching for homologous accessing the related information deposited databases. Functional especially challenging organisms, like many plant species. In such cases, existing free commercial general‐purpose applications may not offer complete accurate results. We present TOA (Taxonomy‐oriented annotation), a Python‐based user‐friendly open source application designed establish pipelines geared towards species that can run Linux/Mac computers, HPCs cloud servers. performs homology searches against proteins stored PLAZA databases, NCBI RefSeq Plant, Nucleotide Database Non‐Redundant Protein Sequence Database, outputs several ontology systems: Gene Ontology, InterPro, EC, KEGG, Mapman MetaCyc. software performance was validated comparing runtimes, total number annotated accuracy benchmark data with other solutions. outperformed terms constitutes good alternative improve plants. recommended gymnosperms or low quality sequence

Language: Английский

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Transcriptome profiling, physiological, and biochemical analyses provide new insights towards drought stress response in sugar maple (Acer saccharum Marshall) saplings

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: April 19, 2023

Sugar maple (Acer saccharum Marshall) is a temperate tree species in the northeastern parts of United States and economically important for its hardwood syrup production. trees are highly vulnerable to changing climatic conditions, especially drought, so understanding physiological, biochemical, molecular responses critical. The sugar saplings were subjected drought stress 7, 14, 21 days physiological data collected at after (DAS) showed significantly reduced chlorophyll Normalized Difference Vegetation Index with increasing time. stress-induced biochemical changes revealed higher accumulation malondialdehyde, proline, peroxidase activity response stress. Transcriptome analysis identified total 14,099 differentially expressed genes (DEGs); 328 common among all periods. Among DEGs, transcription factors (including NAC, HSF, ZFPs, GRFs, ERF), chloroplast-related stress-responsive such as peroxidases, membrane transporters, kinases, protein detoxifiers predominant. GO enrichment KEGG pathway enriched processes related phosphorylation, transmembrane transport, nucleic acids, metabolic, secondary metabolite biosynthesis pathways, circadian rhythm-plant, carotenoid Time-series transcriptomic gene regulation patterns eight different clusters, by individual clusters hub pathways. In addition, qRT-PCR validation selected DEGs that expression consistent transcriptome analysis. results from this study provide insights into dynamics progressive reveal stress-adaptive mechanisms

Language: Английский

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Slower growth prior to the 2018 drought and a high growth sensitivity to previous year summer conditions predisposed European beech to crown dieback

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 912, P. 169068 - 169068

Published: Dec. 2, 2023

The record-breaking drought in 2018 caused premature leaf discoloration and shedding (early browning) many beech (Fagus sylvatica L.) dominated forests Central Europe. However, a high degree of variability response among individual trees was observed. While some were severely impacted by the prolonged water deficits temperatures, others remained vital with no or only minor signs crown vitality loss. Why more susceptible to drought-induced damage than whether growth recovery is possible are poorly understood. Here, we aimed identify characteristics associated between based on sample 470 northern Switzerland. By combining tree measurements condition assessments, also investigated link dieback after drought. Beech early browning exhibited an overall lower vigor before co-occurring trees. This mainly indicated rates, stronger declines past decades, higher growth-climate sensitivity. Particularly, warm previous year summer conditions negatively affected current early-browning These findings suggest that had less access critical resources physiologically limited their predisposing them browning. Following drought, observed potential corresponded amount local climatic balance. Overall, our emphasize beech-dominated Europe under increasing pressure from severe droughts, ultimately reducing competitive ability this species, especially lowland sites shallow soils low holding capacity.

Language: Английский

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Applying molecular and genetic methods to trees and their fungal communities

Applied Microbiology and Biotechnology, Journal Year: 2023, Volume and Issue: 107(9), P. 2783 - 2830

Published: March 29, 2023

Abstract Forests provide invaluable economic, ecological, and social services. At the same time, they are exposed to several threats, such as fragmentation, changing climatic conditions, or increasingly destructive pests pathogens. Trees, inherent species of forests, cannot be viewed isolated organisms. Manifold (micro)organisms associated with trees playing a pivotal role in forest ecosystems. Of these organisms, fungi may have greatest impact on life trees. A multitude molecular genetic methods now available investigate tree their Due smaller genome sizes compared species, whole genomes different routinely compared. Such studies only recently started species. Here, we summarize application conservation genetics, breeding, association genetics well for investigation fungal communities interrelated ecological functions. These techniques valuable insights into basis adaptive traits, impacts management, environmental conditions can enhance tree-breeding cycles due reduced time field testing. It becomes clear that there multifaceted interactions among microbial between organisms We demonstrate versatility approaches based case fungi. Key points • Current knowledge applied Genomic essential conservation, research. Important phytobiomes

Language: Английский

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Transcriptome profiles of Quercus rubra responding to increased O3 stress

BMC Genomics, Journal Year: 2020, Volume and Issue: 21(1)

Published: Feb. 14, 2020

Abstract Background Climate plays an essential role in forest health, and climate change may increase productivity losses due to abiotic biotic stress. Increased temperature leads the increased formation of ozone (O 3 ). Ozone is formed by interaction sunlight, molecular oxygen reactions chemicals commonly found industrial automobile emissions such as nitrogen oxides volatile organic compounds. Although it well known that Northern red oak ( Quercus rubra ) (NRO), ecologically economically important species forests eastern North America, reduced exposure O , limited information available on its responses exogenous stimuli at level gene expression. Results RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, which 42,000 sequences could be annotated through homology-based searches. A total 4140 differential expressed genes (DEGs) were detected response stress, compared their respective controls. Gene Ontology (GO) Kyoto Encyclopedia Genes Genomes (KEGG) enrichment analyses -response DEGs revealed perturbation several biological pathways including energy, lipid, amino acid, carbohydrate terpenoid metabolism plant-pathogen interaction. Conclusion This study provides first reference transcriptome for NRO initial insights into genomic . expression profiling reveals altered primary secondary seedlings, defense biosynthesis.

Language: Английский

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Re-assembly, quality evaluation, and annotation of 678 microbial eukaryotic reference transcriptomes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2018, Volume and Issue: unknown

Published: May 17, 2018

Abstract Background De novo transcriptome assemblies are required prior to analyzing RNAseq data from a species without an existing reference genome or transcriptome. Despite the prevalence of transcriptomic studies, effects using different workflows, “pipelines”, on resulting poorly understood. Here, pipeline was programmatically automated and used assemble annotate raw short read collected by Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP). The were evaluated compared against that previously generated with developed National Center for Genome Research (NCGR). Results New contained majority previous contigs as well new content. On average, 7.8% annotated in novel gene names not found assemblies. Taxonomic trends observed assembly metrics, Dinoflagellata Ciliophora phyla showing higher percentage open reading frames number than transcriptomes other phyla. Conclusions Given current bioinformatics approaches, there is no single ‘best’ particular set data. As optimum moving target, improving (or not) tools programmable pipelines invaluable managing computationally-intensive tasks re-processing large sets samples revised ensuring common evaluation workflow applied all samples. Thus, re-assembling may yield more accurate identification taxon-specific across addition useful products community. Key Points Re-assembly can results Automated be process arbitrarily many Analyzing identifies trends.

Language: Английский

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Characterization of EST-SSRs for European beech (Fagus sylvatica L.) and their transferability to Fagus orientalis Lipsky, Castanea dentata Bork., and Quercus rubra L.

Silvae genetica/Silvae Genetica, Journal Year: 2018, Volume and Issue: 67(1), P. 127 - 132

Published: Dec. 1, 2018

Abstract Due to ongoing climate change, forests are exposed changing environmental conditions, such as increasing temperatures and lower precipitation, which trees have adapt. Successful adaptation variable environments requires sufficient genetic variation within tree populations. Knowledge of the is therefore essential, it provides information for long-term conservation, stability productivity forests. The a species can be analysed with molecular markers. Despite growing genomic resources European beech (Fagus sylvatica L.), one economically ecologically most important forest in Central Europe, number markers population analyses still limited. Therefore, aim work development new EST-SSR this species. A total 72 DNA samples from three widely separated regions Germany were used test 41 primers polymorphism, 35 originally developed American grandifolia Ehrh.) 6 red oak (Quercus rubra L.). Fifteen polymorphic, 13 monomorphic did not amplify. In addition, transferability was successfully tested related Castanea dentata Bork., Fagus orientalis Lipsky Q. rubra. study will useful future extend set available beech.

Language: Английский

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Closely related facultative and constitutive CAM phenotypes show little transcriptomic overlap in the subgenusTillandsia

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 10, 2024

2. Abstract The evolutionary trajectory and genetic architecture of crassulacean acid metabolism (CAM), a water-efficient form photosynthesis that has evolved repeatedly in the plant kingdom, remains elusive. extent to which different CAM phenotypes share basis, forming continuum through varying degrees expression, or exhibit divergence redundancy employed genes their is still debated. subgenus Tillandsia provides an excellent opportunity compare basis forms, given its broad range photosynthetic phenotypes. Through physiological transcriptomic analyses well-watered water-limited accessions closely related species pair, we comprehensively characterized facultative constitutive . By comparing orthologous gene expression orthogroup recruitment, found while both performed upon water-withholding, transcriptional modulation orthogroups stomatal movement, sugar/malate transport, aquaporins starch showed little similarity. Enzymes (de)carboxylation modules exhibited shared patterns, though distinct orthologs PEPC were upregulated at night each species. Our study reveals that, certain core enzymes shared, these substantial CAM-related modulation, revealing CAM’s polygenic nature providing possible hypothesis for evolvability. 1. Highlight We compared bromeliads on level. between phenotypes, highlighting continuum.

Language: Английский

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Genomics and Transcriptomics Advance in Plant Sciences

Energy, environment, and sustainability, Journal Year: 2019, Volume and Issue: unknown, P. 419 - 448

Published: Jan. 1, 2019

Language: Английский

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