scholarly journals Patterns of gene co-expression under water-deficit treatments and pan-genome occupancy in Brachypodium distachyon.

2021 ◽  
Author(s):  
Ruben Sancho ◽  
Pilar Catalan ◽  
Bruno Contreras-Moreira ◽  
Tom Juenger ◽  
David L Des Marais
Keyword(s):  
Brachypodium Distachyon ◽  
Natural Populations ◽  
Genomic Analysis ◽  
Drought Response ◽  
Primary Metabolism ◽  
Environmental Response ◽  
Hub Genes ◽  
Pan Genome ◽  
Expression Of Genes ◽  
Leaf Transcriptome

Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequence complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome, which demonstrate that many genes are absent from the reference genomes whose analysis has dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analyzed weighted gene co-expression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and investigated network topology and differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable occupancy in the pan-genome (genes which are either present in all studied genotypes or missing in some genotypes) show different distributions among co-expression modules. Co-expression analysis united drought genes expressed in drought-stressed plants into 9 modules covering 343 hub genes (440 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 724 hub genes (911 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.

scholarly journals Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Sean P. Gordon ◽  
Bruno Contreras-Moreira ◽  
Daniel P. Woods ◽  
David L. Des Marais ◽  
Diane Burgess ◽  
...  
Keyword(s):  
Population Structure ◽  
Brachypodium Distachyon ◽  
Gene Content ◽  
Pan Genome ◽  
Content Variation

Humic substances affect Arabidopsis physiology by altering the expression of genes involved in primary metabolism, growth and development

2011 ◽  
Vol 74 ◽  
pp. 45-55 ◽  
Author(s):  
Sara Trevisan ◽  
Alessandro Botton ◽  
Silvia Vaccaro ◽  
Alice Vezzaro ◽  
Silvia Quaggiotti ◽  
...  
Keyword(s):  
Humic Substances ◽  
Growth And Development ◽  
Primary Metabolism ◽  
Expression Of Genes

scholarly journals Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Zhiqiu Yin ◽  
Si Zhang ◽  
Yi Wei ◽  
Meng Wang ◽  
Shuangshuang Ma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary Dynamics ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Content Type ◽  
Pan Genome ◽  
Long Time ◽  
Taxonomic Confusion

The taxonomic position of P. shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.

scholarly journals Effects of Exogenous Salicylic Acid on Drought Response and Characterization of Dehydrins in Impatiens walleriana

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1589
Author(s):  
Dragana D. Antonić ◽  
Angelina R. Subotić ◽  
Milan B. Dragićević ◽  
Danijel Pantelić ◽  
Snežana M. Milošević ◽  
...  
Keyword(s):  
Lipid Peroxidation ◽  
Salicylic Acid ◽  
Drought Stress ◽  
De Novo ◽  
Foliar Application ◽  
Drought Response ◽  
Leaf Transcriptome ◽  
Relative Water ◽  
Impatiens Walleriana

Impatiens walleriana is a valued ornamental plant sensitive to drought stress. We investigated whether the foliar application of 2mM salicylic acid (SA) can protect potted I. walleriana plants from drought stress. The plants were divided into: watered plants, drought-stressed plants, watered plants treated with SA and drought-stressed plants treated with SA. The number of flowers and flower buds, relative water content (RWC), contents of malondialdehyde (MDA) and proline (Pro) and the activities of superoxide dismutases, catalases and peroxidases were recorded at different time points. Three dehydrin sequences were identified in de novo assembled leaf transcriptome: IwDhn1, IwDhn2.1 and IwDhn2.2. Drought stress caused wilting, floral abortion, reduction of RWC and increased MDA—an indicator of lipid peroxidation. In response to drought, Impatiens accumulated Pro and induced chloroplastic Cu/ZnSOD and two peroxidase isoforms. The most remarkable drought response was strong induction of IwDhn2.1 and IwDhn2.2. Rehydration restored RWC, Pro level, Cu/ZnSOD activity and dehydrins expression in drought-stressed plants approximately to the values of watered plants.SA had ameliorating effects on plants exposed to drought, including prevention of wilting, preservation of RWC, increased Pro accumulation, modulation of antioxidative activities and remarkable decrease of lipid peroxidation, but without effects on flowers’ preservation.

scholarly journals Isolate specific responses of the non-host grass Brachypodium distachyon to the fungal pathogen Zymoseptoria tritici, compared to wheat.

2020 ◽  
Author(s):  
Ailsing Reilly ◽  
Sujit Jung Karki ◽  
Anthony Twamley ◽  
Anna M.M Tiley ◽  
Steven Kildea ◽  
...  
Keyword(s):  
Fungal Pathogen ◽  
Plant Immunity ◽  
Brachypodium Distachyon ◽  
Septoria Tritici Blotch ◽  
Septoria Tritici ◽  
Pr Genes ◽  
Zymoseptoria Tritici ◽  
Expression Of Genes ◽  
Pathogenesis Related ◽  
Defence Gene Expression

Septoria tritici blotch (STB) is an important foliar disease of wheat that is caused by the fungal pathogen Zymoseptoria tritici. The grass Brachypodium distachyon has been used previously as a model system for cereal-pathogen interactions. In this study, we examined the non-host resistance (NHR) response of B. distachyon to two different Z. tritici isolates in comparison to wheat. These isolates vary in aggressiveness on wheat cv. Remus displaying significant differences in disease and pycnidia coverage. Using microscopy, we found that similar isolate specific responses were observed for H2O2 accumulation and cell death in both wheat and B. distachyon. Despite this, induction of isolate specific patterns of defence gene expression by Z. tritici did differ between B. distachyon and wheat. Our results suggest that phenylalanine ammonia lyase (PAL) expression may be important for NHR in B. distachyon while pathogenesis-related (PR) genes and expression of genes regulating reactive oxygen species (ROS) may be important to limit disease in wheat. Future studies of the B. distachyon-Z. tritici interaction may allow identification of conserved plant immunity targets which are responsible for the isolate specific responses observed in both plant species.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

Sign in / Sign up

Export Citation Format

Share Document