Homogenization of sub-genome secretome gene expression patterns in the allodiploid fungus Verticillium longisporum

AbstractAllopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. The increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their ongoing quest for host immune response evasion. To this end, plant pathogens secrete a plethora of molecules that enable host colonization. Allodiploidization has resulted in the new plant pathogen Verticillium longisporum that infects different hosts than haploid Verticillium species. To reveal the impact of allodiploidization on plant pathogen evolution, we studied the genome and transcriptome dynamics of V. longisporum using next-generation sequencing. V. longisporum genome evolution is characterized by extensive chromosomal rearrangements, between as well as within parental chromosome sets, leading to a mosaic genome structure. In comparison to haploid Verticillium species, V. longisporum genes display stronger signs of positive selection. The expression patterns of the two sub-genomes show remarkable resemblance, suggesting that the parental gene expression patterns homogenized upon hybridization. Moreover, whereas V. longisporum genes encoding secreted proteins frequently display differential expression between the parental sub-genomes in culture medium, expression patterns homogenize upon plant colonization. Collectively, our results illustrate of the adaptive potential of allodiploidy mediated by the interplay of two sub-genomes.Author summaryHybridization followed by whole-genome duplication, so-called allopolyploidization, provides genomic flexibility that is beneficial for survival under stressful conditions or invasiveness into new habitats. Allopolyploidization has mainly been studied in plants, but also occurs in other organisms, including fungi. Verticillium longisporum, an emerging fungal pathogen on brassicaceous plants, arose by allodiploidization between two Verticillium spp. We used comparative genomics to reveal the plastic nature of the V. longisporum genomes, showing that parental chromosome sets recombined extensively, resulting in a mosaic genome pattern. Furthermore, we show that non-synonymous substitutions frequently occurred in V. longisporum. Moreover, we reveal that expression patterns of genes encoding secreted proteins homogenized between the V. longisporum sub-genomes upon plant colonization. In conclusion, our results illustrate the large adaptive potential upon genome hybridization for fungi mediated by genomic plasticity and interaction between sub-genomes.

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Similarities and differences in uterine gene expression patterns caused by treatment with physiological and non-physiological estrogens

Journal of Molecular Endocrinology ◽

10.1677/jme.0.0310487 ◽

2003 ◽

Vol 31 (3) ◽

pp. 487-497 ◽

Cited By ~ 30

Author(s):

H Watanabe ◽

A Suzuki ◽

M Kobayashi ◽

DB Lubahn ◽

H Handa ◽

...

Keyword(s):

Gene Expression ◽

Estrogen Receptor ◽

Reproductive Tract ◽

Stress Proteins ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Response Patterns ◽

Genes Encoding ◽

The Many ◽

Dose Responses

Administration of physiological and non-physiological estrogens during pregnancy or after birth is known to have adverse effects on the development of the reproductive tract and other organs. Although it is believed that both estrogens have similar effects on gene expression, this view has not been tested systematically. To compare the effects of physiological (estradiol; E2) and non-physiological (diethylstilbestrol; DES) estrogens, we used DNA microarray analysis to examine the uterine gene expression patterns induced by the two estrogens. Although E2 and DES induced many genes to respond in the same way, different groups of genes showed varying levels of maximal activities to each estrogen, resulting in different dose-response patterns. Thus, each estrogen has a distinct effect on uterine gene expression. The genes were classified into clusters according to their dose-responses to the two estrogens. Of the eight clusters, only two correlated well with the uterotropic effect of different doses of E2. One of these clusters contained genes that were upregulated by E2, which included genes encoding several stress proteins and transcription factors. The other cluster contained genes that were downregulated by E2, including genes related to metabolism, transcription and detoxification processes. The expression of these genes in estrogen receptor-deficient mice was not affected by E2 treatment, indicating that these genes are affected by the E2-bound estrogen receptor. Thus, of the many genes that are affected by estrogen, it was suggested that only a small number are directly involved in the uterotropic effects of estrogen treatment.

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Gene expression changes of seven stonefly species in responses to a latitudinal-environmental gradient

10.1101/2020.09.22.309179 ◽

2020 ◽

Author(s):

Maribet Gamboa ◽

Yusuke Gotoh ◽

Arnelyn D. Doloiras-Laraño ◽

Kozo Watanabe

Keyword(s):

Gene Expression ◽

Environmental Stress ◽

Environmental Conditions ◽

Latitudinal Gradient ◽

Environmental Changes ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Adaptive Potential ◽

Geographical Regions ◽

Multiple Species

AbstractLatitudinal variation has been known to create strong selection pressure for genomic variation that enables the adaptation and survival of organisms. By altering gene expression patterns, organisms can modify their adaptive potential to heterogeneous environmental conditions along a latitudinal gradient; however, there is a gap in our understanding of how physiological consequences in wild species are affected and how changing environmental conditions act on multiple species. Here, we investigated how seven stream stonefly species sampled from four geographical regions in Japan differ in their responses to latitudinal variations by measuring gene expression (RNA-sequencing) differences within species and gene co-expression among species. We found that a large number of genes (622) were differentially expressed along the latitudinal gradient. The high species-specific gene expression diversity found at higher latitude regions was probably associated with low temperatures and high water discharge, which suggests the adaptive potential of stonefly specie. In contrast, similar gene expression patterns among species was observed at lower latitudes, which suggests that strong environmental stress occurs in warmer regions. Weighted gene co-expression network analysis (WGCNA) identified 22 genes with similar expression patterns among species along the latitudinal gradient. Among the four geographical regions, high differential expression patterns in the co-expressed genes from two regions were found, suggesting that the local environment strongly affects gene expression patterns among species in these regions. Respiration, metabolism, and developmental co-expressed genes exhibited a latitudinal cline, showing clear evidence of divergent adaptive responses to latitude. Our findings demonstrate that stonefly species are differentially adapted to local environmental conditions, and imply that adaptation in gene expression could be shared by multiple species under environmental stress conditions. This study highlights the importance of considering multiple species when evaluating the consequences of environmental changes on aquatic insect communities, and possible mechanisms to cope with environmental changes.

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Linking gene expression patterns with survival studies elucidates adaptive potential in changing environments

Molecular Ecology ◽

10.1111/mec.15389 ◽

2020 ◽

Vol 29 (6) ◽

pp. 1031-1034 ◽

Cited By ~ 1

Author(s):

Mariah H. Meek

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Adaptive Potential ◽

Changing Environments ◽

Survival Studies

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The physiological differentiation along the midgut ofBombyx mori- inspirations from proteomics and gene expression patterns of the secreted proteins in the ectoperitrophic space

Insect Molecular Biology ◽

10.1111/imb.12368 ◽

2017 ◽

Vol 27 (2) ◽

pp. 247-259 ◽

Cited By ~ 4

Author(s):

L. Liu ◽

M. Qu ◽

J. Yang ◽

Q. Yang

Keyword(s):

Gene Expression ◽

Expression Patterns ◽

Secreted Proteins ◽

Gene Expression Patterns

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Gene Expression Patterns in Plants Colonized with Pathogenic and Non-pathogenic Gene Disruption Mutants of Colletotrichum

10.32747/2009.7592112.bard ◽

2009 ◽

Author(s):

Russell J. Rodriguez ◽

Stanley Freeman

Keyword(s):

Gene Expression ◽

Disease Resistance ◽

Gene Disruption ◽

Plant Pathogens ◽

Expression Patterns ◽

Gene Expression Patterns ◽

Growth Enhancement ◽

Colletotrichum Species ◽

Fungal Plant Pathogens ◽

The Us

Fungal plant pathogens are responsible for extensive annual crop and revenue losses throughout the world. To better understand why fungi cause diseases, we performed gene-disruption mutagenesis on several pathogenic Colletotrichum species and demonstrated that pathogenic isolates can be converted to symbionts expressing non-pathogenic lifestyles. One group of nonpathogenic mutants confer disease protection against pathogenic species of Col!etotrichum, Fusarium and Phytophthora; drought tolerance; and growth enhancement to host plants. These mutants have been defined as mutualists and disease resistance correlates to a decrease in the time required for hosts to activate defense systems when exposed to virulent fungi. A second group of non-pathogenic mutants did not confer disease resistance and were classified as commensals. In addition, we have demonstrated that wildtype pathogenic Colletotrichum species can express non-pathogenic lifestyles, including mutualism, on plants they colonize asymptomatically. We have been using wildtype and isogenic gene disruption mutants to characterize gene expression patterns in plants colonized with a pathogen, mutualist or commensal. The US group is contrasting genes expressed during colonization by mutuahstic and commensal mutants of C. magna and a pathogenic wildtype C. coccodes on tomato. The Israeli group is characterizing genes expressed during asymptomatic colonization of tomato by wildtype C. acutatum and a non-pathogenic mutant.To accomplish this we have been utilizing suppressive subtraction hybridization, microarray and sequencing strategies. The expected contribution of this research to agriculture in the US and Israel is: 1) understanding how pathogens colonize certain hosts asymptomatic ally will shed light on the ecology of plant pathogens which has been described as a fundamental deficiency in plant pathology; 2) identifying genes involved in symbiotically conferred disease resistance will help explain why and how pathogens cause disease, and may identify new candidate targets for developing genetically modified disease resistant crop plants.

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Defining a relationship between dietary fatty acids and the cytochrome P450 system in a mouse model of fatty liver disease

Physiological Genomics ◽

10.1152/physiolgenomics.00209.2010 ◽

2011 ◽

Vol 43 (3) ◽

pp. 121-135 ◽

Cited By ~ 13

Author(s):

Monika Gonzalez ◽

Whitney Sealls ◽

Elliot D. Jesch ◽

M. Julia Brosnan ◽

Istvan Ladunga ◽

...

Keyword(s):

Gene Expression ◽

Fatty Acids ◽

Cytochrome P450 ◽

Fatty Liver ◽

Saturated Fatty Acids ◽

Expression Patterns ◽

Dietary Fatty Acids ◽

Gene Expression Patterns ◽

Expression Of Genes ◽

Genes Encoding

Liver-specific ablation of cytochrome P450 reductase in mice (LCN) results in hepatic steatosis that can progress to steatohepatitis characterized by inflammation and fibrosis. The specific cause of the fatty liver phenotype is poorly understood but is hypothesized to result from elevated expression of genes encoding fatty acid synthetic genes. Since expression of these genes is known to be suppressed by polyunsaturated fatty acids, we performed physiological and genomics studies to evaluate the effects of dietary linoleic and linolenic fatty acids (PUFA) or arachidonic and decosahexaenoic acids (HUFA) on the hepatic phenotypes of control and LCN mice by comparison with a diet enriched in saturated fatty acids. The dietary interventions with HUFA reduced the fatty liver phenotype in livers of LCN mice and altered the gene expression patterns in these livers to more closely resemble those of control mice. Importantly, the expression of genes encoding lipid pathway enzymes were not different between controls and LCN livers, indicating a strong influence of diet over POR genotype. These analyses highlighted the impact of POR ablation on expression of genes encoding P450 enzymes and proteins involved in stress and inflammation. We also found that livers from animals of both genotypes fed diets enriched in PUFA had gene expression patterns more closely resembling those fed diets enriched in saturated fatty acids. These results strongly suggest only HUFA supplied from an exogenous source can suppress hepatic lipogenesis.

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