What can the cold-induced transcriptomes of Arctic Brassicaceae tell us about the evolution of cold tolerance?

AbstractBy studying the molecular basis of cold response in plants adapted to some of the world’s coldest biomes, we can gain insight into the evolution of cold tolerance - an important factor in determining plant distributions worldwide.Although cold tolerance in temperate plants have been extensively studied, little is known about the evolutionary changes needed to transition from temperate to the more extreme polar zones.Here, we conducted a time series experiment to examine the transcriptional responses of three Arctic Brassicaceae to low temperatures. RNA was sampled before onset of treatment, and after 3h, 6h, and 24h with 2 °C. We identified sets of genes that were differentially expressed in response to cold and compared them between species, as well as to published data from the temperate Arabidopsis thaliana.We found that the cold response is highly species-specific. Among thousands of differentially expressed genes, ∼200 genes were shared among the three Arctic species and A. thaliana, and only ∼100 genes were specific to the three Arctic species alone. This pattern was also reflected in the functional comparison.Our results show that the cold response of Arctic plant species has mainly evolved independently, although it likely builds on a conserved basis found across Brassicaceae. The findings also confirm that highly polygenic traits, such as cold tolerance, may show less repeatable patterns of adaptation than traits involving only a few genes.

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Comparative analysis of the transcriptional responses of five Leishmania species to trivalent antimony

Parasites & Vectors ◽

10.1186/s13071-021-04915-y ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Julián Medina ◽

Lissa Cruz-Saavedra ◽

Luz Helena Patiño ◽

Marina Muñoz ◽

Juan David Ramírez

Keyword(s):

Comparative Analysis ◽

Differentially Expressed Genes ◽

Metabolic Pathways ◽

Rna Binding ◽

De Novo ◽

Expression Profiles ◽

Differentially Expressed ◽

Orthologous Genes ◽

Transcriptional Responses ◽

Species Specific

Abstract Background Leishmaniasis is a neglected tropical disease caused by several species of Leishmania. The resistance phenotype of these parasites depends on the characteristics of each species, which contributes to increased therapeutic failures. Understanding the mechanism used by the parasite to survive under treatment pressure in order to identify potential common and specific therapeutic targets is essential for the control of leishmaniasis. The aim of this study was to investigate the expression profiles and potential shared and specific resistance markers of the main Leishmania species of medical importance [subgenus L. (Leishmania): L. donovani, L. infantum and L. amazonensis; subgenus L. (Viannia): L. panamensis and L. braziliensis)] resistant and sensitive to trivalent stibogluconate (SbIII). Methods We conducted comparative analysis of the transcriptomic profiles (only coding sequences) of lines with experimentally induced resistance to SbIII from biological replicates of five Leishmania species available in the databases of four articles based on ortholog attribution. Simultaneously, we carried out functional analysis of ontology and reconstruction of metabolic pathways of the resulting differentially expressed genes (DEGs). Results Resistant lines for each species had differential responses in metabolic processes, compound binding, and membrane components concerning their sensitive counterpart. One hundred and thirty-nine metabolic pathways were found, with the three main pathways comprising cysteine and methionine metabolism, glycolysis, and the ribosome. Differentially expressed orthologous genes assigned to species-specific responses predominated, with 899 self-genes. No differentially expressed genes were found in common among the five species. Two common upregulated orthologous genes were found among four species (L. donovani, L. braziliensis, L. amazonensis, and L. panamensis) related to an RNA-binding protein and the NAD(P)H cytochrome-B5-oxidoreductase complex, associated with transcriptional control and de novo synthesis of linoleic acid, critical mechanisms in resistance to antimonials. Conclusion Herein, we identified potential species-specific genes related to resistance to SbIII. Therefore, we suggest that future studies consider a treatment scheme that is species-specific. Despite the limitations of our study, this is the first approach toward unraveling the pan-genus genetic mechanisms of resistance in leishmaniasis. Graphical Abstract

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Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability

BMC Genomics ◽

10.1186/s12864-021-07773-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Gregory M. Weber ◽

Jill Birkett ◽

Kyle Martin ◽

Doug Dixon ◽

Guangtu Gao ◽

...

Keyword(s):

Rainbow Trout ◽

Egg Quality ◽

Transcript Abundance ◽

Differentially Expressed ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Analysis Group ◽

Maternal Transcripts ◽

Single Batch ◽

Insight Into

Abstract Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes.

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Variability in nitrogen-derived trophic levels of Arctic marine biota

Polar Biology ◽

10.1007/s00300-020-02782-4 ◽

2020 ◽

Author(s):

Renske P. J. Hoondert ◽

Nico W. van den Brink ◽

Martine J. van den Heuvel-Greve ◽

Ad M. J. Ragas ◽

A. Jan Hendriks

Keyword(s):

Stable Isotopes ◽

Enrichment Factors ◽

Trophic Levels ◽

The Arctic ◽

Marine Biota ◽

Arctic Ecosystems ◽

Arctic Species ◽

Single Region ◽

Benthic Food ◽

Species Specific

AbstractStable isotopes are often used to provide an indication of the trophic level (TL) of species. TLs may be derived by using food-web-specific enrichment factors in combination with a representative baseline species. It is challenging to sample stable isotopes for all species, regions and seasons in Arctic ecosystems, e.g. because of practical constraints. Species-specific TLs derived from a single region may be used as a proxy for TLs for the Arctic as a whole. However, its suitability is hampered by incomplete knowledge on the variation in TLs. We quantified variation in TLs of Arctic species by collating data on stable isotopes across the Arctic, including corresponding fractionation factors and baseline species. These were used to generate TL distributions for species in both pelagic and benthic food webs for four Arctic areas, which were then used to determine intra-sample, intra-study, intra-region and inter-region variation in TLs. Considerable variation in TLs of species between areas was observed. This is likely due to differences in parameter choice in estimating TLs (e.g. choice of baseline species) and seasonal, temporal and spatial influences. TLs between regions were higher than the variance observed within regions, studies or samples. This implies that TLs derived within one region may not be suitable as a proxy for the Arctic as a whole. The TL distributions derived in this study may be useful in bioaccumulation and climate change studies, as these provide insight in the variability of trophic levels of Arctic species.

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Comparing transcriptional responses to Fusarium crown rot in wheat and barley identified an important relationship between disease resistance and drought tolerance

BMC Plant Biology ◽

10.1186/s12870-020-02818-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Z. Y. Su ◽

J. J. Powell ◽

S. Gao ◽

M. Zhou ◽

C. Liu

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Crown Rot ◽

Differentially Expressed ◽

Transcriptional Responses ◽

Drought Treatment ◽

Crop Species ◽

Fusarium Crown Rot ◽

Important Relationship ◽

The Impact

Abstract Background Fusarium crown rot (FCR) is a chronic disease in cereal production worldwide. The impact of this disease is highly environmentally dependant and significant yield losses occur mainly in drought-affected crops. Results In the study reported here, we evaluated possible relationships between genes conferring FCR resistance and drought tolerance using two approaches. The first approach studied FCR induced differentially expressed genes (DEGs) targeting two barley and one wheat loci against a panel of genes curated from the literature based on known functions in drought tolerance. Of the 149 curated genes, 61.0% were responsive to FCR infection across the three loci. The second approach was a comparison of the global DEGs induced by FCR infection with the global transcriptomic responses under drought in wheat. This analysis found that approximately 48.0% of the DEGs detected one week following drought treatment and 74.4% of the DEGs detected three weeks following drought treatment were also differentially expressed between the susceptible and resistant isolines under FCR infection at one or more timepoints. As for the results from the first approach, the vast majority of common DEGs were downregulated under drought and expressed more highly in the resistant isoline than the sensitive isoline under FCR infection. Conclusions Results from this study suggest that the resistant isoline in wheat was experiencing less drought stress, which could contribute to the stronger defence response than the sensitive isoline. However, most of the genes induced by drought stress in barley were more highly expressed in the susceptible isolines than the resistant isolines under infection, indicating that genes conferring drought tolerance and FCR resistance may interact differently between these two crop species. Nevertheless, the strong relationship between FCR resistance and drought responsiveness provides further evidence indicating the possibility to enhance FCR resistance by manipulating genes conferring drought tolerance.

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Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics

Microorganisms ◽

10.3390/microorganisms9040760 ◽

2021 ◽

Vol 9 (4) ◽

pp. 760

Author(s):

Tatyana V. Butina ◽

Yurij S. Bukin ◽

Ivan S. Petrushin ◽

Alexey E. Tupikin ◽

Marsel R. Kabilov ◽

...

Keyword(s):

Lake Baikal ◽

Biological Diversity ◽

Anthropogenic Impacts ◽

Lake Ecosystem ◽

Published Data ◽

Full Diversity ◽

True Diversity ◽

Viral Communities ◽

Diversity Studies ◽

Insight Into

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake’s viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake. There was a strict distinction of viral communities in areas with different environmental conditions. Comparative analysis with other freshwater lakes revealed the highest similarity of Baikal viromes with those of the Asian lakes Soyang and Biwa. Analysis of new data, together with previously published data allowed us to get a deeper insight into the diversity and functional potential of Baikal viruses; however, the true diversity of Baikal viruses in the lake ecosystem remains still unknown. The new metaviromic data will be useful for future studies of viral composition, distribution, and the dynamics associated with global climatic and anthropogenic impacts on this ecosystem.

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Integrated Insight into the Molecular Mechanisms of Spontaneous Abortion during Early Pregnancy in Pigs

International Journal of Molecular Sciences ◽

10.3390/ijms22126644 ◽

2021 ◽

Vol 22 (12) ◽

pp. 6644

Author(s):

Xupeng Zang ◽

Ting Gu ◽

Wenjing Wang ◽

Chen Zhou ◽

Yue Ding ◽

...

Keyword(s):

Immune Response ◽

Spontaneous Abortion ◽

Molecular Mechanisms ◽

Gene Set Enrichment Analysis ◽

Differentially Expressed ◽

Gene Set ◽

Cerna Network ◽

Major Interest ◽

End Stage ◽

Insight Into

Due to the high rate of spontaneous abortion (SAB) in porcine pregnancy, there is a major interest and concern on commercial pig farming worldwide. Whereas the perturbed immune response at the maternal–fetal interface is an important mechanism associated with the spontaneous embryo loss in the early stages of implantation in porcine, data on the specific regulatory mechanism of the SAB at the end stage of the implantation remains scant. Therefore, we used high-throughput sequencing and bioinformatics tools to analyze the healthy and arresting endometrium on day 28 of pregnancy. We identified 639 differentially expressed lncRNAs (DELs) and 2357 differentially expressed genes (DEGs) at the end stage of implantation, and qRT-PCR was used to verify the sequencing data. Gene set variation analysis (GSVA), gene set enrichment analysis (GSEA), and immunohistochemistry analysis demonstrated weaker immune response activities in the arresting endometrium compared to the healthy one. Using the lasso regression analysis, we screened the DELs and constructed an immunological competitive endogenous RNA (ceRNA) network related to SAB, including 4 lncRNAs, 11 miRNAs, and 13 genes. In addition, Blast analysis showed the applicability of the constructed ceRNA network in different species, and subsequently determined HOXA-AS2 in pigs. Our study, for the first time, demonstrated that the SAB events at the end stages of implantation is associated with the regulation of immunobiological processes, and a specific molecular regulatory network was obtained. These novel findings may provide new insight into the possibility of increasing the litter size of sows, making pig breeding better and thus improving the efficiency of animal husbandry production.

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Simulation of P2X-mediated calcium signaling in microglia

10.1101/354142 ◽

2018 ◽

Author(s):

Ben Chun ◽

Bradley D. Stewart ◽

Darin Vaughan ◽

Adam D. Bachstetter ◽

Peter M. Kekenes-Huskey

Keyword(s):

Computational Model ◽

Purinergic Receptor ◽

Receptor Activation ◽

Quantitative Model ◽

Published Data ◽

Transcriptional Responses ◽

Extracellular Adenosine ◽

Wide Range ◽

Intracellular Ca

AbstractMicroglia function is orchestrated through highly-coupled signaling pathways that depend on calcium (Ca2+). In response to extracellular adenosine triphosphate (ATP), transient increases in intracellular Ca2+ driven through the activation of purinergic receptors, P2X and P2Y, are sufficient to promote cytokine synthesis and potentially their release. While steps comprising the pathways bridging purinergic receptor activation with transcriptional responses have been probed in great detail, a quantitative model for how these steps collectively control cytokine production has not been established. Here we developed a minimal computational model that quantitatively links extracellular stimulation of two prominent ionotropic puriner-gic receptors, P2X4 and P2X7, with the graded production of a gene product, namely the tumor necrosis factor α (TNFα) cytokine. In addition to Ca2+ handling mechanisms common to eukaryotic cells, our model includes microglia-specific processes including ATP-dependent P2X4 and P2X7 activation, activation of NFAT transcription factors, and TNFα production. Parameters for this model were optimized to reproduce published data for these processes, where available. With this model, we determined the propensity for TNFα production in microglia, subject to a wide range of ATP exposure amplitudes, frequencies and durations that the cells could encounter in vivo. Furthermore, we have investigated the extent to which modulation of the signal transduction pathways influence TNFα production. Our key findings are that TNFα production via P2X4 is maximized at low ATP when subject to high frequency ATP stimulation, whereas P2X7 contributes most significantly at millimolar ATPranges. Given that Ca2+ homeostasis in microglia is profoundly important to its function, this computational model provides a quantitative framework to explore hypotheses pertaining to microglial physiology.

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Identification of cold stress responsive microRNAs in cold tolerant and susceptible Hemerocallis fulva by high throughput sequencing

10.21203/rs.3.rs-41470/v1 ◽

2020 ◽

Author(s):

Changbing Huang ◽

Chun Jiang ◽

limin Jin ◽

Huanchao Zhang

Keyword(s):

Low Temperature ◽

Cold Stress ◽

Cold Tolerance ◽

Temperature Stress ◽

Stress Responses ◽

Target Genes ◽

Low Temperature Stress ◽

Differentially Expressed ◽

Differentially Expressed Mirnas ◽

Cold Tolerant

Abstract Background:Hemerocallis fulva is a perennial herb belonging to Hemerocallis of Hemerocallis. Because of the large and bright colors, it is often used as a garden ornamental plant. But most varieties of H. fulva on the market will wither in winter, which will affect their beauty. It is very important to study the effect of low temperature stress on the physiological indexes of H. fulva and understand the cold tolerance of different H. fulva. MiRNA is a kind of endogenous non coding small molecular RNA with length of 21-24nt. It mainly inhibits protein translation by cutting target genes, and plays an important role in the development of organisms, gene expression and biological stress. Low temperature is the main abiotic stress affecting the production of H. fulva in China, which hinders the growth and development of plants. A comprehensive understanding of the expression pattern of microRNA in H. fulva under low temperature stress can improve our understanding of microRNA mediated stress response. Although there are many studies on miRNAs of various plants under cold stress at home and abroad, there are few studies on miRNAs related to cold stress of H. fulva. It is of great significance to explore the cold stress resistant gene resources of H. fulva, especially the identification and functional research of miRNA closely related to cold stress, for the breeding of excellent H. fulva.Results A total of 5619 cold-responsive miRNAs, 315 putative novel and 5 304 conserved miRNAs, were identified from the leaves and roots of two different varieties ‘Jinyan’ (cold-tolerant) and ‘Lucretius ’ (cold-sensitive), which were stressed under -4 oC for 24 h. Twelve conserved and three novel miRNAs (novel-miR10, novel-miR19 and novel-miR48) were differentially expressed in leaves of ‘Jinyan’ under cold stress. Novel-miR19, novel-miR29 and novel-miR30 were up-regulated in roots of ‘Jinyan’ under cold stress. Thirteen and two conserved miRNAs were deferentially expressed in leaves and roots of ‘Lucretius’ after cold stress. The deferentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR156, miR166 and miR319 families. A total of 6 598 target genes for 6 516 known miRNAs and 82 novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Ten differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR(q-PCR), and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR156a-3-p, miR319a, and novel-miR19) may play important roles in plant response to cold stress.Conclusions Our study indicates that some putative target genes and miRNA mediated metabolic processes and stress responses are significant to cold tolerance in H. fulva.

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Bichir external gills arise via heterochronic shift that accelerates hyoid arch development

eLife ◽

10.7554/elife.43531 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 7

Author(s):

Jan Stundl ◽

Anna Pospisilova ◽

David Jandzik ◽

Peter Fabian ◽

Barbora Dobiasova ◽

...

Keyword(s):

Pharyngeal Arch ◽

Developmental Sequence ◽

Free Living ◽

Pharyngeal Arches ◽

Hyoid Arch ◽

Early Appearance ◽

Evolutionary Changes ◽

Insight Into ◽

Living Group ◽

Early Larvae

In most vertebrates, pharyngeal arches form in a stereotypic anterior-to-posterior progression. To gain insight into the mechanisms underlying evolutionary changes in pharyngeal arch development, here we investigate embryos and larvae of bichirs. Bichirs represent the earliest diverged living group of ray-finned fishes, and possess intriguing traits otherwise typical for lobe-finned fishes such as ventral paired lungs and larval external gills. In bichir embryos, we find that the anteroposterior way of formation of cranial segments is modified by the unique acceleration of the entire hyoid arch segment, with earlier and orchestrated development of the endodermal, mesodermal, and neural crest tissues. This major heterochronic shift in the anteroposterior developmental sequence enables early appearance of the external gills that represent key breathing organs of bichir free-living embryos and early larvae. Bichirs thus stay as unique models for understanding developmental mechanisms facilitating increased breathing capacity.

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Identification and characterization of differentially expressed genes in Caenorhabditis elegans in response to pathogenic and nonpathogenic Stenotrophomonas maltophilia

10.21203/rs.2.14106/v2 ◽

2019 ◽

Author(s):

Leah J Radeke ◽

Michael Herman

Keyword(s):

Candidate Genes ◽

Differentially Expressed Genes ◽

Stenotrophomonas Maltophilia ◽

Defense Mechanisms ◽

Virulent Strain ◽

Differentially Expressed ◽

Transcriptional Responses ◽

Transcriptomic Response ◽

C Elegans ◽

Realistic Interaction

Abstract Background: Stenotrophomonas maltophilia is an emerging nosocomial pathogen that causes infection in immunocompromised patients. S. maltophilia isolates are genetically diverse, contain diverse virulence factors, and are variably pathogenic within several host species. Members of the Stenotrophomonas genus are part of the native microbiome of C. elegans , being found in greater relative abundance within the worm than its environment, suggesting that these bacteria accumulate within C. elegans . Thus, study of the C. elegans-Stenotrophomonas interaction is of both medical and ecological significance. To identify host defense mechanisms, we analyzed the C. elegans transcriptomic response to S. maltophilia strains of varying pathogenicity: K279a, an avirulent clinical isolate, JCMS, a virulent strain isolated in association with soil nematodes near Manhattan, KS, and JV3, an even more virulent environmental isolate. Results: Overall, we found 145 genes that are commonly differentially expressed in response to pathogenic S. maltophilia strains, 89% of which are upregulated, with many even further upregulated in response to JV3 as compared to JCMS. There are many more JV3-specific differentially expressed genes (225, 11% upregulated) than JCMS-specific differentially expressed genes (14, 86% upregulated), suggesting JV3 has unique pathogenic mechanisms that could explain its increased virulence. We used connectivity within a gene network model to choose pathogen-specific and strain-specific differentially expressed candidate genes for functional analysis. Mutations in 13 of 22 candidate genes caused significant differences in C. elegans survival in response to at least one S. maltophilia strain, although not always the strain that induced differential expression, suggesting a dynamic response to varying levels of pathogenicity. Conclusions: Variation in observed pathogenicity and differences in host transcriptional responses to S. maltophilia strains reveal that strain-specific mechanisms play important roles in S. maltophilia pathogenesis. Furthermore, utilizing bacteria closely related to strains found in C. elegans natural environment provides a more realistic interaction for understanding host-pathogen response.

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