scholarly journals Transcriptomic signature of rapidly evolving immune genes in a highland fish

2019 ◽  
Author(s):  
Chao Tong ◽  
Miao Li ◽  
Kai Zhao
Keyword(s):  
Fish Species ◽  
Complement Activation ◽  
Expression Patterns ◽  
Adaptive Immune System ◽  
Head Kidney ◽  
Immune Gene ◽  
Gene Repertoire ◽  
Immune Genes ◽  
Genome Wide ◽  
Insight Into

AbstractRecent genome-wide studies have begun to elucidate the genomic basis of hypoxia, long-term cold and high saline and alkaline adaptation in highland fish, and a number of key genes contributed to its highland adaptation were identified. An increasing number of studies indicated that immune genes of Tibetan endemic fish species underwent positive selection towards functional shift, while the insight into immune gene repertoire of Tibetan highland fishes from genome-wide studies has largely lagged behind. In this study, we performed one of the first comparative genomics study in particular focusing on the signatures of immune genes in a highland fish, Gymnocypris przewalskii based on immune-relevant tissue transcriptome assemblies. We identified seven putative rapidly evolving immune genes with elevated molecular evolutionary rate (dN/dS) relative to lowland fish species. Using tissue-transcriptome data, we found most of rapidly evolving immune genes were broadly expressed in head-kidney, spleen, gills and skin tissues, which significantly enriched for complement activation and inflammatory response processes. In addition, we found a set of complement activation related genes underwent accelerated evolution and showed consistently repressed expression patterns in response to parasite Ichthyophthirius multifiliis infection. Moreover, we detected a number of immune genes involved in adaptive immune system exhibited distinct signature of upregulated expression patterns after parasite infection. Taken together, this study provided putative transcriptomic signatures of rapidly evolving immune genes, and will gain the insight into Schizothoracine fish adaptation to high-altitude extreme aquatic environments including diversified pathogen challenge.

scholarly journals Evolution and Expression of the Immune System of a Facultatively Anadromous Salmonid

2021 ◽  
Vol 12 ◽  
Author(s):  
Thomas J. Colgan ◽  
Peter A. Moran ◽  
Louise C. Archer ◽  
Robert Wynne ◽  
Stephen A. Hutton ◽  
...  
Keyword(s):  
Life Cycle ◽  
Immune System ◽  
Brown Trout ◽  
Salmo Trutta ◽  
Whole Genome Duplication ◽  
Genome Duplication ◽  
Immune Gene ◽  
Whole Genome ◽  
Gene Repertoire ◽  
Immune Genes

Vertebrates have evolved a complex immune system required for the identification of and coordinated response to harmful pathogens. Migratory species spend periods of their life-cycle in more than one environment, and their immune system consequently faces a greater diversity of pathogens residing in different environments. In facultatively anadromous salmonids, individuals may spend parts of their life-cycle in freshwater and marine environments. For species such as the brown trout Salmo trutta, sexes differ in their life-histories with females more likely to migrate to sea while males are more likely to stay and complete their life-cycle in their natal river. Salmonids have also undergone a lineage-specific whole genome duplication event, which may provide novel immune innovations but our current understanding of the differences in salmonid immune expression between the sexes is limited. We characterized the brown trout immune gene repertoire, identifying a number of canonical immune genes in non-salmonid teleosts to be duplicated in S. trutta, with genes involved in innate and adaptive immunity. Through genome-wide transcriptional profiling (“RNA-seq”) of male and female livers to investigate sex differences in gene expression amplitude and alternative splicing, we identified immune genes as being generally male-biased in expression. Our study provides important insights into the evolutionary consequences of whole genome duplication events on the salmonid immune gene repertoire and how the sexes differ in constitutive immune expression.

scholarly journals Integrative Transcriptomic Analysis Reveals the Immune Mechanism for A CyHV-3-Resistant Common Carp Strain

2020 ◽  
Author(s):  
Zhiying Jia ◽  
Nan Wu ◽  
Xiaona Jiang ◽  
Heng Li ◽  
Jiaxin Sun ◽  
...  
Keyword(s):  
Gene Ontology ◽  
Common Carp ◽  
Resistance Mechanism ◽  
Head Kidney ◽  
Immune Gene ◽  
Immune Mechanism ◽  
Protein Coding ◽  
Immune Genes ◽  
Comparison Groups ◽  
Immune Related Genes

ABSTRACTAnti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Mortality studies suggested that a breeding strain of common carp is resistant to this disease. This study illustrates the immune mechanisms involved in anti-CyHV-3 ability. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was also performed. Tissues from the head kidney of common carp were extracted at day 0 (the healthy control) and day 7 after CyHV-3 infection (the survivors), and used to analyze the transcriptome through both Illumina and Pac-bio sequencing. Following analysis of the Kyoto Encyclopedia of Genes and Genomes pathways and Gene Ontology terms involved, the immune-related genes were merged. These genes were filtered using the current common carp immune gene library, and information on the immune process was detailed. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used for the regulation of immune genes lncRNA. The results demonstrated that the breeding carp strain develops marked resistance to CyHV-3 through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and mucin 3 (MUC3). Moreover, the immune suppressive signals, such as suppression of interleukin 21 receptor (IL21R) on STAT3, PI3K mediated the inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLR family CARD domain containing 3 (NLRC3) on STING during a steady state. Possible susceptible factors for CyHV-3, such as integrin beta 1 (ITGB1), toll-like receptor 18 (TLR18), and C-C motif chemokine ligand 4 (CCL4), were also revealed from the common strain. The results of this study suggested that the regulation of galectin 3 (LGALS3) and T cell leukemia homeobox 3 (TLX3) by lncRNA may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

scholarly journals Immune gene diversity in archaic and present-day humans

2018 ◽  
Author(s):  
David Reher ◽  
Felix M. Key ◽  
Aida M. Andrés ◽  
Janet Kelso
Keyword(s):  
Gene Diversity ◽  
Innate Immune ◽  
Immune Gene ◽  
Similar Reduction ◽  
Protein Coding ◽  
Immune Genes ◽  
Genome Wide ◽  
Show Evidence ◽  
Functional Consequences ◽  
Immune Related Genes

Genome-wide analyses of two Neandertals and a Denisovan have shown that these archaic humans had lower genetic heterozygosity than present-day people. A similar reduction in genetic diversity of protein-coding genes (gene diversity) was found in exome sequences of three Neandertals. Reduced gene diversity, and particularly in genes involved in immunity, may have important functional consequences. In fact, it has been suggested that reduced diversity in immune genes may have contributed to Neandertal extinction. We therefore explored gene diversity in different human groups and at different time points on the Neandertal lineage with a particular focus on the diversity of genes involved in innate immunity and genes of the Major Histocompatibility Complex (MHC).We find that the two Neandertals and the Denisovan have similar gene diversity, both significantly lower than any present-day human. This is true across gene categories, with no gene set showing an excess decrease in diversity compared to the genome-wide average. Innate immune-related genes show a similar reduction in diversity to other genes, both in present-day and archaic humans. There is also no observable decrease in gene diversity over time in Neandertals, suggesting that there may have been no ongoing reduction in gene diversity in later Neandertals, although this needs confirmation with a larger sample size. In both archaic and present-day humans, genes with the highest levels of diversity are enriched for MHC-related functions. In fact, in archaic humans the MHC genes show evidence of having retained more diversity than genes involved only in the innate immune system.

scholarly journals Characterization of the gene repertoire and environmentally driven expression patterns in Tanner crab (Chionoecetes bairdi)

2021 ◽  
Author(s):  
Grace Crandall ◽  
Pamela C Jensen ◽  
Sam White ◽  
Steven Roberts
Keyword(s):  
Disease Transmission ◽  
Expression Patterns ◽  
Ocean Warming ◽  
Lipid Storage ◽  
Host Susceptibility ◽  
Gene Repertoire ◽  
Important Species ◽  
Tanner Crab ◽  
Chionoecetes Bairdi ◽  
Insight Into

Tanner crab (Chionoecetes bairdi) are an economically important species that is threatened by ocean warming and Bitter Crab Disease, which is caused by an endoparasitic dinoflagellate, Hematodinium. Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To provide a transcriptomic resource for the Tanner crab we generated a suite of RNA-seq libraries encompassing pooled hemolymph samples from crab displaying differing infection status and maintained at different temperatures (ambient (7.5˚C), elevated (10˚C), or decreased (4˚C)). After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection, and detected some of those genes over time at the individual level using RNAseq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm.

scholarly journals Genome-Wide Analysis and Identification of the Aux/IAA Gene Family in Peach

2019 ◽  
Vol 20 (19) ◽  
pp. 4703 ◽  
Author(s):  
Dan Guan ◽  
Xiao Hu ◽  
Donghui Diao ◽  
Fang Wang ◽  
Yueping Liu
Keyword(s):  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Fruit Maturation ◽  
Auxin Response ◽  
Genome Wide ◽  
Potential Development ◽  
Fold Induction ◽  
Indole 3 Acetic Acid ◽  
Insight Into ◽  
Stony Hard

The Auxin/indole-3-acetic acid (Aux/IAA) repressor genes down-regulate the auxin response pathway during many stages of plant and fruit development. In order to determine if and how Aux/IAAs participate in governing texture and hardness in stone fruit maturation, we identified 23 Aux/IAA genes in peach, confirmed by the presence of four conserved domains. In this work, we used fluorescence microscopy with PpIAA-GFP fusion reporters to observe their nuclear localization. We then conducted PCR-based differential expression analysis in “melting” and “stony hard” varieties of peach, and found that in the “melting” variety, nine PpIAAs exhibited peak expression in the S4-3 stage of fruit maturation, with PpIAA33 showing the highest (>120-fold) induction. The expression of six PpIAAs peaked in the S4-2 stage, with PpIAA14 expressed the most highly. Only PpIAA15/16 showed higher expression in the “stony hard” variety than in the “melting” variety, both peaking in the S3 stage. In contrast, PpIAA32 had the highest relative expression in buds, flowers, young and mature leaves, and roots. Our study provides insights into the expression patterns of Aux/IAA developmental regulators in response to auxin during fruit maturation, thus providing insight into their potential development as useful markers for quantitative traits associated with fruit phenotype.

scholarly journals Genome-wide identification and characterization of the ALOG gene family in Petunia

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Feng Chen ◽  
Qin Zhou ◽  
Lan Wu ◽  
Fei Li ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Reproductive Organs ◽  
Genome Wide ◽  
Domain Of Unknown Function ◽  
Intron Structure ◽  
Identification And Characterization ◽  
Insight Into

Abstract Background The ALOG (Arabidopsis LSH1 and Oryza G1) family of proteins, namely DUF640 (domain of unknown function 640) domain proteins, were found in land plants. Functional characterization of a few ALOG members in model plants such as Arabidopsis and rice suggested they play important regulatory roles in plant development. The information about its evolution, however, is largely limited, and there was no any report on the ALOG genes in Petunia, an important ornamental species. Results The ALOG genes were identified in four species of Petunia including P. axillaris, P. inflata, P. integrifolia, and P. exserta based on the genome and/or transcriptome databases, which were further confirmed by cloning from P. hybrida ‘W115’ (Mitchel diploid), a popular laboratorial petunia line susceptible to genetic transformation. Phylogenetic analysis indicated that Petunia ALOG genes (named as LSHs according to their closest Arabidopsis homologs) were grouped into four clades, which can be further divided into eight groups, and similar exon-intron structure and motifs are reflected in the same group. The PhLSH genes of hybrid petunia ‘W115’ were mainly derived from P. axillaris. The qPCR analysis revealed distinct spatial expression patterns among them suggesting potentially functional diversification. Moreover, over-expressing PhLSH7a and PhLSH7b in Arabidopsis uncovered their functions in the development of both vegetative and reproductive organs. Conclusions Petunia genome includes 11 ALOG genes that can be divided into eight distinct groups, and they also show different expression patterns. Among these genes, PhLSH7b and PhLSH7a play significant roles in plant growth and development, especially in fruit development. Our results provide new insight into the evolution of ALOG gene family and have laid a good foundation for the study of petunia LSH gene in the future.

scholarly journals Integrative Transcriptomic Analysis Reveals the Immune Mechanism for a CyHV-3-Resistant Common Carp Strain

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhiying Jia ◽  
Nan Wu ◽  
Xiaona Jiang ◽  
Heng Li ◽  
Jiaxin Sun ◽  
...  
Keyword(s):  
Common Carp ◽  
Resistance Mechanism ◽  
Head Kidney ◽  
Immune Gene ◽  
Immune Mechanism ◽  
Protein Coding ◽  
Immune Genes ◽  
Kegg Pathways ◽  
Comparison Groups ◽  
Galectin 3

Anti-disease breeding is becoming the most promising solution to cyprinid herpesvirus-3 (CyHV-3) infection, the major threat to common carp aquaculture. Virus challenging studies suggested that a breeding strain of common carp developed resistance to CyHV-3 infection. This study illustrates the immune mechanisms involved in both sensitivity and anti-virus ability for CyHV3 infection in fish. An integrative analysis of the protein-coding genes and long non-coding RNAs (lncRNAs) using transcriptomic data was performed. Tissues from the head kidney of common carp were extracted at days 0 (the healthy control) and 7 after CyHV-3 infection (the survivors) and used to analyze the transcriptome through both Illumina and PacBio sequencing. Following analysis of the GO terms and KEGG pathways involved, the immune-related terms and pathways were merged. To dig out details on the immune aspect, the DEGs were filtered using the current common carp immune gene library. Immune gene categories and their corresponding genes in different comparison groups were revealed. Also, the immunological Gene Ontology terms for lncRNA modulation were retained. The weighted gene co-expression network analysis was used to reveal the regulation of immune genes by lncRNA. The results demonstrated that the breeding carp strain develops a marked resistance to CyHV-3 infection through a specific innate immune mechanism. The featured biological processes were autophagy, phagocytosis, cytotoxicity, and virus blockage by lectins and MUC3. Moreover, the immune-suppressive signals, such as suppression of IL21R on STAT3, PI3K mediated inhibition of inflammation by dopamine upon infection, as well as the inhibition of NLRC3 on STING during a steady state. Possible susceptible factors for CyHV-3, such as ITGB1, TLR18, and CCL4, were also revealed from the non-breeding strain. The results of this study also suggested that Nramp and PAI regulated by LncRNA could facilitate virus infection and proliferation for infected cells respectively, while T cell leukemia homeobox 3 (TLX3), as well as galectin 3 function by lncRNA, may play a role in the resistance mechanism. Therefore, immune factors that are immunogenetically insensitive or susceptible to CyHV-3 infection have been revealed.

scholarly journals Genome-wide association studies suggest limited immune gene enrichment in schizophrenia compared to five autoimmune diseases

2015 ◽  
Author(s):  
Jennie G. Pouget ◽  
Vanessa F. Gonçalves ◽  
Sarah L. Spain ◽  
Hilary K. Finucane ◽  
Soumya Raychaudhuri ◽  
...  
Keyword(s):  
Association Studies ◽  
Genome Wide Association ◽  
Future Research ◽  
Immune Gene ◽  
Genome Wide Association Studies ◽  
Immune Genes ◽  
Genome Wide ◽  
Immune Alterations ◽  
Pathway Analyses ◽  
Immune Loci

AbstractThere has been intense debate over the immunological basis of schizophrenia, and the potential utility of adjunct immunotherapies. The major histocompatibility complex is consistently the most powerful region of association in genome-wide association studies (GWASs) of schizophrenia, and has been interpreted as strong genetic evidence supporting the immune hypothesis. However, global pathway analyses provide inconsistent evidence of immune involvement in schizophrenia, and it remains unclear whether genetic data support an immune etiology per se. Here we empirically test the hypothesis that variation in immune genes contributes to schizophrenia. We show that there is no enrichment of immune loci outside of the MHC region in the largest genetic study of schizophrenia conducted to date, in contrast to five diseases of known immune origin. Among 108 regions of the genome previously associated with schizophrenia, we identify six immune candidates (DPP4, HSPD1, EGR1, CLU, ESAM, NFATC3) encoding proteins with alternative, nonimmune roles in the brain. While our findings do not refute evidence that has accumulated in support of the immune hypothesis, they suggest that genetically mediated alterations in immune function may not play a major role in schizophrenia susceptibility. Instead, there may be a role for pleiotropic effects of a small number of immune genes that also regulate brain development and plasticity. Whether immune alterations drive schizophrenia progression is an important question to be addressed by future research, especially in light of the growing interest in applying immunotherapies in schizophrenia.

scholarly journals Characterization of the Gene Repertoire and Environmentally Driven Expression Patterns in Tanner Crab ( Chionoecetes Bairdi )

2021 ◽  
Author(s):  
Grace Crandall ◽  
Pamela Jensen ◽  
Sam White ◽  
Steven Roberts
Keyword(s):  
Disease Transmission ◽  
Expression Patterns ◽  
Ocean Warming ◽  
Lipid Storage ◽  
Host Susceptibility ◽  
Gene Repertoire ◽  
Important Species ◽  
Tanner Crab ◽  
Chionoecetes Bairdi ◽  
Insight Into

Abstract Tanner crab ( Chionoecetes bairdi ) are an economically important species that is threatened by ocean warming and Bitter Crab Disease, which is caused by an endoparasitic dinoflagellate, Hematodinium . Little is known about disease transmission or its link to host mortality, or how ocean warming will affect pathogenicity or host susceptibility. To betterunderstand how temperature and infection influence host physiology, we performed a temporal transcriptomic analysis on crab infected with Hematodinium and uninfected crab exposed to either ambient (7.5˚C), elevated (10˚C), or decreased (4˚C) temperature treatments. After assembling a transcriptome and performing a multifactor differential gene expression analysis, we found genes influenced by temperature in relation to infection, and detected some of those genes over time at the individual level using RNAseq data from one crab. Biological processes associated with those genes include lipid storage, transcription, response to oxidative stress, cell adhesion, and morphogenesis. Alteration in lipid storage and transcription provide insight into how temperature impacts energy allocation in Hematodinium infected crabs. Alteration in expression patterns in genes associated with morphogenesis could suggest hemocytes were changing morphology and/or type in response to temperature. This project provides insight into how Hematodinium infection could influence crab physiology as oceans warm.

scholarly journals Genome-Wide Analysis of Carboxylesterases (COEs) in the Whitefly, Bemisia tabaci (Gennadius)

2019 ◽  
Vol 20 (20) ◽  
pp. 4973
Author(s):  
Jixing Xia ◽  
Haifeng Xu ◽  
Zezhong Yang ◽  
Huipeng Pan ◽  
Xin Yang ◽  
...  
Keyword(s):  
Bemisia Tabaci ◽  
Expression Patterns ◽  
Invasive Pest ◽  
Neighbor Joining ◽  
Functional Categories ◽  
Genome Database ◽  
Genome Wide ◽  
A Genome ◽  
Multifunctional Enzymes ◽  
Insight Into

The whitefly (Bemisia tabaci), an important invasive pest that causes severe damage to crops worldwide, has developed resistance to a variety of insecticides. Carboxylesterases (COEs) are important multifunctional enzymes involved in the growth, development, and xenobiotic metabolism of insects. However, systematic studies on the COEs of B. tabaci are scarce. Here, 42 putative COEs in different functional categories were identified in the Mediterranean species of B. tabaci (B. tabaci MED) based on a genome database and neighbor-joining phylogeny. The expression patterns of the COEs were affected by the development of B. tabaci. The expression levels of six COEs were positively correlated with the concentration of imidacloprid to which B. tabaci adults were exposed. The mortality of B. tabaci MED adults fed dsBTbe5 (67.5%) and dsBTjhe2 (58.4%) was significantly higher than the adults fed dsEGFP (41.1%) when treated with imidacloprid. Our results provide a basis for functional research on COEs in B. tabaci and provide new insight into the imidacloprid resistance of B. tabaci.

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