scholarly journals Genomic analysis of dingoes identifies genomic regions under reversible selection during domestication and feralization

2018 ◽  
Author(s):  
Shao-jie Zhang ◽  
Guo-Dong Wang ◽  
Pengcheng Ma ◽  
Liang-liang Zhang ◽  
Ting-Ting Yin ◽  
...  
Keyword(s):  
Hippocampal Neurons ◽  
Genomic Analysis ◽  
Neural Spine ◽  
Diet Change ◽  
Distinct Population ◽  
Domestic Species ◽  
Behavioral Adaptations ◽  
Endogenous Expression ◽  
Wild Canids ◽  
Genomic Regions

AbstractDingoes (Canis dingo) are wild canids living in Australia. They have lived isolated from both the wild and the domestic ancestor and are a unique model for studying feralization, the process in which a domestic species escapes human control, adapts to the wild, and diverges from the domestic ancestor into a genetically distinct population. Here, we sequenced the genomes of 10 dingoes and 2 New Guinea Singing Dogs, to study the origins and feralization process of the dingo. Phylogenetic and demographic analyses show that dingoes originate from domestic dogs in southern East Asia, which migrated via Island Southeast Asia to reach Australia 4300-5000 years ago, and subsequently diverged into a genetically distinct population. Selection analysis identified 99 positively selected genes enriched in starch and fat metabolism pathways, indicating a diet change during feralization of dingoes. Interestingly, we found that 14 genes have shifted allele frequencies compared to dogs but not compared to wolves. This suggests that the selection affecting these genes during domestication of the wolf was reversed in the feralization process. One of these genes, ARHGEF7, may promote the formation of neural spine and synapses in hippocampal neurons. Functional assays showed that an A to G mutation in ARHGEF7, located in a transcription factor-binding site, decreases the endogenous expression. This suggests that ARHGEF7 may have been under selection for behavioral adaptations related to the transitions in environment both from wild to domestic and from domestic back to wild. Our results indicate that adaptation to domestication and feralization primarily affected different genomic regions, but that some genes, related to neurodevelopment, metabolism and reproduction, may have been reversibly affected in the two processes.

scholarly journals Understanding potential implications for non-trophic parasite transmission based on vertebrate behavior at mesocarnivore carcass sites

2021 ◽  
Author(s):  
Moisés Gonzálvez ◽  
Carlos Martínez-Carrasco ◽  
Marcos Moleón
Keyword(s):  
Red Fox ◽  
Close Contact ◽  
Infection Risk ◽  
Camera Traps ◽  
Emerging Pathogens ◽  
Domestic Species ◽  
Time Period ◽  
Wild Canids ◽  
Rubbing Behavior ◽  
Trophically Transmitted Parasites

AbstractHigh infection risk is often associated with aggregations of animals around attractive resources. Here, we explore the behavior of potential hosts of non-trophically transmitted parasites at mesocarnivore carcass sites. We used videos recorded by camera traps at 56 red fox (Vulpes vulpes) carcasses and 10 carcasses of other wild carnivore species in three areas of southeastern Spain. Scavenging species, especially wild canids, mustelids and viverrids, showed more frequent rubbing behavior at carcass sites than non-scavenging and domestic species, suggesting that they could be exposed to a higher potential infection risk. The red fox was the species that most frequently contacted carcasses and marked and rubbed carcass sites. Foxes contacted heterospecific carcasses more frequently and earlier than conspecific ones and, when close contact occurred, it was more likely to be observed at heterospecific carcasses. This suggests that foxes avoid contact with the type of carcass and time period that have the greatest risk as a source of parasites. Overall, non-trophic behaviors of higher infection risk were mainly associated with visitor-carcass contact and visitor contact with feces and urine, rather than direct contact between visitors. Moreover, contact events between scavengers and carnivore carcasses were far more frequent than consumption events, which suggests that scavenger behavior is more constrained by the risk of acquiring meat-borne parasites than non-trophically transmitted parasites. This study contributes to filling key gaps in understanding the role of carrion in the landscape of disgust, which may be especially relevant in the current global context of emerging and re-emerging pathogens. Graphical abstract

scholarly journals MyD88-5 links mitochondria, microtubules, and JNK3 in neurons and regulates neuronal survival

2007 ◽  
Vol 204 (9) ◽  
pp. 2063-2074 ◽  
Author(s):  
Younghwa Kim ◽  
Ping Zhou ◽  
Liping Qian ◽  
Jen-Zen Chuang ◽  
Jessica Lee ◽  
...  
Keyword(s):  
Hippocampal Neurons ◽  
Artificial Chromosome ◽  
Adaptor Proteins ◽  
Innate Immune ◽  
Molecular Structures ◽  
Endogenous Expression ◽  
Microbial Products ◽  
The Brain ◽  
Deficient Mice

The innate immune system relies on evolutionally conserved Toll-like receptors (TLRs) to recognize diverse microbial molecular structures. Most TLRs depend on a family of adaptor proteins termed MyD88s to transduce their signals. Critical roles of MyD88-1–4 in host defense were demonstrated by defective immune responses in knockout mice. In contrast, the sites of expression and functions of vertebrate MyD88-5 have remained elusive. We show that MyD88-5 is distinct from other MyD88s in that MyD88-5 is preferentially expressed in neurons, colocalizes in part with mitochondria and JNK3, and regulates neuronal death. We prepared MyD88-5/GFP transgenic mice via a bacterial artificial chromosome to preserve its endogenous expression pattern. MyD88-5/GFP was detected chiefly in the brain, where it associated with punctate structures within neurons and copurified in part with mitochondria. In vitro, MyD88-5 coimmunoprecipitated with JNK3 and recruited JNK3 from cytosol to mitochondria. Hippocampal neurons from MyD88-5–deficient mice were protected from death after deprivation of oxygen and glucose. In contrast, MyD88-5–null macrophages behaved like wild-type cells in their response to microbial products. Thus, MyD88-5 appears unique among MyD88s in functioning to mediate stress-induced neuronal toxicity.

scholarly journals Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus

2020 ◽  
Vol 8 (3) ◽  
pp. 366
Author(s):  
Jarred Yasuhara-Bell ◽  
Mohammad Arif ◽  
Grethel Y. Busot ◽  
Rachel Mann ◽  
Brendan Rodoni ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
The United States ◽  
Grass Species ◽  
Comparative Genomic ◽  
Underrepresented Populations ◽  
System A ◽  
Genome Wide ◽  
The Family ◽  
Study Support ◽  
Genomic Regions

Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.

A reappraisal of the California Roach/Hitch (Cypriniformes, Cyprinidae, Hesperoleucus/Lavinia) species complex

Zootaxa ◽  
2019 ◽  
Vol 4543 (2) ◽  
pp. 221 ◽  
Author(s):  
JASON BAUMSTEIGER ◽  
PETER B. MOYLE
Keyword(s):  
Species Complex ◽  
Genomic Analysis ◽  
Clear Lake ◽  
Distinct Population ◽  
Morphological Studies ◽  
Hierarchical Levels ◽  
Russian River ◽  
Tomales Bay ◽  
Management And Conservation ◽  
Hesperoleucus Symmetricus

The California Roach (Hesperoleucus symmetricus) and Hitch (Lavinia exilicauda) form a species complex largely endemic to California (CA), USA. Using previous studies of this complex along with a recent comprehensive genomic analysis, we developed a highly supported taxonomic hierarchy of two genera, five species, four subspecies and multiple distinct population segments within two presently recognized species. The genera Lavinia and Hesperoleucus are supported as representing distinct lineages, despite occasional hybridization between them. While hybridization is one pathway to some speciation in this complex, hierarchical levels correlate nicely between genomic results and earlier morphological work. Hesperoleucus symmetricus is newly divided into four species (H. parvipinnis—Gualala Roach, H. mitrulus—Northern Roach, H. venustus—Coastal Roach, and H. symmetricus—California Roach) and two subspecies (H. s. serpentinus—Red Hills Roach, H. s. symmetricus—California Roach). Within H. venustus, two subspecies are identified (H. v. navarroensis—Northern Coastal Roach, and H. v. subditus—Southern Coastal Roach), which are supported by previous morphological studies but resolve discrepancies between those studies. Finally, six distinct population segments are identified within different species/subspecies: Kaweah, Russian River, Navarro River, Monterey, and Tomales Bay. Clear Lake Roach are introgressed between California and Coastal Roach, making them distinct but difficult to formally name. Results should greatly improve management and conservation of each taxonomic entity and help resolve past ambiguities. Additional studies are needed to improve range-wide boundaries and to investigate population structure within all species and subspecies identified in both Lavinia and Hesperoleucus lineages. 

scholarly journals Identification of a Hypervariable Region Containing New Legionella pneumophila Icm/Dot Translocated Substrates by Using the Conserved icmQ Regulatory Signature

2008 ◽  
Vol 76 (10) ◽  
pp. 4581-4591 ◽  
Author(s):  
Tal Zusman ◽  
Elena Degtyar ◽  
Gil Segal
Keyword(s):  
Legionella Pneumophila ◽  
Regulatory Element ◽  
Hypervariable Region ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Genomic Region ◽  
Host Cells ◽  
Regulatory Sequence ◽  
Dependent Manner ◽  
Genomic Regions

ABSTRACT Legionella pneumophila is an intracellular pathogen that has been shown to utilize the Icm/Dot type IV secretion system for pathogenesis. This system was shown to be composed of Icm/Dot complex components, accessory proteins, and a large number of translocated substrates. In this study, comparison of the icmQ regulatory regions from many Legionella species revealed a conserved regulatory sequence that includes the icmQ −10 promoter element. Mutagenesis of this conserved regulatory element indicated that each of the nucleotides in it affects the level of expression of the icmQ gene but not in a uniform fashion. A genomic analysis discovered that four additional genes in L. pneumophila contain this conserved regulatory sequence, which was found to function similarly in these genes as well. Examination of these four genes indicated that they are dispensable for intracellular growth, but two of them were found to encode new Icm/Dot translocated substrates (IDTS). Comparison of the genomic regions encoding these two IDTS among the four available L. pneumophila genomic sequences indicated that one of these genes is located in a hypervariable genomic region, which was shown before to contain an IDTS-encoding gene. Translocation analysis that was performed for nine proteins encoded from this hypervariable genomic region indicated that six of them are new IDTS which are translocated into host cells in an Icm/Dot-dependent manner. Furthermore, a bioinformatic analysis indicated that additional L. pneumophila genomic regions that contain several neighboring IDTS-encoding genes are hypervariable in gene content.

scholarly journals Genomic analysis of GBS data reveals genes associated with facial pigmentation in Xinyang blue-shelled layers

2020 ◽  
Vol 63 (2) ◽  
pp. 483-491
Author(s):  
Haobin Hou ◽  
Xiaoliang Wang ◽  
Caiyun Zhang ◽  
Yingying Tu ◽  
Wenwei Lv ◽  
...  
Keyword(s):  
Skin Color ◽  
Genome Wide Association Study ◽  
Laying Hens ◽  
Genomic Analysis ◽  
Significant Snps ◽  
Pure Line ◽  
Genomic Region ◽  
High Quality Snps ◽  
A Genome ◽  
Genomic Regions

Abstract. Facial pigmentation is an important economic trait of chickens, especially for laying hens, which will affect the carcass appearance of eliminated layers. Therefore, identifying the genomic regions and exploring the function of this region that contributes to understanding the variation of skin color traits is significant for breeding. In the study, 291 pure-line Xinyang blue-shelled laying hens were selected, of which 75 were dark-faced chickens and 216 were white-faced chickens. The population was sequenced and typed by GBS genotyping technology. The obtained high-quality SNPs and pigmentation phenotypes were analyzed by a genome-wide association study (GWAS) and a FST scan. Based on the two analytical methods, we identified a same genomic region (10.70–11.60 Mb) on chromosome 20 with 68 significant SNPs (−log 10(P)>6), mapped to 10 known genes, including NPEPL1, EDN3, GNAS, C20orf85, VAPB, BMP7, TUBB1, ELMO2, DDX27, and NCOA5, which are associated with dermal hyperpigmentation.

scholarly journals Long non-coding RNA NEAT1 aggravates epilepsy and seizure-induced neuronal damage by regulating microRNA-139/ROCK1 axis

2020 ◽  
Author(s):  
Xiaowan Li ◽  
Fang Hao ◽  
Shuxin Tao ◽  
Weihua Wang ◽  
Xinxing Xiao ◽  
...  
Keyword(s):  
Cell Apoptosis ◽  
Hippocampal Neurons ◽  
Neuronal Damage ◽  
Inflammatory Factors ◽  
Luciferase Reporter ◽  
Endogenous Expression ◽  
Non Coding Rna ◽  
Gene Assay ◽  
Lncrna Neat1 ◽  
Long Non Coding Rna

Abstract Background Both long non-coding RNA (lncRNA) NEAT1 and microRNA (miR)-139 are crucial gene regulators in various disorders. This study aims to investigate their role in epilepsy and seizure-induced neuronal damage. Methods In this research, rat model of epilepsy was established by pilocarpine induction. The RNA and protein expression in hippocampal tissues and neurons were determined by RT-qPCR and Western blot analysis, respectively. Microarray analysis was used to predict the relationship between NEAT1 and miR-139 or between miR-139 and ROCK1, and dual luciferase reporter gene assay was performed to verify the interaction. The endogenous expression of related genes was modulated by recombinant plasmids and cell transfection. The cell apoptosis, levels of inflammatory factors and cell proliferation were detected by flow cytometry, ELISA and EdU assay. Results LncRNA NEAT1 and ROCK1 was upregulated, while the miR-139 was downregulated in hippocampal tissues and neurons of epileptic rats. Overexpression of NEAT1 decreased the activity of neurons, increased cell apoptosis, and increased the level of inflammatory factors. NEAT1 negatively targeted miR-139 to upregulate ROCK1. The RhoA/ROCK1 signaling pathway was activated by NEAT1 overexpression and miR-139 downregulation. Conclusion LncRNA NEAT1 suppressed pilocarpine-induced epilepsy by inhibiting apoptosis of hippocampal neurons through miR-139/RhoA/ROCK1 axis, and thereby inhibiting neuronal injury induced by seizure.

scholarly journals FANCD2 tunes the UPR preventing mitochondrial stress-­induced common fragile site instability

2019 ◽  
Author(s):  
Philippe Fernandes ◽  
Benoit Miotto ◽  
Claude Saint-Ruf ◽  
Viola Nähse ◽  
Silvia Ravera ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Instability ◽  
Fragile Site ◽  
Transcriptional Response ◽  
Genomic Analysis ◽  
Fragile Sites ◽  
The Unfolded Protein Response ◽  
And Function ◽  
Large Genes ◽  
Genomic Regions

AbstractCommon fragile sites (CFSs) are genomic regions frequently involved in cancer-associated rearrangements. Most CFSs lie within large genes, and their instability relies on transcription- and replication-dependent mechanisms. Here, we uncover a role for the UBL5-dependent branch of the unfolded protein response pathway (UPR) in the maintenance of CFS stability. We show that genetic or pharmacological UPR activation induces CFS gene expression and concomitant relocalization of FANCD2, a master regulator of CFS stability, to CFSs. Furthermore, a genomic analysis of FANCD2 binding sites identified an enrichment for mitochondrial UPR transcriptional response elements in FANCD2 bound regions. We demonstrated that depletion of FANCD2 increases CFS gene transcription and their instability while also inducing mitochondrial dysfunction and triggering the activation of the UPR pathway. Depletion of UBL5, a mediator of the UPR, but not ATF4, reduces CFS gene expression and breakage in FANCD2-depleted cells. We thus demonstrate that FANCD2 recruitment and function at CFSs depends on transcription and UPR signaling, and in absence of transcription or UBL5, FANCD2 is dispensable for CFS stability. We propose that FANCD2 coordinates nuclear and mitochondrial activities by tuning the UPR to prevent genome instability.

scholarly journals Phylogenomics reveals dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism

2018 ◽  
Author(s):  
Steven A. Higgins ◽  
Christopher W. Schadt ◽  
Patrick B. Matheny ◽  
Frank E. Löffler
Keyword(s):  
Nitric Oxide ◽  
Secondary Metabolism ◽  
Genomic Analysis ◽  
Primary Role ◽  
Ancestral State ◽  
The Novel ◽  
Gene Duplications ◽  
Genes Encoding ◽  
Denitrification Genes ◽  
Genomic Regions

AbstractFungi expressing P450nor, an unconventional nitric oxide (NO) reducing cytochrome P450, are thought to be significant contributors to soil nitrous oxide (N2O) emissions. However, fungal contributions to N2O emissions remain uncertain due to inconsistencies in measurements of N2O formation by fungi. Much of the N2O emitted from antibiotic-amended soil microcosms is attributed to fungal activity, yet fungal isolates examined in pure culture are poor N2O producers. To assist in reconciling these conflicting observations and produce a benchmark genomic analysis of fungal denitrifiers, genes underlying fungal denitrification were examined in >700 fungal genomes. Of 167p450nor–containing genomes identified, 0, 30, and 48 also harbored the denitrification genesnarG,napAornirK, respectively. Compared tonapAandnirK,p450norwas twice as abundant and exhibited two to five-fold more gene duplications, losses, and transfers, indicating a disconnect betweenp450norpresence and denitrification potential. Furthermore, co-occurrence ofp450norwith genes encoding NO-detoxifying flavohemoglobins (Spearman r = 0.87,p= 1.6e−10) confounds hypotheses regarding P450nor’s primary role in NO detoxification. Instead, ancestral state reconstruction united P450nor with actinobacterial cytochrome P450s (CYP105) involved in secondary metabolism (SM) and 19 (11 %)p450nor-containing genomic regions were predicted to be SM clusters. Another 40 (24 %) genomes harbored genes nearbyp450norpredicted to encode hallmark SM functions, providing additional contextual evidence linkingp450norto SM. These findings underscore the potential physiological implications of widespreadp450norgene transfer, support the novel affiliation ofp450norwith fungal SM, and challenge the hypothesis ofp450nor’s primary role in denitrification.

scholarly journals A Comparative Genomic Analysis of the Barley Pathogen Pyrenophora teres f. teres Identifies Subtelomeric Regions as Drivers of Virulence

2020 ◽  
Vol 33 (2) ◽  
pp. 173-188 ◽  
Author(s):  
Nathan A. Wyatt ◽  
Jonathan K. Richards ◽  
Robert S. Brueggeman ◽  
Timothy L. Friesen
Keyword(s):  
Genomic Analysis ◽  
Effector Proteins ◽  
Comparative Genomic ◽  
Pyrenophora Teres ◽  
Structural Variations ◽  
Evolution Of Virulence ◽  
Reference Quality ◽  
Genomic Characterization ◽  
Genomic Regions ◽  
Subtelomeric Regions

Pyrenophora teres f. teres causes net form net blotch of barley and is an economically important pathogen throughout the world. However, P. teres f. teres is lacking in the genomic resources necessary to characterize the mechanisms of virulence. Recently a high-quality reference genome was generated for P. teres f. teres isolate 0-1. Here, we present the reference quality sequence and annotation of four new isolates and we use the five available P. teres f. teres genomes for an in-depth comparison, resulting in the generation of hypotheses pertaining to the potential mechanisms and evolution of virulence. Comparative analyses were performed between all five P. teres f. teres genomes, examining genomic organization, structural variations, and core and accessory genomic content, specifically focusing on the genomic characterization of known virulence loci and the localization of genes predicted to encode secreted and effector proteins. We showed that 14 of 15 currently published virulence quantitative trait loci (QTL) span accessory genomic regions, consistent with these accessory regions being important drivers of host adaptation. Additionally, these accessory genomic regions were frequently found in subtelomeric regions of chromosomes, with 10 of the 14 accessory region QTL localizing to subtelomeric regions. Comparative analysis of the subtelomeric regions of P. teres f. teres chromosomes revealed translocation events in which homology was detected between nonhomologous chromosomes at a significantly higher rate than the rest of the genome. These results indicate that the subtelomeric accessory genomic compartments not only harbor most of the known virulence loci but, also, that these regions have the capacity to rapidly evolve.

Sign in / Sign up

Export Citation Format

Share Document