Genetic Bases Of Aposematic Traits: Insights from the Skin Transcriptional Profiles of Oophaga Poison Frogs

Mapping Intimacies ◽

10.1101/706655 ◽

2019 ◽

Author(s):

Andrés Posso-Terranova ◽

José Andres

Keyword(s):

Functional Annotation ◽

Expression Profiles ◽

Resistance Mechanisms ◽

Chemical Defenses ◽

South American ◽

Warning Signals ◽

Closely Related Species ◽

Poison Frogs ◽

Skin Coloration ◽

American Clade

AbstractAposematic organisms advertise their defensive toxins to predators using a variety of warning signals, including bright coloration. While most Neotropical poison frogs (Dendrobatidae) rely on crypsis to avoid predators, Oophaga poison frogs from South America advertise their chemical defenses, a complex mix of diet-derived alkaloids, by using conspicuous hues. The present study aimed to characterize the skin transcriptomic profiles of the South American clade of Oophaga poison frogs (O. anchicayensis, O. solanensis, O. lehmanni and O. sylvatica). Our analyses showed very similar transcriptomic profiles for these closely related species in terms of functional annotation and relative abundance of gene ontology terms expressed. Analyses of expression profiles of Oophaga and available skin transcriptomes of cryptic anurans allowed us to propose possible mechanisms for the active sequestration of alkaloid-based chemical defenses and to highlight some genes that may be potentially involved in resistance mechanisms to avoid self-intoxication and skin coloration. In doing so, we provide an important molecular resource for the study of warning signals that will facilitate the assembly and annotation of future poison frog genomes.

Mechanisms of convergent egg-provisioning in poison frogs

10.1101/653501 ◽

2019 ◽

Cited By ~ 1

Author(s):

Eva K. Fischer ◽

Alexandre B. Roland ◽

Nora A. Moskowitz ◽

Charles Vidoudez ◽

Ndimbintsoa Ranaivorazo ◽

...

Keyword(s):

Molecular Mechanisms ◽

Field Studies ◽

Brain Regions ◽

Chemical Defenses ◽

Lateral Septum ◽

Neuron Activity ◽

South American ◽

Poison Frogs ◽

Provisioning Behavior ◽

Maternal Provisioning

AbstractParental provisioning of offspring with physiological products occurs in many animals. Within amphibians, maternal provisioning has evolved multiple times, including in South American dendrobatid and Malagasy mantellid poison frogs. In some of these species, mothers feed unfertilized eggs to their developing tadpoles for several months until tadpoles complete metamorphosis. We conducted field studies in Ecuador and Madagascar to ask whether convergence at the behavioral level provides similar benefits to offspring and whether nursing behavior relies on shared neural mechanisms across frogs and vertebrates more broadly. At an ecological level, we found that nursing allows poison frog mothers to provide chemical defenses to their tadpoles in both species. At the level of brain regions, nursing behavior was associated with increased neural activity in the lateral septum and preoptic area in both species, demonstrating recruitment of shared brain regions in the convergent evolution of maternal care within frogs and across vertebrates. In contrast at a molecular level, only mantellids showed increased oxytocin neuron activity akin to that in nursing mammals. Taken together, our findings demonstrate that convergently evolved maternal provisioning behavior provides similar benefits to offspring and relies on similar brain regions. However, the molecular mechanisms underlying the convergence in nursing behavior may be different, suggesting evolutionary versatility in the mechanisms promoting maternal behavior.

Salicornia cuscoensis (Amaranthaceae/Chenopodiaceae), a new species from Peru (South America)

Phytotaxa ◽

10.11646/phytotaxa.319.3.4 ◽

2017 ◽

Vol 319 (3) ◽

pp. 254 ◽

Cited By ~ 1

Author(s):

M. ÁNGELES ALONSO ◽

MANUEL B. CRESPO ◽

HELMUT FREITAG

Keyword(s):

New Species ◽

South America ◽

Morphological Characters ◽

Tierra Del Fuego ◽

South American ◽

Habitat Distribution ◽

Closely Related Species ◽

Molecular Analyses ◽

Southern Patagonia ◽

A New Species

The name Salicornia cuscoensis given to a plant from high Andean saltmarshes near Cusco [Cuzco] and Ayacucho, Peru (South America) is validated by a diagnosis and description. The main morphological characters that separate S. cuscoensis from other closely related species are creeping habit, delicate branches, inflorescence of short and thin spikes, and seed indumentum. The new species clearly differs from other perennial Salicornia taxa growing in high Andean saltmarshes such as S. pulvinata and S. andina. The former forms small compact cushions producing very short, few-flowered inflorescences. The latter shows woody stems and forms larger rounded carpets. Morphologically, S. cuscoensis is also similar to S. magellanica, a species growing along the seashore in southern Patagonia and Tierra del Fuego, but the latter has shorter and wider inflorescences and larger seeds with a different type and arrangement of indumentum. Molecular analyses also supported the separation of S. cuscoensis. Data on habitat, distribution and phylogenetic relationships are presented for the new species and its relatives, and an identification key is given for the South American taxa of the genus Salicornia.

Electrophoretic Comparison of Blood Proteins of Two Closely Related Species of South American Tortoises

Copeia ◽

10.2307/1442152 ◽

1967 ◽

Vol 1967 (2) ◽

pp. 481 ◽

Cited By ~ 1

Author(s):

Richard J. Newcomer ◽

John W. Crenshaw

Keyword(s):

Related Species ◽

South American ◽

Blood Proteins ◽

Closely Related Species

Identification of Molecular Mechanisms in Parkinson’s Disease Pathogenesis: Significance of Survival and Inflammation Pathways

10.21203/rs.3.rs-41609/v1 ◽

2020 ◽

Author(s):

Zerrin Karaaslan ◽

Ozlem Timirci Kahraman ◽

Elif Sanli ◽

Hayriye Arzu Ergen ◽

Basar Bilgic ◽

...

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Functional Annotation ◽

Molecular Mechanisms ◽

Mononuclear Cells ◽

Neuronal Degeneration ◽

Expression Profiles ◽

Quantitative Polymerase Chain Reaction ◽

Rt Pcr ◽

Peripheral Blood Mononuclear

Abstract Background: Our aim was to identify the differentially expressed genes (DEGs) between Parkinson’s disease (PD) patients and controls by microarray technology and analysis of related molecular pathways by functional annotation. Methods: Thirty PD patients and 30 controls were enrolled. Agilent Human 8X60 K Oligo Microarray was used for gene level expression identification. Gene ontology and pathway enrichment analyses were used for functional annotation of DEGs. Protein-protein interaction analyses were performed with STRING. Expression levels of randomly selected 5 genes among DEGs were quantified by real time quantitative polymerase chain reaction (RT-PCR) for validation. Flow cytometry was done to determine frequency of regulatory T cells (Tregs) in peripheral blood mononuclear cells. Results: A total of 361 DEGs (143 upregulated and 218 downregulated) were identified after GeneSpring analysis. DEGs were involved in 28 biological processes, 12 cellular components and 26 molecular functions. Pathway analyses demonstrated that upregulated genes mainly enriched in p53 (CASP3, TSC2, ATR, MDM4, CCNG1) and PI3K/Akt (IL2RA, IL4R, TSC2, VEGFA, PKN2, PIK3CA, ITGA4, BCL2L11) signaling pathways. TP53 and PIK3CA were identified as most significant hub proteins. Expression profiles obtained by RT-PCR were consistent with microarray findings. PD patients showed increased proportions of CD49d+ Tregs, which correlated with disability scores. Discussion: Survival pathway genes were upregulated putatively to compensate neuronal degeneration. Bioinformatics analysis showed an association between survival and inflammation genes. Increased CD49d+ Treg ratios might signify the attempt of the immune system to suppress ongoing inflammation. Conclusion: Altered functions of Tregs might have an important role in PD pathogenesis and CD49d expression could be a prognostic biomarker of PD.

Differential Expression Profiles of the Transcriptome and miRNA Interactome in Synovial Fibroblasts of Rheumatoid Arthritis Revealed by Next Generation Sequencing

Diagnostics ◽

10.3390/diagnostics9030098 ◽

2019 ◽

Vol 9 (3) ◽

pp. 98

Author(s):

Chia-Chun Tseng ◽

Ling-Yu Wu ◽

Wen-Chan Tsai ◽

Tsan-Teng Ou ◽

Cheng-Chin Wu ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Differential Expression ◽

Regulatory Network ◽

Functional Annotation ◽

Interaction Analysis ◽

Expression Profiles ◽

Synovial Fibroblasts ◽

Rna Seq ◽

Network Mapping ◽

Generation Sequencing

Using next-generation sequencing to decipher the molecular mechanisms underlying aberrant rheumatoid arthritis synovial fibroblasts (RASF) activation, we performed transcriptome-wide RNA-seq and small RNA-seq on synovial fibroblasts from rheumatoid arthritis (RA) subject and normal donor. Differential expression of mRNA and miRNA was integrated with interaction analysis, functional annotation, regulatory network mapping and experimentally verified miRNA–target interaction data, further validated with microarray expression profiles. In this study, 3049 upregulated mRNA and 3552 downregulated mRNA, together with 50 upregulated miRNA and 35 downregulated miRNA in RASF were identified. Interaction analysis highlighted contribution of miRNA to altered transcriptome. Functional annotation revealed metabolic deregulation and oncogenic signatures of RASF. Regulatory network mapping identified downregulated FOXO1 as master transcription factor resulting in altered transcriptome of RASF. Differential expression in three miRNA and corresponding targets (hsa-miR-31-5p:WASF3, hsa-miR-132-3p:RB1, hsa-miR-29c-3p:COL1A1) were also validated. The interactions of these three miRNA–target genes were experimentally validated with past literature. Our transcriptomic and miRNA interactomic investigation identified gene signatures associated with RASF and revealed the involvement of transcription factors and miRNA in an altered transcriptome. These findings help facilitate our understanding of RA with the hope of serving as a springboard for further discoveries relating to the disease.

Geographic variation in a South American clade of mormoopid bats, Pteronotus (Phyllodia), with description of a new species

Journal of Mammalogy ◽

10.1093/jmammal/gyy048 ◽

2018 ◽

Vol 99 (3) ◽

pp. 624-645 ◽

Cited By ~ 11

Author(s):

Ana C Pavan ◽

Paulo E D Bobrowiec ◽

Alexandre R Percequillo

Keyword(s):

New Species ◽

Geographic Variation ◽

South American ◽

American Clade ◽

A New Species

Plant antiherbivore defenses in Fabaceae species of the Chaco

Brazilian Journal of Biology ◽

10.1590/1519-6984.12815 ◽

2016 ◽

Vol 77 (2) ◽

pp. 299-303 ◽

Cited By ~ 1

Author(s):

T. E. Lima ◽

A. L. B. Sartori ◽

M. L. M. Rodrigues

Keyword(s):

Protease Inhibitors ◽

Plant Species ◽

Reproductive Organs ◽

Chemical Defenses ◽

South American ◽

Defense Proteins ◽

Climatic Variations ◽

Physical Defenses ◽

Physical And Chemical ◽

First Time

Abstract The establishment and maintenance of plant species in the Chaco, one of the widest continuous areas of forests in the South American with sharp climatic variations, are possibly related to biological features favoring plants with particular defenses. This study assesses the physical and chemical defenses mechanisms against herbivores of vegetative and reproductive organs. Its analyses of 12 species of Fabaceae (Leguminosae) collected in remnants of Brazilian Chaco shows that 75% present structural defense characters and 50% have chemical defense – defense proteins in their seeds, like protease inhibitors and lectins. Physical defenses occur mainly on branches (78% of the species), leaves (67%), and reproductive organs (56%). The most common physical characters are trichomes and thorns, whose color represents a cryptic character since it does not contrast with the other plant structures. Defense proteins occur in different concentrations and molecular weight classes in the seeds of most species. Protease inhibitors are reported for the first time in seeds of: Albizia niopoides, Anadenanthera colubrina, Mimosa glutinosa, Prosopis rubriflora, and Poincianella pluviosa. The occurrence of physical and chemical defenses in members of Fabaceae indicate no associations between defense characters in these plant species of the Chaco.

Weak genetic divergence between the two South American toad-headed turtles Mesoclemmys dahli and M. zuliae (Testudines: Pleurodira: Chelidae)

Amphibia-Reptilia ◽

10.1163/15685381-00002840 ◽

2012 ◽

Vol 33 (3-4) ◽

pp. 373-385 ◽

Cited By ~ 3

Author(s):

Mario Vargas-Ramírez ◽

Jan Michels ◽

Olga Victoria Castaño-Mora ◽

Gladys Cárdenas-Arevalo ◽

Natalia Gallego-García ◽

...

Keyword(s):

Habitat Preferences ◽

Divergence Time ◽

South American ◽

Mitochondrial Cytochrome ◽

Closely Related Species ◽

Turtle Species ◽

American Toad ◽

Distribution Ranges ◽

Mountain Chain ◽

Relaxed Molecular Clock

Mesoclemmys dahli and M. zuliae are two endangered, little-known toad-headed turtles with small distribution ranges in Colombia and Venezuela, respectively. Using the mitochondrial cytochrome b gene as a marker, we investigate their phylogeographic differentiation. Furthermore, based on 2341 bp of mtDNA and 2109 bp of nDNA of M. dahli, M. zuliae and allied chelid turtles, we infer their divergence time using a fossil-calibrated relaxed molecular clock approach. Mesoclemmys dahli and M. zuliae are closely related species, with an estimated mean divergence time of 10.6 million years. This estimate correlates with the uplift of the Serranía de Perijá, an Andean mountain chain separating their distribution ranges, suggesting that this event could have caused the evolution of the two species. Haplotype and nucleotide diversities of M. dahli are markedly higher than in Podocnemis lewyana, another endemic turtle species of Colombia. This pronounced dissimilarity may reflect differences in the phylogeographies and demographic histories of the two species, but also different habitat preferences.

Beyond gene ontology (GO): using biocuration approach to improve the gene nomenclature and functional annotation of rice S-domain kinase subfamily

PeerJ ◽

10.7717/peerj.11052 ◽

2021 ◽

Vol 9 ◽

pp. e11052

Author(s):

Sushma Naithani ◽

Daemon Dikeman ◽

Priyanka Garg ◽

Noor Al-Bader ◽

Pankaj Jaiswal

Keyword(s):

Gene Ontology ◽

Abiotic Stress ◽

Differential Expression ◽

Functional Annotation ◽

Expression Profiles ◽

Abiotic Stress Tolerance ◽

Family Members ◽

Gene Families ◽

Structural Features ◽

Response Expression

The S-domain subfamily of receptor-like kinases (SDRLKs) in plants is poorly characterized. Most members of this subfamily are currently assigned gene function based on the S-locus Receptor Kinase from Brassica that acts as the female determinant of self-incompatibility (SI). However, Brassica like SI mechanisms does not exist in most plants. Thus, automated Gene Ontology (GO) pipelines are not sufficient for functional annotation of SDRLK subfamily members and lead to erroneous association with the GO biological process of SI. Here, we show that manual bio-curation can help to correct and improve the gene annotations and association with relevant biological processes. Using publicly available genomic and transcriptome datasets, we conducted a detailed analysis of the expansion of the rice (Oryza sativa) SDRLK subfamily, the structure of individual genes and proteins, and their expression.The 144-member SDRLK family in rice consists of 82 receptor-like kinases (RLKs) (67 full-length, 15 truncated),12 receptor-like proteins, 14 SD kinases, 26 kinase-like and 10 GnK2 domain-containing kinases and RLKs. Except for nine genes, all other SDRLK family members are transcribed in rice, but they vary in their tissue-specific and stress-response expression profiles. Furthermore, 98 genes show differential expression under biotic stress and 98 genes show differential expression under abiotic stress conditions, but share 81 genes in common.Our analysis led to the identification of candidate genes likely to play important roles in plant development, pathogen resistance, and abiotic stress tolerance. We propose a nomenclature for 144 SDRLK gene family members based on gene/protein conserved structural features, gene expression profiles, and literature review. Our biocuration approach, rooted in the principles of findability, accessibility, interoperability and reusability, sets forth an example of how manual annotation of large-gene families can fill in the knowledge gap that exists due to the implementation of automated GO projections, thereby helping to improve the quality and contents of public databases.

What does mitogenomics tell us about the evolutionary history of the Drosophila buzzatii cluster (repleta group)

10.1101/712232 ◽

2019 ◽

Author(s):

Nicolás N. Moreyra ◽

Julián Mensch ◽

Juan Hurtado ◽

Francisca Almeida ◽

Cecilia Laprida ◽

...

Keyword(s):

Phylogenetic Relationships ◽

Evolutionary Biology ◽

Large Scale ◽

South American ◽

Phylogenetic Studies ◽

Drosophila Buzzatii ◽

Molecular Phylogenetic ◽

History Of ◽

Tree Topologies ◽

American Clade

AbstractThe Drosophila repleta group is an array of more than 100 cactophilic species endemic to the “New World”. The acquisition of the ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in the American deserts. Within this group, the Drosophila buzzatii cluster is a South American clade of seven cactophilic closely related species in different stages of divergence, a feature that makes it a valuable model system for evolutionary research. However, even though substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, the issue is still controversial. In effect, molecular phylogenetic studies performed to date generated ambiguous results since tree topologies depend on the kind of molecular marker employed. Curiously, even though mitochondrial DNA has become a popular marker in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far belongs to this cluster. In this work we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, D. seriema and two strains of D. koepferae, with the aim to revisit the phylogenetic relationships and divergence times by means of a mitogenomic approach. The recovered topology using complete mitogenomes gives support to the hypothesis of the monophyly of that the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains) and the other the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes but in conflict with the results of a recent large-scale nuclear phylogeny, suggesting that nuclear and mitochondrial genomes depict different evolutionary histories.