scholarly journals Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog, Dendrobates auratus

2018 ◽  
Author(s):  
Adam M. M. Stuckert ◽  
Emily Moore ◽  
Kaitlin P. Coyle ◽  
Ian Davison ◽  
Matthew D. MacManes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Networks ◽  
De Novo ◽  
Poison Frog ◽  
Color Morphs ◽  
Survival And Reproduction ◽  
Genetic Mechanisms ◽  
Differential Gene ◽  
Different Color ◽  
Dendrobates Auratus

AbstractColor and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa. Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrpl, lefl, leol, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgapl, arfgap2, airc, and gairt). Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.

scholarly journals Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Adam M. M. Stuckert ◽  
Emily Moore ◽  
Kaitlin P. Coyle ◽  
Ian Davison ◽  
Matthew D. MacManes ◽  
...  
Keyword(s):  
Gene Expression ◽  
Poison Frog ◽  
Pigmentation Gene ◽  
Color Morphs ◽  
Dendrobates Auratus

scholarly journals The genomics of mimicry: gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

2019 ◽  
Author(s):  
Adam M M Stuckert ◽  
Mathieu Chouteau ◽  
Melanie McClure ◽  
Troy M LaPolice ◽  
Tyler Linderoth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Evolutionary Biology ◽  
De Novo ◽  
Color Pattern ◽  
De Novo Genome Assembly ◽  
Structural Colors ◽  
Müllerian Mimicry ◽  
Color Morphs ◽  
Genetic Mechanisms ◽  
Mullerian Mimicry

AbstractA common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defense, are excellent models to understand the link between vivid color pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of color production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid color and pattern are produced in a Müllerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp and 93% of expected tetrapod genes. We then leveraged this genome to conduct gene expression analyses throughout development of four color morphs of R. imitator and two color morphs from both R. fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development, and guanine synthesis. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in color between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colors within these frogs.

scholarly journals The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Saivageethi Nuthikattu ◽  
Dragan Milenkovic ◽  
John Rutledge ◽  
Amparo Villablanca
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Differential Expression ◽  
Differential Gene Expression ◽  
Gene Networks ◽  
Molecular Mechanisms ◽  
Western Diet ◽  
Protein Coding ◽  
Female Mice ◽  
Differential Gene

AbstractHyperlipidemia is a risk factor for dementia, and chronic consumption of a Western Diet (WD) is associated with cognitive impairment. However, the molecular mechanisms underlying the development of microvascular disease in the memory centers of the brain are poorly understood. This pilot study investigated the nutrigenomic pathways by which the WD regulates gene expression in hippocampal brain microvessels of female mice. Five-week-old female low-density lipoprotein receptor deficient (LDL-R−/−) and C57BL/6J wild type (WT) mice were fed a chow or WD for 8 weeks. Metabolics for lipids, glucose and insulin were determined. Differential gene expression, gene networks and pathways, transcription factors, and non-protein coding RNAs were evaluated by genome-wide microarray and bioinformatics analysis of laser captured hippocampal microvessels. The WD resulted in differential expression of 2,412 genes. The majority of differential gene expression was attributable to differential regulation of cell signaling proteins and their transcription factors, approximately 7% was attributable to differential expression of miRNAs, and a lesser proportion was due to other non-protein coding RNAs, primarily long non-coding RNAs (lncRNAs) and small nucleolar RNAs (snoRNAs) not previously described to be modified by the WD in females. Our findings revealed that chronic consumption of the WD resulted in integrated multilevel molecular regulation of the hippocampal microvasculature of female mice and may provide one of the mechanisms underlying vascular dementia.

scholarly journals Performance of gene expression analyses using de novo assembled transcripts in polyploid species

2019 ◽  
Vol 35 (21) ◽  
pp. 4314-4320 ◽  
Author(s):  
Ling-Yun Chen ◽  
Diego F Morales-Briones ◽  
Courtney N Passow ◽  
Ya Yang
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
De Novo ◽  
Supplementary Information ◽  
Polyploid Species ◽  
Network Analyses ◽  
The Past ◽  
Gene Expression Analyses ◽  
Differential Gene

Abstract Motivation Quality of gene expression analyses using de novo assembled transcripts in species that experienced recent polyploidization remains unexplored. Results Differential gene expression (DGE) analyses using putative genes inferred by Trinity, Corset and Grouper performed slightly differently across five plant species that experienced various polyploidy histories. In species that lack recent polyploidy events that occurred in the past several millions of years, DGE analyses using de novo assembled transcriptomes identified 54–82% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species that experienced more recent polyploidy events, the percentage decreased to 21–65%. Gene co-expression network analyses using de novo assemblies versus mapping to the reference genes recovered the same module that significantly correlated with treatment in one species that lacks recent polyploidization. Availability and implementation Commands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: 10.5061/dryad.4p6n481. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals De novo transcriptome assembly and analysis of differential gene expression in response to drought in European beech

PLoS ONE ◽  
2017 ◽  
Vol 12 (9) ◽  
pp. e0184167 ◽  
Author(s):  
Markus Müller ◽  
Sarah Seifert ◽  
Torben Lübbe ◽  
Christoph Leuschner ◽  
Reiner Finkeldey
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
European Beech ◽  
De Novo Transcriptome Assembly ◽  
De Novo Transcriptome ◽  
Differential Gene

scholarly journals Transcriptome Sequencing of Trichoderma Koningiopsis Strain Tk1 to Identify and Analyze Differential Gene Expression Patterns

2020 ◽  
Author(s):  
Mei Luo ◽  
Zhangyong Dong ◽  
Yongxin Shu ◽  
Mobing Chen
Keyword(s):  
Gene Expression ◽  
Expression Pattern ◽  
Differential Gene Expression ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Antimicrobial Effect ◽  
Carbohydrate Active Enzymes ◽  
Differential Gene

Abstract Background: Trichoderma koningiopsis strain Tk1 shows good biocontrol potential. However, its biocontrol function may differ under different conditions. The objective of this study is to elucidate the biological and transcriptome differences of T. koningiopsis Tk1 under different media. Results: In this study, the mycelium weight and sporulation of T. koningiopsis Tk1 was found to differ in various media. Further, the Tk1 strain inhibited the growth of the pathogen Fusarium oxysporum in the three media tested. Fries3, PD, and PS were collected for RNA sequencing of Tk1 mycelia to identify the genes that are differentially expressed genes (DEGs) between Tk1 grown on different media. De novo transcriptome assembly resulted in identification of 14,208 unigenes. The differential gene expression pattern was more similar between the Fries3 and PS samples, whereas PD samples showed a different expression pattern. The DEGs were enriched in some metabolic and biosynthetic pathways. Additional analysis of the DEGs identified a set of carbohydrate-active enzymes that are upregulated or downregulated under different conditions.Conclusions: These results indicate that the Tk1 strain cultured in Fires3 and PS mediums can produce specific metabolic and carbohydrate-active enzymes to enhance their antimicrobial effect, providing a foundation for the subsequent mining of specific genes.

scholarly journals Performance of gene expression analyses using de novo assembled transcripts in polyploid species

2018 ◽  
Author(s):  
Ling-Yun Chen ◽  
Diego F. Morales-Briones ◽  
Courtney N. Passow ◽  
Ya Yang
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Reference Genes ◽  
De Novo ◽  
Differentially Expressed ◽  
Supplementary Information ◽  
Network Analyses ◽  
Gene Expression Analyses ◽  
Polyploidy Event ◽  
Differential Gene

AbstractMotivationQuality of gene expression analyses using de novo assembled transcripts in species experienced recent polyploidization is yet unexplored.ResultsFive plant species with various polyploidy history were used for differential gene expression (DGE) analyses. DGE analyses using putative genes inferred by Trinity performed similar to or better than Corset and Grouper in precision, but lower in sensitivity. In species that lack polyploidy event in the past few million years, DGE analyses using de novo assembled transcriptome identified 50–76% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species with more recent polyploidy event, the percentage decreased to 7–30%. In addition, 7–89% of differentially expressed genes from de novo assembly are contaminations. Gene co-expression network analyses using de novo assemblies vs. mapping to the reference genes recovered the same module that significantly correlated with treatment in one of the five species tested.Availability and ImplementationCommands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: [email protected] informationSupplementary data are available at Bioinformatics online

Sign in / Sign up

Export Citation Format

Share Document