DEgenes Hunter - A Flexible R Pipeline for Automated RNA-seq Studies in Organisms without Reference Genome

Gayte, Isabel González; Moreno, Rocío Bautista; Zonjic, Pedro Seoane; Claros, Manuel Gonzalo

doi:10.18547/gcb.2017.vol3.iss3.e31

Cited by 24 publications

(16 citation statements)

References 32 publications

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“…Therefore, in order to obtain an accurate mapping of generated reads, we used as reference our recently reported species-specific transcriptome of Citrus aurantifolia [26], and the corresponding orthologs were annotated from A. thaliana TAIR10 database. Then, we carried out a differential expression analysis by means DEgenes-Hunter [28]. A principal component (PC) analysis showed a correlation between biological replicates demonstrating the reliability and consistency of transcriptional data (Figure 4).…”

Section: Discussionmentioning

confidence: 96%

“…Transcript counts were obtained using Sam2count.py. Data normalization and differential expression studies were carried out using DEgenes-Hunter [28] with EdgeR and DESeq2 package; any differentially expressed candidate gene must appear in both algorithms with |log2ratio| ≥ 1 and false discovery rate (FDR) <0.05. Enriched gene ontology term annotations were identified using Singular Enrichment Analysis (SEA) in agriGO v.2 [29].…”

Section: Differential Expression Analysismentioning

confidence: 99%

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Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

et al. 2020

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Nowadays, Huanglongbing (HLB) disease, associated with Candidatus Liberibacter asiaticus (CLas), seriously affects citriculture worldwide, and no cure is currently available. Transcriptomic analysis of host-pathogen interaction is the first step to understand the molecular landscape of a disease. Previous works have reported the transcriptome profiling in response to HLB in different susceptible citrus species; however, similar studies in tolerant citrus species, including Mexican lime, are limited. In this work, we have obtained an RNA-seq-based differential expression profile of Mexican lime plants challenged against CLas infection, at both asymptomatic and symptomatic stages. Typical HLB-responsive differentially expressed genes (DEGs) are involved in photosynthesis, secondary metabolism, and phytohormone homeostasis. Enrichment of DEGs associated with biotic response showed that genes related to cell wall, secondary metabolism, transcription factors, signaling, and redox reactions could play a role in the tolerance of Mexican lime against CLas infection. Interestingly, despite some concordance observed between transcriptional responses of different tolerant citrus species, a subset of DEGs appeared to be species-specific. Our data highlights the importance of studying the host response during HLB disease using as model tolerant citrus species, in order to design new and opportune diagnostic and management methods.

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Section: Discussionmentioning

confidence: 96%

Section: Differential Expression Analysismentioning

confidence: 99%

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

et al. 2020

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“…Finally, its suitability for RNA-seq studies was demonstrated using an experimental study that investigates the role of RA on metamorphic larvae by using a specific RA-receptor agonist or a RA synthesis blocker. The bioinformatic analysis was performed using an improved version of DEGenes Hunter 30 .…”

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confidence: 99%

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae

Córdoba-Caballero

Seoane

Jabato

et al. 2020

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Senegalese sole is an economically important flatfish species in aquaculture and an attractive model to decipher the molecular mechanisms governing the severe transformations occurring during metamorphosis, where retinoic acid seems to play a key role in tissue remodeling. In this study, a robust sole transcriptome was envisaged by reducing the number of assembled libraries (27 out of 111 available), fine-tuning a new automated and reproducible set of workflows for de novo assembling based on several assemblers, and removing low confidence transcripts after mapping onto a sole female genome draft. From a total of 96 resulting assemblies, two “raw” transcriptomes, one containing only Illumina reads and another with Illumina and GS-FLX reads, were selected to provide SOLSEv5.0, the most informative transcriptome with low redundancy and devoid of most single-exon transcripts. It included both Illumina and GS-FLX reads and consisted of 51,348 transcripts of which 22,684 code for 17,429 different proteins described in databases, where 9527 were predicted as complete proteins. SOLSEv5.0 was used as reference for the study of retinoic acid (RA) signalling in sole larvae using drug treatments (DEAB, a RA synthesis blocker, and TTNPB, a RA-receptor agonist) for 24 and 48 h. Differential expression and functional interpretation were facilitated by an updated version of DEGenes Hunter. Acute exposure of both drugs triggered an intense, specific and transient response at 24 h but with hardly observable differences after 48 h at least in the DEAB treatments. Activation of RA signalling by TTNPB specifically increased the expression of genes in pathways related to RA degradation, retinol storage, carotenoid metabolism, homeostatic response and visual cycle, and also modified the expression of transcripts related to morphogenesis and collagen fibril organisation. In contrast, DEAB mainly decreased genes related to retinal production, impairing phototransduction signalling in the retina. A total of 755 transcripts mainly related to lipid metabolism, lipid transport and lipid homeostasis were altered in response to both treatments, indicating non-specific drug responses associated with intestinal absorption. These results indicate that a new assembling and transcript sieving were both necessary to provide a reliable transcriptome to identify the many aspects of RA action during sole development that are of relevance for sole aquaculture.

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“…Samtools (v.0.1.19) quantified known transcripts (count reads per transcripts) ( 53 ), and transcripts were annotated using Full-Lengther-Next ( 54 ). Statistical comparisons of transcript expression between diet groups and between atopic and healthy dogs were performed using DEgenes-Hunter (v.2.0.11) ( 55 ), a tool that imputes raw read counts generated by Bowtie2/Samtools into the EdgeR ( 56 ) and DESeq2 ( 57 ) algorithms. Fold change (FC) ≥2, and a false discovery rate (FDR) corrected p < 0.05 were set as thresholds.…”

Section: Methodsmentioning

confidence: 99%

The Effect of Atopic Dermatitis and Diet on the Skin Transcriptome in Staffordshire Bull Terriers

et al. 2020

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Canine atopic dermatitis (CAD) has a hereditary basis that is modified by interactions with the environment, including diet. Differentially expressed genes in non-lesional skin, determined by RNA sequencing before and after a dietary intervention, were compared between dogs with naturally occurring CAD (n = 4) and healthy dogs (n = 4). The dogs were fed either a common commercial heat-processed high carbohydrate food (kibble diet) (n = 4), or a non-processed high fat food (raw meat-based diet) (n = 4). At the end of the diet intervention, 149 differentially expressed transcripts were found between the atopic and healthy dogs. The main canonical pathways altered by the dysregulation of these genes were angiopoietin signaling, epidermal growth factor signaling, activation of angiogenesis, and alterations in keratinocyte proliferation and lipid metabolism. On the other hand, 33 differently expressed transcripts were found between the two diet groups, of which 8 encode genes that are annotated in the current version of the dog genome: immunoglobulin heavy constant mu (IGHM), immunoglobulin lambda-like polypeptide 5 (IGLL5), B-cell antigen receptor complex-associated protein beta chain (CD79B), polymeric immunoglobulin receptor (PIGR), cystathionine β-synthase (CBS), argininosuccinate synthase 1 (ASS1), secretory leukocyte peptidase inhibitor (SLPI), and mitochondrial ribosome recycling factor (MRRF). All genes were upregulated in the raw diet group. In conclusion the findings of this study suggest alterations in lipid and keratinocyte metabolism as well as angiogenesis in the skin of atopic dogs. Additionally, a possible enhancement of innate immunity and decrease in oxidative stress was seen in raw food fed dogs, which could have an important role in preventing hypersensitivities and disturbed immunity at young age.

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DEgenes Hunter - A Flexible R Pipeline for Automated RNA-seq Studies in Organisms without Reference Genome

Cited by 24 publications

References 32 publications

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

Gene Expression Profile of Mexican Lime (Citrus aurantifolia) Trees in Response to Huanglongbing Disease caused by Candidatus Liberibacter asiaticus

An improved de novo assembling and polishing of Solea senegalensis transcriptome shed light on retinoic acid signalling in larvae

The Effect of Atopic Dermatitis and Diet on the Skin Transcriptome in Staffordshire Bull Terriers

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