FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation

Chen, Ting-Wen; Gan, Ruei Chi; Fang, Yi; Chien, Kun-Yi; Liao, Wei; Chen, Chia Chun; Wu, Timothy; Chang, Ian Yi‐Feng; Yang, Chi; Huang, Po-Jung; Yeh, Yuan Ming; Chiu, Cheng Hsun; Huang, Tzu Wen; Tang, Petrus

doi:10.1038/s41598-017-10952-4

Cited by 32 publications

(32 citation statements)

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“…In order to obtain a comprehensive annotation of our final sets of transcripts we used FunctionAnnotator, which is especially well-suited for non-model organism annotation [12] . The uploaded final transcriptome of Common quail in FunctionAnnotator was used for homology searches against the NCBI-NR (Non-redundant) protein sequences database with a cut-off e -value of 1e −3 .…”

Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix)

et al. 2020

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The Common or European quail ( Coturnix coturnix ) is a Galliform bird of ecological importance for research in the field of animal migration. The Common quail is also a game bird, thus, of great interest for recreational activities and conservation management. Here, we generated a high quality de novo transcriptome for the Common quail for which no reference genome is to date publicly available. The transcriptome was obtained from a population of Common quail originated from captive founders raised under laboratory conditions. Paired-end RNA-Sequencing reads were obtained from extracted total RNA of brain tissue punches (preoptic-hypothalamic region) of 23 quails, which yielded to 5.5–11.2 million reads per individual bird for a total of 236 million reads. After assembly optimization, we used a stringent filtering analysis pipeline to remove redundant and low confidence transcripts. The final transcriptome consisted of 22,293 transcripts of which 21,551 (97%) were provided with annotation data. Our data offers a high quality pipeline for compiling transcriptomes of complex non-genomic species. Our data also provide a robust reference for gene expression studies in this species or other related Galliform species, including the Japanese quail.

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Section: Experimental Design Materials and Methodsmentioning

confidence: 99%

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix)

et al. 2020

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“…Transcripts per million (TPM) was calculated using Salmon tool. The contigs were assembled against National Center for Biotechnology Information (NCBI) non-redundant (NR) database, with the aid of FunctionAnnotator website available at http://163.25.92.60/index.php [ 25 ], and specific anuran antimicrobial peptides (AMP) database DADP [ 26 ] using the blastx algorithm, to obtain the functional annotation. The resulting annotated sequences were the ones with cut-off value of significance lower than 1 × 10 − 5 , coverage higher than 70% and protein identity (pident) higher than 60.…”

Section: Methodsmentioning

confidence: 99%

Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion

Shibao

Cologna

Filho

et al. 2018

J Venom Anim Toxins Incl Trop Dis

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BackgroundAnimal poisons and venoms are sources of biomolecules naturally selected. Rhinella schneideri toads are widespread in the whole Brazilian territory and they have poison glands and mucous gland. Recently, protein from toads’ secretion has gaining attention. Frog skin is widely known to present great number of host defense peptides and we hypothesize toads present them as well. In this study, we used a RNA-seq analysis from R. schneideri skin and biochemical tests with the gland secretion to unravel its protein molecules.MethodsTotal RNA from the toad skin was extracted using TRizol reagent, sequenced in duplicate using Illumina Hiseq2500 in paired end analysis. The raw reads were trimmed and de novo assembled using Trinity. The resulting sequences were submitted to functional annotation against non-redundant NCBI database and Database of Anuran Defense Peptide. Furthermore, we performed caseinolytic activity test to assess the presence of serine and metalloproteases in skin secretion and it was fractionated by fast liquid protein chromatography using a reverse-phase column. The fractions were partially sequenced by Edman’s degradation.ResultsWe were able to identify several classes of antimicrobial peptides, such as buforins, peroniins and brevinins, as well as PLA2, lectins and galectins, combining protein sequencing and RNA-seq analysis for the first time. In addition, we could isolate a PLA2 from the skin secretion and infer the presence of serine proteases in cutaneous secretion.ConclusionsWe identified novel toxins and proteins from R. schneideri mucous glands. Besides, this is a pioneer study that presented the in depth characterization of protein molecules richness from this toad secretion. The results obtained herein showed evidence of novel AMP and enzymes that need to be further explored.Electronic supplementary materialThe online version of this article (10.1186/s40409-018-0173-8) contains supplementary material, which is available to authorized users.

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“…Annotation was performed using BLAST2GO 5.2 software for identification of Gene Ontology (GO) terms [16]. Exhaustive functional annotations of the transcript sequences were performed through Function annotator [17]. Function Annotator assisted in annotation of enzymes, best hits to NCBI nr database, GO terms, conserved domain, transmembrane protein, lipoprotein peptide, signal peptide and also subcellular localization.KEGG orthology designation was obtained based on homology searches in KAAS [18].…”

Section: Reads Mapping and Annotationmentioning

confidence: 99%

Transcriptomic analysis ofLentinus squarrosulusprovide insights into its biodegradation ability

Ravichandran

Kolte

Dhali

et al. 2020

Preprint

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Basidiomycetes are of special interest in biotechnological research for their versatile potential in degradation of lignocellulosic biomass. This study accordingly reports analysis of transcriptome of a white-rot Basidiomycete L.squarrosulus grown in simple potato dextrose broth supplemented with aromatic compound, reactive black dye to gain an insight into the degradation ability of the fungus. RNA was sequenced using Illumina NextSeq 500 to obtain 6,679,162 high quality paired end reads that were assembled de novo using CLC assembly cell to generate 25,244 contigs.Putative functions were assigned for the 10,494 transcripts based on sequence similarities through BLAST2GO 5.2 and Function annotator. Functional assignments revealed enhanced oxidoreductase activity through the expression of diverse biomass degrading enzymes and their corresponding co-regulators. CAZyme analysis through dbCAN and CUPP revealed the presence of 6 families of polysaccharide lyases, 51 families of glycoside hydrolases, 23 families of glycoside transferases, 7 families of carbohydrate esterases and 10 families of Auxiliary activities.Genes encoding the ligninolytic enzymes and auxiliary activities among the transcript sequences were identified through gene prediction by AUGUSTUS and FGENESH. Biochemical analysis of a couple of biomass degrading enzymes substantiated the functional predictions. In essence, L.squarrosulus grown in a simple medium devoid of lignocellulosic substrate demonstrated presence of a repertoire of lignocellulose degrading enzymesimplying that source of lignocellulose is not required for expression of these biomass degrading enzymes. The study hereby underlines the significance of L.squarrosulus in biomass degradation and its future functional exploitation in biomass conversion applications.

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FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation

Cited by 32 publications

References 50 publications

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix)

Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix)

Deep sequencing analysis of toad Rhinella schneideri skin glands and partial biochemical characterization of its cutaneous secretion

Transcriptomic analysis ofLentinus squarrosulusprovide insights into its biodegradation ability

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