OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Wang, Yi; Coleman‐Derr, Devin; Chen, Guoping; Gu, Yong

doi:10.1093/nar/gkv487

Cited by 626 publications

(302 citation statements)

References 36 publications

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“…Genome wide comparison and annotation of orthologous genes across multiple species were performed using OrthoVenn (Wang et al, 2015). The orthologous clusters were identified with default parameters, 1 e - 5 e -value cutoff for all protein similarity comparisons, and 1.5 inflation value for the generation of orthologous clusters.…”

Section: Methodsmentioning

confidence: 99%

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Nguyen

Gwak

et al. 2018

Front. Microbiol.

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Soil acidification is accelerated by anthropogenic and agricultural activities, which could significantly affect global methane cycles. However, detailed knowledge of the genomic properties of methanotrophs adapted to acidic soils remains scarce. Using metagenomic approaches, we analyzed methane-utilizing communities enriched from acidic forest soils with pH 3 and 4, and recovered near-complete genomes of proteobacterial methanotrophs. Novel methanotroph genomes designated KS32 and KS41, belonging to two representative clades of methanotrophs (Methylocystis of Alphaproteobacteria and Methylobacter of Gammaproteobacteria), were dominant. Comparative genomic analysis revealed diverse systems of membrane transporters for ensuring pH homeostasis and defense against toxic chemicals. Various potassium transporter systems, sodium/proton antiporters, and two copies of proton-translocating F1F0-type ATP synthase genes were identified, which might participate in the key pH homeostasis mechanisms in KS32. In addition, the V-type ATP synthase and urea assimilation genes might be used for pH homeostasis in KS41. Genes involved in the modification of membranes by incorporation of cyclopropane fatty acids and hopanoid lipids might be used for reducing proton influx into cells. The two methanotroph genomes possess genes for elaborate heavy metal efflux pumping systems, possibly owing to increased heavy metal toxicity in acidic conditions. Phylogenies of key genes involved in acid adaptation, methane oxidation, and antiviral defense in KS41 were incongruent with that of 16S rRNA. Thus, the detailed analysis of the genome sequences provides new insights into the ecology of methanotrophs responding to soil acidification.

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Section: Methodsmentioning

confidence: 99%

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Nguyen

Gwak

et al. 2018

Front. Microbiol.

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“…The same quality control and pipelines applied for L. albus were implemented to obtain high-quality contigs of the additional species. Transcripts of the six species were translated and used for comparisons of orthologous clusters with the OrthoVenn software75 using default parameters to identify GO categories and any GO enrichment.…”

Section: Methodsmentioning

confidence: 99%

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

Gaitán‐Espitía

Sánchez

Bruning

2016

Sci Rep

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The edible sea urchin Loxechinus albus (Molina, 1782) is a keystone species in the littoral benthic systems of the Pacific coast of South America. The international demand for high-quality gonads of this echinoderm has led to an extensive exploitation and decline of its natural populations. Consequently, a more thorough understanding of L. albus gonad development and gametogenesis could provide valuable resources for aquaculture applications, management, conservation and studies about the evolution of functional and structural pathways that underlie the reproductive toolkit of marine invertebrates. Using a high-throughput sequencing technology, we explored the male gonad transcriptome of this highly fecund sea urchin. Through a de novo assembly approach we obtained 42,530 transcripts of which 15,544 (36.6%) had significant alignments to known proteins in public databases. From these transcripts, approximately 73% were functionally annotated allowing the identification of several candidate genes that are likely to play a central role in developmental processes, nutrient reservoir activity, sexual reproduction, gamete generation, meiosis, sex differentiation, sperm motility, male courtship behavior and fertilization. Additionally, comparisons with the male gonad transcriptomes of other echinoderms revealed several conserved orthologous genes, suggesting that similar functional and structural pathways underlie the reproductive development in this group and other marine invertebrates.

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“…KOG analyses reveal that most of the genes are involved in metabolism: amino acid (≈ 437 proteins / strain), carbohydrates (≈ 771 proteins / strain), lipid (≈ 482 proteins / strain) or secondary metabolites (≈ 422 proteins / strain). In the case of OrthoMCL analysis compares amino acid sequences of different genomes through BlastP analyses, clustering them according to their identity (threshold: 50% similarity) [36]. An OrthoMCL analysis was performed on A. tubingensis G131, A. tubingensis CBS 134.48, A. niger CBS 513.88 and A. kawachii IFO 4308.…”

Section: Genome Annotationmentioning

confidence: 99%

“…Genome wide analysis of orthologous clusters was done through the interactive plateform OrthoVenn [36] using A. tubingensis G131, A. tubingensis CBS 134.48 [20], A. niger CBS 513.88 [13] and A. kawachii IFO 4308 [21] predicted proteomes.…”

Section: Genome Comparative Analyses Comparative Wide Comparison Of Omentioning

confidence: 99%

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

Choque

Klopp²,

Valière³

et al. 2018

BMC Genomics

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Background: Black Aspergilli represent one of the most important fungal resources of primary and secondary metabolites for biotechnological industry. Having several black Aspergilli sequenced genomes should allow targeting the production of certain metabolites with bioactive properties. Results: In this study, we report the draft genome of a black Aspergilli, A. tubingensis G131, isolated from a French Mediterranean vineyard. This 35 Mb genome includes 10,994 predicted genes. A genomic-based discovery identifies 80 secondary metabolites biosynthetic gene clusters. Genomic sequences of these clusters were blasted on 3 chosen black Aspergilli genomes: A. tubingensis CBS 134.48, A. niger CBS 513.88 and A. kawachii IFO 4308. This comparison highlights different levels of clusters conservation between the four strains. It also allows identifying seven unique clusters in A. tubingensis G131. Moreover, the putative secondary metabolites clusters for asperazine and naphthogamma-pyrones production were proposed based on this genomic analysis. Key biosynthetic genes required for the production of 2 mycotoxins, ochratoxin A and fumonisin, are absent from this draft genome. Even if intergenic sequences of these mycotoxins biosynthetic pathways are present, this could not lead to the production of those mycotoxins by A. tubingensis G131.

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OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species

Cited by 626 publications

References 36 publications

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Genomic Insights Into the Acid Adaptation of Novel Methanotrophs Enriched From Acidic Forest Soils

Functional insights into the testis transcriptome of the edible sea urchin Loxechinus albus

Whole-genome sequencing of Aspergillus tubingensis G131 and overview of its secondary metabolism potential

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