Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Sievers, Fabian; Wilm, Andreas; Dineen, David; Gibson, Toby J.; Karplus, Kevin; Li, Weizhong; López, Rodrigo; McWilliam, Hamish; Remmert, Michael; Söding, Johannes; Thompson, Julie; Higgins, Desmond G.

doi:10.1038/msb.2011.75

Cited by 13,537 publications

(10,884 citation statements)

References 26 publications

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“…For creating the multiple sequence alignments, the protein sequences were aligned using the C lustal O mega algorithm (Sievers et al ., 2011) and graphically visualized by J al V iew v.2.8.0b1 using default C lustal X colour code (Waterhouse et al ., 2009). …”

Section: Methodsmentioning

confidence: 99%

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

et al. 2017

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Summary N6‐adenosine methylation (m6A) of mRNA is an essential process in most eukaryotes, but its role and the status of factors accompanying this modification are still poorly understood.Using combined methods of genetics, proteomics and RNA biochemistry, we identified a core set of mRNA m6A writer proteins in Arabidopsis thaliana.The components required for m6A in Arabidopsis included MTA, MTB, FIP37, VIRILIZER and the E3 ubiquitin ligase HAKAI. Downregulation of these proteins led to reduced relative m6A levels and shared pleiotropic phenotypes, which included aberrant vascular formation in the root, indicating that correct m6A methylation plays a role in developmental decisions during pattern formation.The conservation of these proteins amongst eukaryotes and the demonstration of a role in writing m6A for the E3 ubiquitin ligase HAKAI is likely to be of considerable relevance beyond the plant sciences.

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Section: Methodsmentioning

confidence: 99%

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

et al. 2017

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“…They were constructed using the “sptree_raxml_all” workflow as implemented in ETE3 v3.0.0b36 (Huerta‐Cepas et al , 2016a). In brief, multiple sequence alignments were built for the 40 marker proteins using Clustal Omega v1.2.1 (Sievers et al , 2011), translated into codon alignments, concatenated, and used to infer a phylogeny by RAxML v8.1.20 (Stamatakis, 2014). …”

Section: Methodsmentioning

confidence: 99%

Subspecies in the global human gut microbiome

Costea

Coelho

Sunagawa

et al. 2017

Molecular Systems Biology

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143

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Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large‐scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture‐independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single‐nucleotide variation clearly indicates the existence of sub‐populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies‐specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro‐inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.

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“…Briefly, the ortholog sequences were aligned with Clustal Omega v1.2.0 (Sievers et al., 2011) and concatenated gap‐free with Gblocks v0.91 (Castresana, 2000). The tree was constructed using neighbor‐joining method (Saitou & Nei, 1987) in Mega 6.06 (Tamura, Stecher, Peterson, Filipski & Kumar, 2013) and calibrated using the estimates of divergence time in the literature.…”

Section: Methodsmentioning

confidence: 99%

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

Avanesov

Porter

et al. 2018

Aging Cell

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SummaryLifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life‐history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer‐lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing. Interestingly, these gene expression patterns resembled those of flies under dietary restriction and several other lifespan‐extending interventions, although on the individual gene level, there was no significant overlap with genes previously reported to have lifespan‐extension effects. We experimentally tested the lifespan regulation potential of several candidate genes and found no consistent effects, suggesting that individual genes generally do not explain the observed longevity patterns. Instead, it appears that lifespan regulation across species is modulated by complex relationships at the system level represented by global gene expression.

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Cited by 13,537 publications

References 26 publications

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Subspecies in the global human gut microbiome

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

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Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

Cited by 13,537 publications

References 26 publications

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m6A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Subspecies in the global human gut microbiome

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

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Product

Resources

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Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI

Identification of factors required for m⁶A mRNA methylation in Arabidopsis reveals a role for the conserved E3 ubiquitin ligase HAKAI