ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Steenwyk, Jacob L.; Buida, Thomas J.; Li, Yuanning; Shen, Xing‐Xing; Rokas, Antonis

doi:10.1101/2020.06.08.140384

Cited by 25 publications

(12 citation statements)

References 22 publications

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“…First, the rpS3 sequences were aligned with MAFFT linsi v7.453 ( Katoh and Standley, 2013 ) and for poorly aligning sequences we performed homology searches with BLASTp against NCBI’s nr ( Altschul et al, 1990 ) to confirm their origin (e.g., eukaryotic, misannotations, potential misassemblies) and remove them. The remaining sequences were fused with the Hug dataset, realigned, and trimmed with ClipKIT (mode: kpic-gappy) ( Steenwyk et al, 2020 ). A Maximum-Likelihood phylogeny was reconstructed in IQ-TREE 2 ( Minh et al, 2020 ), under a model selected with ModelFinder ( Kalyaanamoorthy et al, 2017 ), and branch supports calculated with 1000 ultrafast bootstraps ( Hoang et al, 2018 ), 1000 SH-aLRT replicates ( Guindon et al, 2010 ), and aBayes ( Anisimova et al, 2011 ).…”

Section: Methodsmentioning

confidence: 99%

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

et al. 2020

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Organisms of the candidate phylum Saccharibacteria have frequently been detected as active members of hydrocarbon degrading communities, yet their actual role in hydrocarbon degradation remained unclear. Here, we analyzed three enrichment cultures of hydrocarbon-amended groundwater samples using genome-resolved metagenomics to unravel the metabolic potential of indigenous Saccharibacteria. Community profiling based on ribosomal proteins revealed high variation in the enrichment cultures suggesting little reproducibility although identical cultivation conditions were applied. Only 17.5 and 12.5% of the community members were shared between the three enrichment cultures based on ribosomal protein clustering and read mapping of reconstructed genomes, respectively. In one enrichment, two Saccharibacteria strains dominated the community with 16.6% in relative abundance and we were able to recover near-complete genomes for each of them. A detailed analysis of their limited metabolism revealed the capacity for peptide degradation, lactate fermentation from various hexoses, and suggests a scavenging lifestyle with external retrieval of molecular building blocks. In contrast to previous studies suggesting that Saccharibacteria are directly involved in hydrocarbon degradation, our analyses provide evidence that these organisms can be highly abundant scavengers acting rather as organic carbon sinks than hydrocarbon degraders in these communities.

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Section: Methodsmentioning

confidence: 99%

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

et al. 2020

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“…Specifically, the following parameters were used: --op 1.0 --maxiterate 1000 --retree 1 --genafpair. The resulting alignment was trimmed using ClipKIT, v0.1 (Steenwyk et al, 2020b), with default ‘gappy’ mode. The trimmed alignment was then used to infer the evolutionary history of tef1 sequences using IQ-TREE2 (Minh et al, 2020).…”

Section: Methodsmentioning

confidence: 99%

“…Next, nucleotide sequences were threaded onto the protein alignments using function thread_dna in PhyKIT, v0.0.1 (Steenwyk et al, 2020a). The resulting codon-based alignments were then trimmed using ClipKIT, v0.1 (Steenwyk et al, 2020b), using the gappy mode. The resulting aligned and trimmed alignments were then concatenated into a single matrix with 7,133,367 sites using the PhyKIT function create_concat.…”

Section: Maximum Likelihood Molecular Phylogeneticsmentioning

confidence: 99%

Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates ofAspergillus fumigatus

Steenwyk

Mead

Castro

et al. 2020

Preprint

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The ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 2019 (COVID-19) first described from Wuhan, China. A subset of COVID-19 patients has been reported to have acquired secondary infections by microbial pathogens, such as fungal opportunistic pathogens from the genus Aspergillus. To gain insight into COVID-19 associated pulmonary aspergillosis (CAPA), we analyzed the genomes and characterized the phenotypic profiles of four CAPA isolates of Aspergillus fumigatus obtained from patients treated in the area of North Rhine-Westphalia, Germany. By examining the mutational spectrum of single nucleotide polymorphisms, insertion-deletion polymorphisms, and copy number variants among 206 genes known to modulate A. fumigatus virulence, we found that CAPA isolate genomes do not exhibit major differences from the genome of the Af293 reference strain. By examining virulence in an invertebrate moth model, growth in the presence of osmotic, cell wall, and oxidative stressors, and the minimum inhibitory concentration of antifungal drugs, we found that CAPA isolates were generally, but not always, similar to A. fumigatus reference strains Af293 and CEA17. Notably, CAPA isolate D had more putative loss of function mutations in genes known to increase virulence when deleted (e.g., in the FLEA gene, which encodes a lectin recognized by macrophages). Moreover, CAPA isolate D was significantly more virulent than the other three CAPA isolates and the A. fumigatus reference strains tested. These findings expand our understanding of the genomic and phenotypic characteristics of isolates that cause CAPA.

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“…From these phylogenies we isolated the sequences forming well-supported branches corresponding to the ones in (Lombard, 2016), albeit with increased diversity plus some additional clades of potential interest. The individual datasets (archaeal, bacterial, eukaryotic) were then fused into single Alg13/EpsF-like and Alg14/EpsE-like datasets that were aligned as above and trimmed with ClipKIT (kpigappy) (Steenwyk et al, 2020). Then phylogenies were inferred with IQ-TREE 2.0.5 (Minh et al, 2020) under the model selected by ModelFinder (Kalyaanamoorthy et al, 2017), and ultrafast bootstrap (Hoang et al, 2018), aLRT SH-like (Guindon et al, 2010), and approximate Bayesian (Anisimova et al, 2011) branch support tests (-m MFP -bb 1000 -alrt 1000 -abayes).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

N-glycan chitobiose core biosynthesis by Agl24 strengthens the hypothesis of an archaeal origin of the eukaryal N-glycosylation

Meyer

Wagstaff

Adam

et al. 2021

Preprint

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Protein N-glycosylation is one of the most common posttranslational modifications found in all three domains of life. The crenarchaeal N-glycosylation begins with the synthesis of a lipid-linked chitobiose core structure, identical to that in eukaryotes. Here, we report the first identification of a thermostable archaeal beta-1,4-N-acetylglucosaminyltransferase, named archaeal glycosylation enzyme 24 (Agl24), responsible for the synthesis of the N-glycan chitobiose core. Biochemical characterization confirmed the function as an inverting β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase. Substitution of a highly conserved histidine residue, found also in the eukaryotic and bacterial homologs, demonstrated its importance for the function of Agl24. Furthermore, bioinformatics and structural modeling revealed strong similarities between Agl24 and both the eukaryotic Alg14/13 and a distant relation to the bacterial MurG, which catalyze the identical or a similar process, respectively. Our data, complemented by phylogenetic analysis of Alg13 and Alg14, revealed similar sequences in Asgardarchaeota, further supporting the hypothesis that the Alg13/14 homologs in eukaryotes have been acquired during eukaryogenesis.HighlightsFirst identification and characterization of a thermostable β-D-GlcNAc-(1→4)-α-D-GlcNAc-diphosphodolichol glycosyltransferase (GT family 28) in Archaea.A highly conserved histidine, within a GGH motif in Agl24, Alg14, and MurG, is essential for function of Agl24.Agl24-like homologs are broadly distributed among Archaea.The eukaryotic Alg13 and Alg14 are closely related to the Asgard homologs, suggesting their acquisition during eukaryogenesis.Cover Art

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ClipKIT: a multiple sequence alignment-trimming algorithm for accurate phylogenomic inference

Cited by 25 publications

References 22 publications

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

Genomic and phenotypic analysis of COVID-19-associated pulmonary aspergillosis isolates ofAspergillus fumigatus

N-glycan chitobiose core biosynthesis by Agl24 strengthens the hypothesis of an archaeal origin of the eukaryal N-glycosylation

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