PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Tice, Alexander K.; Žihala, David; Pánek, Tomáš; Jones, Robert E.; Salomaki, Eric D.; Nenarokov, Serafim; Burki, Fabien; Eliáš, Marek; Eme, Laura; Roger, Andrew J.; Rokas, Antonis; Shen, Xing‐Xing; Strassert, Jürgen F. H.; Kolísko, Martin; Brown, Matthew W.

doi:10.1371/journal.pbio.3001365

Cited by 59 publications

(88 citation statements)

References 37 publications

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“…The copyright holder for this preprint this version posted November 2, 2021. ; https://doi.org/10.1101/2021.10.30.466607 doi: bioRxiv preprint "spurious_sequence" function in PhyKIT (Steenwyk et al, 2021b). Other tools, such as PhyloFisher, UPhO, and other orthology inference pipelines employ similar strategies to refine orthology inference (Yang and Smith, 2014;Ballesteros and Hormiga, 2016;Tice et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Steenwyk

Goltz²,

Buida³

et al. 2021

Preprint

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Molecular evolution studies, such as phylogenomic studies and genome-wide surveys of positive selection, often rely on gene families of single-copy orthologs (SC-OGs). In contrast, large gene families with multiple homologs in one or more species—a phenomenon observed among several important families of genes such as transporters and transcription factors—are often ignored because identifying and retrieving SC-OGs nested within them is challenging. To address this issue and increase the number of markers used in molecular evolution studies, we developed orthoSNAP, a software that uses a phylogenetic framework to simultaneously split gene families into SC-OGs and prune species-specific inparalogs. We term SC-OGs identified by orthoSNAP as SNAP-OGs because they are identified using a splitting and pruning procedure. From 46,645 orthologous groups of genes inferred using graph-based clustering of sequence similarity scores across four separate eukaryotic datasets, we identified 6,634 SC-OGs; using orthoSNAP on the remaining 40,011 orthologous groups of genes, we identified an additional 6,630 SNAP-OGs. Comparison of SNAP-OGs and SC-OGs revealed that their phylogenetic information content was similar. orthoSNAP is useful for increasing the number of markers used in molecular evolution data matrices, a critical step for robustly inferring and exploring the tree of life.

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Section: Discussionmentioning

confidence: 99%

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Steenwyk

Goltz²,

Buida³

et al. 2021

Preprint

Self Cite

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“…Both datasets were grouped into a larger dataset composed by 312 non-redundant orthologues. All orthologues were I) filtered with Prequal 139 to remove non-homologous residues, ii) aligned with mafft, iii) filtered with divvier 140 to remove alignment errors, iv) trimed with trimAl 141 and v) merged into the super matrix by using the script matrix_constructor.py available with PhyloFisher 142 . The maximum likelihood tree was built with IQ-Tree2 under LG+C60+G+F 143 .…”

Section: Methodsmentioning

confidence: 99%

Marine gregarine genomes reveal the breadth of apicomplexan diversity and provide new insights on gliding motility

Boisard¹,

Duvernois-Berthet

Duval

et al. 2021

Preprint

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Apicomplexans, parasite protists of a very wide diversity of metazoan hosts, are mostly known from species infecting human. Absence or limited data for basal lineages prevents a comprehensive view of evolutionary history and adaptive capacities of Apicomplexa. Here, we characterized the genome of the marine eugregarine Porospora gigantea, remarkable for the gigantic size of its vegetative feeding forms (trophozoites) and their speed of gliding movement, the fastest so far recorded for an Apicomplexa. Not a single but two highly related genomes named A and B were assembled. Highly syntenic, of similar size (9 Mb) and coding capacities (~5300 genes), they display a 10.8% divergence at nucleotide level corresponding to 16-38 My divergent time. Orthogroups analyses across 25 (proto)Apicomplexa including Gregarina niphandrodes showed that A and B are highly divergent from all other known apicomplexan species, revealing an unexpected diversity. These two related species branch in phylogenetic studies at the base of Cephaloidophoroidea, forming a new family in these crustacean gregarines. Gliding proteins data mining found a strong conservation of actin-related proteins, as well as of regulatory factors, within apicomplexan. In contrast, the conservation of core glideosome proteins and adhesion proteins appears to be highly variable among apicomplexan lineages, especially in gregarines. These results confirm the importance of studying gregarines to widen our biological and evolutionary view of apicomplexan parasites, to better apprehend species diversity and revise our understanding of the molecular bases of some key functions such as observed for the glideosome.

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“…Gene regulation relationship data, i.e., "controls-expression-of", were sourced from the Pathway Commons database (http://www.pathwaycommons.org/pc/home.do, June 15, 2021). Subnetworks were identified from the networks of up-and down-regulated genes using the Markov cluster algorithm (MCL) clustering function [24].…”

Section: Expression Regulation Network Analysismentioning

confidence: 99%

Identification of Regulatory Factors and Prognostic Markers in Amyotrophic Lateral Sclerosis

Sun

et al. 2022

Antioxidants

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Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive degeneration of motor neurons, leading to muscle atrophy, paralysis and even death. Immune disorder, redox imbalance, autophagy disorder, and iron homeostasis disorder have been shown to play critical roles in the pathogenesis of ALS. However, the exact pathogenic genes and the underlying mechanism of ALS remain unclear. The purpose of this study was to screen for pathogenic regulatory genes and prognostic markers in ALS using bioinformatics methods. We used Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, gene set enrichment analysis (GSEA), and expression regulation network analysis to investigate the function of differentially expressed genes in the nerve tissue, lymphoid tissue, and whole blood of patients with ALS. Our results showed that the up-regulated genes were mainly involved in immune regulation and inflammation, and the down-regulated genes were mainly involved in energy metabolism and redox processes. Eleven up-regulated transcription factors (CEBPB, CEBPD, STAT5A, STAT6, RUNX1, REL, SMAD3, GABPB2, FOXO1, PAX6, and FOXJ1) and one down-regulated transcription factor (NOG) in the nerve tissue of patients with ALS likely play important regulatory roles in the pathogenesis of ALS. Based on construction and evaluation of the ALS biomarker screening model, cluster analysis of the identified characteristic genes, univariate Cox proportional hazards regression analysis, and the random survival forest algorithm, we found that MAEA, TPST1, IFNGR2, and ALAS2 may be prognostic markers regarding the survival of ALS patients. High expression of MAEA, TPST1, and IFNGR2 and low expression of ALAS2 in ALS patients may be closely related to short survival of ALS patients. Taken together, our results indicate that immune disorders, inflammation, energy metabolism, and redox imbalance may be the important pathogenic factors of ALS. CEBPB, CEBPD, STAT5A, STAT6, RUNX1, REL, SMAD3, GABPB2, FOXO1, PAX6, FOXJ1, and NOG may be important regulatory factors linked to the pathogenesis of ALS. MAEA, TPST1, IFNGR2, and ALAS2 are potential important ALS prognostic markers. Our findings provide evidence on the pathogenesis of ALS, potential targets for the development of new drugs for ALS, and important markers for predicting ALS prognosis.

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PhyloFisher: A phylogenomic package for resolving eukaryotic relationships

Cited by 59 publications

References 37 publications

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

OrthoSNAP: a tree splitting and pruning algorithm for retrieving single-copy orthologs from gene family trees

Marine gregarine genomes reveal the breadth of apicomplexan diversity and provide new insights on gliding motility

Identification of Regulatory Factors and Prognostic Markers in Amyotrophic Lateral Sclerosis

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