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eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Jaime Huerta-Cepas, Damian Szklarczyk, Kristoffer Forslund, Helen Cook, Davide Heller, Mathias C. Walter, Thomas Rattei, Daniel R. Mende, Shinichi Sunagawa, Michael Kuhn, Lars Juhl Jensen, Christian von Mering (+1 others)
2015 Nucleic Acids Research  
http://eggnog.embl. de. von Mering, Christian; Bork, Peer (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.  ...  eggNOG is a public resource that provides Orthologous Groups (OGs) of proteins at different taxonomic levels, each with integrated and summarized functional annotations.  ...  ACKNOWLEDGEMENTS Valuable feedback helping to guide some of the improvements to eggNOG was received within the Quest for Orthologs initiative.  ... 
doi:10.1093/nar/gkv1248 pmid:26582926 pmcid:PMC4702882 fatcat:cdzsgymezrd7hbk373no5tmpxy

MicrobComp – graphical user interface enables an in-silico comparison of taxonomic differences between two amplicon datasets [article]

Thomas Nussbaumer
2019 bioRxiv   pre-print
Amplicon sequencing is still widely adapted and standard procedure to determine key species in a biological sample and despite a high number of different datasets being steadily generated and fed into  ...  The experimental and computational analysis of microbes is in the focus of basic and applied research for several decades already and has massively extended our knowledge of role and impact of microbes  ...  "eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences." Nucleic acids research 44.D1 (2015): D286-D293. 13.  ... 
doi:10.1101/717231 fatcat:fbwibwogo5el7fi7m2exxegery

The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

Endang Rahmat, Inkyu Park, Youngmin Kang
2021 G3: Genes, Genomes, Genetics  
The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins.  ...  The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set.  ...  ., 2015 eggNOG 4.5: a hierarchical orthology framework with improved 249 functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res.  ... 
doi:10.1093/g3journal/jkab246 pmid:34849782 pmcid:PMC8527480 fatcat:say5ob37wjcfbhmdf4rxinqgoq

De novo assembly and annotation of the larval transcriptome of two spadefoot toads widely divergent in developmental rate [article]

H. Christoph Liedtke, Jessica Gomez Garrido, Anna Esteve-Codina, Marta Gut, Tyler Alioto, Ivan Gomez-Mestre
2018 bioRxiv   pre-print
Amphibians are a highly vulnerable and highly diverse group of vertebrates for which we still have modest genomic resources.  ...  In particular, amphibian larvae are a key component of continental wetlands, where they have strong influences on energy fluxes, nutrient cycling, and community structure.  ...  Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a 314 hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic 315 and  ... 
doi:10.1101/421446 fatcat:o6mbbgz4wvewfldcixyeqklpvu

Improved draft reference genome for the Glassy-winged Sharpshooter (Homalodisca vitripennis), a vector for Pierce's disease [article]

Cassandra L Ettinger, Frank J Byrne, Matthew A Collin, Derreck Carter-House, Linda L Walling, Peter W Atkinson, Rick A Redak, Jason E Stajich
2021 bioRxiv   pre-print
To improve on this effort, we used a combination of Oxford Nanopore long-read sequencing technology combined with Illumina sequencing reads to generate a better assembly and first-pass annotation of the  ...  The improved genome assembly and annotation for H. vitripennis, curated set of candidate genes, and endosymbiont MAGs will be invaluable resources for future research of H. vitripennis.  ...  ., 2016 eggNOG 4.5: a 469 hierarchical orthology framework with improved functional annotations for eukaryotic, 470 prokaryotic and viral sequences. Nucleic Acids Res. 44: D286-93. 471 Hunter, W.  ... 
doi:10.1101/2021.06.04.447158 fatcat:sxe4vahh75hfxpur5ihb4pbspi

Genotypic differences between strains of the opportunistic pathogen Corynebacterium bovis isolated from humans, cows, and rodents

Christopher Cheleuitte-Nieves, Christopher A. Gulvik, John R. McQuiston, Ben W. Humrighouse, Melissa E. Bell, Aaron Villarma, Vincent A. Fischetti, Lars F. Westblade, Neil S. Lipman, Feng Gao
2018 PLoS ONE  
Little is known about the genetic characteristics and genomic diversity of C. bovis because only a single draft genome is available for the species.  ...  Interestingly, the average nucleotide identity demonstrated that the C. bovis isolates clustered by host, with human and bovine isolates clustering together, and the mouse and rat isolates forming a separate  ...  Christopher Manuel of the University of Colorado-Denver for providing the C. bovis isolate CUAMC1 (small and large colony variant) and Dr.  ... 
doi:10.1371/journal.pone.0209231 pmid:30586440 pmcid:PMC6306256 fatcat:6z63shonmzby5gnop4nd53ec6i

An integrative method to unravel the host-parasite interactome: An orthology-based approach [article]

Yesid Cuesta Astroz, Alberto Santos, Guilherme Oliveira, Lars Juhl Jensen
2017 bioRxiv   pre-print
Besides, the host proteome is filtered for proteins expressed in selected cellular localizations and tissues supporting the parasites growth.  ...  The resulting PPI networks were compared across parasites to identify common mechanisms that may define a global pathogenic hallmark.  ...  Huerta-Cepas J, Szklarczyk D, Forslund K, Cook H, Heller D, Walter MC, et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences  ... 
doi:10.1101/147868 fatcat:rveo5uyw6jcpxpasjajao6bri4

Cell cycle transcriptomics of Capsaspora provides insights into the evolution of cyclin-CDK machinery

Alberto Pérez-Posada, Omaya Dudin, Eduard Ocaña-Pallarès, Iñaki Ruiz-Trillo, Andrej Ondracka, Joseph Heitman
2020 PLoS Genetics  
We developed a protocol for cell cycle synchronization in Capsaspora cultures and assessed gene expression over time across the entire cell cycle.  ...  In addition, many otherwise conserved cell cycle regulators have been lost and independently evolved in yeast, a widely used model organism for cell cycle research.  ...  We also acknowledge the UPF Flow Cytometry Core Facility for assistance with flow cytometry, and the CRG Genomics Unit for mRNA library preparation and Illumina sequencing.  ... 
doi:10.1371/journal.pgen.1008584 pmid:32176685 fatcat:x5277licgfen5gkke52vupaqvu

Insights into the molecular features of the von Hippel-Lindau like protein [article]

Federica Quaglia, Giovanni Minervini, Francesco Tabaro, Silvio C E Tosatto
2018 bioRxiv   pre-print
These may occur at precise hypoxia levels where functional overlap with pVHL may permit a finer modulation of pVHL functions.  ...  Our findings show that VLP may share at least seven interactors with pVHL, suggesting novel functional roles for this under- studied human protein.  ...  Acknowledgements The authors are grateful to members of the BioComputingUP group for insightful discussions. Conflict of interest and funding  ... 
doi:10.1101/407353 fatcat:6poh6glfqvfzfa2kcrg6o7rejq

Genome-Enabled Insights Into The Ecophysiology Of The Comammox BacteriumCandidatusNitrospira nitrosa [article]

Pamela Y. Camejo, Jorge Santo Domingo, Katherine D. McMahon, Daniel R. Noguera
2017 bioRxiv   pre-print
In this study, we identifiedNitrospirastrains dominating the nitrifying community of a sequencing batch reactor (SBR) performing BNR under micro-aerobic conditions.  ...  Overall, our analysis expanded our understanding of the genetic functional features ofCa.Nitrospira nitrosa, and identified genomic traits that further illuminate the phylogenetic diversity and metabolic  ...  J.; von Mering, C.; Bork, P., 575 eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for 576 eukaryotic, prokaryotic and viral sequences.  ... 
doi:10.1101/144600 fatcat:vhjoakre7vcahgyifvz2pzwnty

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Edoardo Pasolli, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, Paolo Manghi, Adrian Tett, Paolo Ghensi, Maria Carmen Collado, Benjamin L. Rice (+6 others)
2019 Cell  
We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000).  ...  The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations.  ...  ., et al. (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44 (D1), D286-D293.  ... 
doi:10.1016/j.cell.2019.01.001 pmid:30661755 pmcid:PMC6349461 fatcat:tthplpl3nvcgvilpf2mgmhjowq

Host–Symbiont Interactions in Deep-Sea Chemosymbiotic Vesicomyid Clams: Insights From Transcriptome Sequencing

Yi Lan, Jin Sun, Weipeng Zhang, Ting Xu, Yu Zhang, Chong Chen, Dong Feng, Hongbin Wang, Jun Tao, Jian-Wen Qiu, Pei-Yuan Qian
2019 Frontiers in Marine Science  
C., et al. (2016). eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.  ...  Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper. Mol. Biol.  ... 
doi:10.3389/fmars.2019.00680 fatcat:xs2ozkvmorguxahayhixa2ilzi

Protein citrullination was introduced into animals by horizontal gene transfer from cyanobacteria [article]

Thomas FM Cummings, Kevin Gori, Luis Sanchez-Pulido, Gabriel Gavriilidis, David Moi, Abigail R. Wilson, Elizabeth P Murchison, Christophe Dessimoz, Chris Ponting, Maria A. Christophorou
2020 bioRxiv   pre-print
We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues.  ...  This study reveals the unusual evolution of a pleiotropic protein modification with clear relevance in human physiology and disease.  ...  EGGNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. (2016). doi:10.1093/nar/gkv1248 56. Jones, D.  ... 
doi:10.1101/2020.06.13.150037 fatcat:2grg4uqahzd57kuhll3sn6aeza

Integrated transcriptomic and metabolomic analyses of yellow horn (Xanthoceras sorbifolia) in response to cold stress

Juan Wang, Jinping Guo, Yunxiang Zhang, Xingrong Yan, Tapan Kumar Mondal
2020 PLoS ONE  
Xanthoceras sorbifolia, a medicinal and oil-rich woody plant, has great potential for biodiesel production.  ...  Annotation of DEGs revealed that amino acid metabolism, glycolysis/gluconeogenesis, starch and sucrose metabolism, galactose metabolism, fructose and mannose metabolism, and the citrate cycle (TCA) were  ...  All authors have read and approved the final manuscript.  ... 
doi:10.1371/journal.pone.0236588 pmid:32706804 fatcat:74mlbcbuxvh3zpsxkm3ju2m4ui

Supplementary Methods and Figures from Combined cultivation and single-cell approaches to the phylogenomics of nucleariid amoebae, close relatives of fungi

Luis Javier Galindo, Guifré Torruella, David Moreira, Yana Eglit, Alastair G. B. Simpson, Eckhard Völcker, Steffen Clauß, Purificación López-García
2019 Figshare  
The phylogeny of the complete 18S rRNA sequences of Pompholyxophrys and Lithocolla confirmed their suggested evolutionary relatedness to nucleariid amoebae, although with moderate support for internal  ...  To improve the phylogenetic framework of nucleariids, we carried out phylogenomic analyses based on two datasets of, respectively, 264 conserved proteins and 74 single-copy protein domains.  ...  Huerta-Cepas J et al. 2016 EGGNOG 4.5: A hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286-D293.  ... 
doi:10.6084/m9.figshare.9741875.v1 fatcat:bj5m4axixzfmlju62drkukoryu
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