Tag: EggNOG

No genes mapped in clusterprofiler gseGO

Hello! I’m having issues generating an adequate geneList for running gseGO in clusterProfiler, using keytype = “GO” Similar issues have been described here: No gene mapped gseGO code is: gse <- gseGO(geneList = gene_List, ont = “ALL”, #ont one of “BP”, “MF”, “CC” or “ALL” OrgDb = OrgDb, minGSSize =…

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Significance of Dashes (-) as COG category in EGGNOG-Mapper

Significance of Dashes (-) as COG category in EGGNOG-Mapper 0 Seeking clarification on COG categories analysed via eggnog-mapper. while analyzing the output derived from EGGNOG-mapper, I noticed dashes (“-“) in some COG categories, and I’m curious if this indicates non-applicability or undefined functional assignments for associated proteins. Could someone confirm…

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Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Dobson, G. E. On a new genus and species of Rhinolophidae, with description of a new species of Vesperus, and notes on some other species of insectivorous bats from Persia. J. Asiat. Soc. Bengal. 40, 455–461 (1871). Google Scholar  Bates, P., Bumrungsri, S., Francis, C., Csorba, G. & Furey, N….

Continue Reading Chromosome-level genome assembly of the Stoliczka’s Asian trident bat (Aselliscus stoliczkanus)

Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…

Continue Reading Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica

Topological structures and syntenic conservation in sea anemone genomes

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

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Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Bark preparation Spruce bark was obtained from the Iggesund pulp and paper mill (Iggesund, Holmen AB, Sweden), from a bark pile resulting from stripping of spruce logs at the mill after harvest, with the average age of trees at harvest being ~70 years. The bark was left to dry at…

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Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

Wang, P. et al. The genome evolution and domestication of tropical fruit mango. Genome Biol 21 (2020). Tang, C. et al. The rubber tree genome reveals new insights into rubber production and species adaptation. Nat Plants 2 (2016). Bredeson, J. V. et al. Sequencing wild and cultivated cassava and related…

Continue Reading Haplotype-resolved genome of heterozygous African cassava cultivar TMEB117 (Manihot esculenta)

How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.

How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package. 0 @3e18707b Last seen 10 hours ago India I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command. How can I use…

Continue Reading How can we use the organism database created by makeorgPackageFromNCBI to KEGG and GO analysis using clusterprofiler package.

Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Inhibition effect of strain SH-1471 on plant pathogenic fungi The results of the plate confrontation experiment showed that B. velezensis SH-1471 had good inhibitory effects on various pathogenic microorganisms (Fig. 1). Specifically, our experiment showed that its inhibition rates on Sclerotinia scrotiorum, Phoma mateuciicola, and Fusarium oxysporum were 93.5%, 90.3%, and…

Continue Reading Whole genome sequencing provides evidence for Bacillus velezensis SH-1471 as a beneficial rhizosphere bacterium in plants

Taxonomic and environmental distribution of bacterial amino acid auxotrophies

Tripp, H. J. et al. SAR11 marine bacteria require exogenous reduced sulphur for growth. Nature 452, 741–744 (2008). Article  ADS  CAS  PubMed  Google Scholar  Yu, X. J., Walker, D. H., Liu, Y. & Zhang, L. Amino acid biosynthesis deficiency in bacteria associated with human and animal hosts. Infect. Genet. Evol….

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Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

Fierer, N. & Jackson, R. B. The diversity and biogeography of soil bacterial communities. Proc. Natl. Acad. Sci. USA. 103, 626–631 (2006). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Gao, C. & Guo, L. Progress on microbial species diversity, community assembly and functional traits. Biodivers. Sci. 30, 22429 (2022)….

Continue Reading Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient

A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources

40,039 MAGs reconstructed from large-scale genome-resolved metagenomics To reconstruct previously unexplored bacterial and archaeal genomes, we performed a large-scale single-sample metagenomic assembly on 3304 soil metagenomes across the globe (Fig. 1a), including 363 metagenomes from the in-house dataset and 2941 from publicly available metagenomes. The soil samples were mainly collected from…

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Unzipped chromosome-level genomes reveal allopolyploid nematode origin pattern as unreduced gamete hybridization

Nematode materials and species identification Mi, Mj, and Mg were collected from farmlands in Wuhan city of Hubei province, Longyan city of Fujian province, and Changsha city of Hunan Provinces, respectively. Two Ma samples were collected from farmlands in Shenyang city of Liaoning province and Shiping city of Yunnan province….

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Diagnostic and commensal Staphylococcus pseudintermedius genomes reveal niche adaptation through parallel selection of defense mechanisms

Bond, R. & Loeffler, A. What’s happened to Staphylococcus intermedius? Taxonomic revision and emergence of multi-drug resistance. J. Small Anim. Pr. 53, 147–154 (2012). Article  CAS  Google Scholar  Carroll, K. C., Burnham, C. D. & Westblade, L. F. From canines to humans: clinical importance of Staphylococcus pseudintermedius. PLoS Pathog. 17,…

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Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]

Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…

Continue Reading Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls [PeerJ]

Identification and cultivation of anaerobic bacterial scavengers of dead cells

Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article  CAS  PubMed  PubMed Central  Google Scholar  Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article  CAS  PubMed  Google Scholar  Liang…

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Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Falkowski P. G., Raven J. A. Aquatic Photosynthesis (Princeton Univ. Press, 2013). Sanchez-Baracaldo, P., Bianchini, G., Wilson, J. D. & Knoll, A. H. Cyanobacteria and biogeochemical cycles through earth history. Trends Microbiol. 30, 143–157 (2022). Article  CAS  PubMed  Google Scholar  Blankenship, R. E. Early evolution of photosynthesis. Plant Physiol. 154,…

Continue Reading Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

orthologues – Error with eggNOG-mapper jobs

I recently tried using eggNOG-mapper for pan-genome and core genome analysis of files from OrthoFinder, specifically the ‘Orthogroup_Sequences’ which contains a huge list of protein files in fasta format. As instructed, the folder was compressed into a tar.gz zip file and uploaded. If the upload was successful, an email is…

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A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins

Construction of integrated PCEG and PCEP To the best of our knowledge, the present study is the first to develop a comprehensive catalog of plastic-contaminated soils using an integrated bioinformatic workflow. Five datasets were used to produce 53,300,583 unique genes and proteins. Quality control of reads, trimming, assembly, and binning…

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Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria

Ramanan R, Kim BH, Cho DH, Oh HM, Kim HS. Algae–bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv. 2016;34:14–29. Article  CAS  PubMed  Google Scholar  Falkowski PG, Fenchel T, Delong EF. The microbial engines that drive earth’s biogeochemical cycles. Science. 2008;320:1034–9. Article  CAS  PubMed  Google Scholar  Buchan A, LeCleir GR,…

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Metabolite interactions in the bacterial Calvin cycle and implications for flux regulation

Cultivations and harvest Cupriavidus necator strain DSMZ 428 was grown in Ralstonia Minimal Media (RMM) with 100 mM HEPES pH 7.5 under chemostat conditions in a Photon Systems Instruments Multi-Cultivator MC-1000 OD. Each reactor tube was set up to a volume of 55 mL, OD600 0.05 and 3.5 g/L fructose. Once growth ceased,…

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Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India

Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial…

Continue Reading Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India

One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

Isolation and microscopy of Mantamonas sphyraenae sp. nov Mantamonas sphyraenae SRT-306 was collected on 26 Sep. 2013 from the surface of a barracuda caught in a lagoon on Iriomote Island, Taketomi, Okinawa Prefecture, Japan (24° 23′ 36.762″ N, 123° 45′ 22.572″ E). It was isolated manually from the rough sample…

Continue Reading One high quality genome and two transcriptome datasets for new species of Mantamonas, a deep-branching eukaryote clade

A comprehensive genomic catalog from global cold seeps

Joye, S. B. The geology and biogeochemistry of hydrocarbon seeps. Annu. Rev. Earth Pl. Sci. 48, 205–231 (2020). Article  ADS  CAS  Google Scholar  Al-Shayeb, B. et al. Borgs are giant genetic elements with potential to expand metabolic capacity. Nature 610, 731–736 (2022). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar …

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EggNOG mapper annotation results

I am new with Bioinformatics, I used eggnog to annotate a group of protein sequences The results obtained with eggnog are not very well explained, how do you interpret these results? Query | seed_ortholog | evalue | score | eggNOG_OGs | max_annot_lvl | COG_category | Description | Preferred_name | GOs…

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Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin

Magnabosco C, Lin LH, Dong H, Bomberg M, Ghiorse W, Stan-Lotter H, et al. The biomass and biodiversity of the continental subsurface. Nat Geosci. 2018;11:707–17. Article  CAS  Google Scholar  LaRowe DE, Amend JP. Catabolic rates, population sizes and doubling/replacement times of microorganisms in natural settings. Am J Sci. 2015;315:167–203. Article …

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Comparative analysis of carbapenem-resistant K. pneumoniae

Introduction The worldwide spread of Klebsiella pneumoniae is a major global public health threat.1,2 K. pneumoniae is an opportunistic pathogen that colonizes the human gut and respiratory tract and possibly causes infection in immunocompromised hosts. Gut colonized K. pneumoniae is one of the important pathogens causing nosocomial infections, although the…

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Viruses in deep-sea cold seep sediments harbor diverse survival mechanisms and remain genetically conserved within species

Dong X, Peng Y, Wang M, Woods L, Wu W, Wang Y, et al. Evolutionary ecology of microbial populations inhabiting deep sea sediments associated with cold seeps. Nat Commun. 2023;14:1127. Article  CAS  PubMed  PubMed Central  Google Scholar  Dong X, Rattray JE, Campbell DC, Webb J, Chakraborty A, Adebayo O, et…

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Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors

Morphological observation of continuous in vitro cultured B. gibsoni (Wuhan isolate) Babesia gibsoni was successfully cultured in vitro in 20% serum. After splitting, parasitemia reached 10% ± 1.5% on day 3 (Fig. 1A). Fig. 1 Changes in parasitemia and morphology of in vitro cultured B. gibsoni (Wuhan isolate). A Changes in parasitemia of…

Continue Reading Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors

Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

Soltis, P. S. & Soltis, D. E. Polyploidy and Genome Evolution (Springer, 2012). Chen, J. Z. & Birchler, J. A. Polyploid and Hybrid Genomics (Wiley-Blackwell, 2013). Ye, C. Y. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant 13, 1298–1310…

Continue Reading Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips

Genome sequencing and assembly After filtering the adapters and low-quality reads, approximately 30.58 Gb of clean reads (~100×) were retained by Illumina paired-end short-reads sequencing, and about 63.24 Gb of subreads (~200×) were obtained by PacBio long-reads sequencing. The PacBio reads had an average length of 16.34 kb, with an N50 length of…

Continue Reading A chromosome-level genome assembly of Stenchaetothrips biformis and comparative genomic analysis highlights distinct host adaptations among thrips

A predicted CRISPR-mediated symbiosis between uncultivated archaea

Garneau, J. E. et al. The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 468, 67 (2010). Article  CAS  PubMed  Google Scholar  Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008). Article  CAS  PubMed  Google…

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Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont

Psyllid sampling, tissue collection and DNA isolation Adult D. citri newly emerged (five days old) was initially harvested from Citrus Tachibana uninfected CLas in 2020 at Guangxi province, China, and was successively reared on Murraya paniculata at Guangxi Special Crops Research Institute for more than 15 generations. All cages and…

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Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites | BMC Medicine

Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan. China JAMA. 2020;323(11):1061–9. Article  CAS  PubMed  Google Scholar  Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression…

Continue Reading Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites | BMC Medicine

Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution

Lieph, R., Veloso, F. A. & Holmes, D. S. Thermophiles like hot T. Trends Microbiol. 14, 423–426 (2006). Article  CAS  PubMed  Google Scholar  Hedlund, B. P. et al. Uncultivated thermophiles: current status and spotlight on ‘Aigarchaeota’. Curr. Opin. Microbiol. 25, 136–145 (2015). Article  CAS  PubMed  Google Scholar  Kato, S. et…

Continue Reading Identification of a deep-branching thermophilic clade sheds light on early bacterial evolution

Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

Booth, B. C. & Marchant, H. J. Parmales, a new order of marine chrysophytes, with desriptions of three new genera and seven new species. J. Phycol. 23, 245–260 (1987). Article  Google Scholar  Ichinomiya, M. et al. Diversity and oceanic distribution of the Parmales (Bolidophyceae), a picoplanktonic group closely related to…

Continue Reading Genome analysis of Parmales, the sister group of diatoms, reveals the evolutionary specialization of diatoms from phago-mixotrophs to photoautotrophs

First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]

Introduction Vultures are obligate scavengers, birds of prey that provide several ecological services such as nutrient recycling or avoiding soil contamination by carcass feeding, which help to reduce the spread of diseases in their habitats (Ogada, Keesing & Virani, 2012; Chung et al., 2015; Buechley & Şekercioğlu, 2016). Vultures are…

Continue Reading First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome [PeerJ]

Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease | Molecular Neurodegeneration

Aim, design and setting of the study We aim to address our research question – how does microbial diversity affect PD pathology with ageing at the molecular level and can early intervention in the microbiome modulate the disease course? Herein, we have studied longitudinally the gut microbiome dynamics with ageing and report that with ageing,…

Continue Reading Overexpression of human alpha-Synuclein leads to dysregulated microbiome/metabolites with ageing in a rat model of Parkinson disease | Molecular Neurodegeneration

Parallel and convergent genomic changes underlie independent subterranean colonization across beetles

Conway Morris, S. The predictability of evolution: glimpses into a post-Darwinian world. Naturwissenschaften 96, 1313–1337 (2009). Article  ADS  CAS  PubMed  Google Scholar  Stern, D. L. The genetic causes of convergent evolution. Nat. Rev. Genet. 14, 751–764 (2013). Article  CAS  PubMed  Google Scholar  Christiansen, K. Convergence and parallelism in cave entomobryinae….

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Whole-Genome Sequencing of Pseudomonas koreensis Isolated from Diseased Tor tambroides

Parte AC, Carbasse JS, Meier-Kolthoff JP et al (2020) List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 70(11):5607–5612. doi.org/10.1099/ijsem.0.004332 Article  PubMed  PubMed Central  Google Scholar  Duman M, Mulet M, Altun S et al (2021) The diversity of Pseudomonas species isolated…

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Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster | BMC Infectious Diseases

Luo T, Comas I, Luo D, et al. Southern East Asian origin and coexpansion of Mycobacterium tuberculosis Beijing family with Han Chinese. Proc Natl Acad Sci USA. 2015;112:8136–41. Article  CAS  PubMed  PubMed Central  Google Scholar  Yin QQ, Liu HC, Jiao WW, et al. Evolutionary history and ongoing transmission of phylogenetic…

Continue Reading Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster | BMC Infectious Diseases

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017). Article  CAS  PubMed  Google Scholar  Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015). Article …

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Host-adaptive traits in the plant-colonizing Pseudomonas donghuensis P482 revealed by transcriptomic responses to exudates of tomato and maize

P. donghuensis P482 achieved high populations on the roots of soil-grown tomato and maize, confirming it to be a suitable model for studying bacterial adaptations to different hosts P482 Rif was present on the roots of 18-day-old tomato and maize plants grown in soil from inoculated seeds. Based on arithmetic…

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Group B Streptococcus Cas9 variants provide insight into programmable gene repression and CRISPR-Cas transcriptional effects

Amino acid sequence comparisons between GAS and GBS Cas9 identify orthologous active sites Relationships between the amino acid sequence of GBS Cas9 endonuclease and its molecular functions can be deduced from detailed studies of its GAS ortholog, SpyCas9 (Supplementary Fig. 1). As a first step in locating DNA complementary to a…

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What statistical test should I use to analyse my two set of transcriptomique data?

What statistical test should I use to analyse my two set of transcriptomique data? 0 I have an assembled transcriptome. I performed analyses on this transcriptome to extract candidate sequences involved in the production of a substance. Then, I annotated both sets of data using the Eggnog Mapper tool. This…

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Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

Genome sequencing and assembly We sequenced and assembled genomes for the sandalwood species S. album and S. yasi (Fig. 1). In total, ~23 Gb and ~25 Gb of clean short reads of S. album and S. yasi were obtained for the genomic survey, respectively (Supplementary Tables 1 and 2). According to k-mer analysis, the…

Continue Reading Chromosome-level genome assemblies from two sandalwood species provide insights into the evolution of the Santalales

The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

Continue Reading The draft genome sequence of the Japanese rhinoceros beetle Trypoxylus dichotomus septentrionalis towards an understanding of horn formation

Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB

Summary of genes and pathways in SMDB Using keywords (e.g., sulfur, sulfate) to retrieve 284,541 literature reports from 1976 to 2021 in Web of Science and then obtained records of sulfur genes through a web crawler with Python. After manual verification, 875 related literature reports (representative literature was recruited) and…

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Antimicrobial activity of Limosilactobacillus fermentum strains isolated from the human oral cavity against Streptococcus mutans

Welch, J. L. M., Dewhirst, F. E. & Borisy, G. G. Biogeography of the oral microbiome: The site-specialist hypothesis. Annu. Rev. Microbiol. 73, 335–358. doi.org/10.1146/annurev-micro-090817-062503 (2019). Article  CAS  Google Scholar  Cornejo Ulloa, P., van der Veen, M. H. & Krom, B. P. Review: Modulation of the oral microbiome by the…

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Highly host-linked viromes in the built environment possess habitat-dependent diversity and functions for potential virus-host coevolution

Manrique, P., Dills, M. & Young, M. J. The human gut phage community and its implications for health and disease. Viruses 9, 141 (2017). Article  PubMed  PubMed Central  Google Scholar  Li, Z. et al. Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity. ISME J….

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Adding ‘gene_name’ attribute to each row of GTF/GFF file (missing for CDS, transcript, and exon rows)

Hello, Can someone please help me with this issue I’m having? Thank you in advance! I have a GFF file, and I have the gene_name attribute in my GFF file, but it’s only present for each gene entry (i.e., it’s absent from the transcript, cds, and exon rows). I want…

Continue Reading Adding ‘gene_name’ attribute to each row of GTF/GFF file (missing for CDS, transcript, and exon rows)

New Developments in Techniques Like Metagenomics and Metaproteomics for Isolation, Identification, and Characterization of Microbes from Varied Environment

Ashton PM, Nair S, Dallman T et al (2015) MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island. Nat Biotechnol 33:296–302 CrossRef  CAS  PubMed  Google Scholar  Fenn JB, Mann M, Meng CK et al (1990) ChemInform abstract: electrospray ionization for mass spectrometry of large biomolecules….

Continue Reading New Developments in Techniques Like Metagenomics and Metaproteomics for Isolation, Identification, and Characterization of Microbes from Varied Environment

Assessing the biogeography of marine giant viruses in four oceanic transects

Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19. Article  CAS  PubMed  PubMed Central  Google Scholar  Wilhelm S, Bird J, Bonifer K, Calfee B, Chen T, Coy S, et al. A…

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Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

Ma, Y. et al. Gut microbiota adaptation to high altitude in indigenous animals. Biochem. Biophys. Res. Commun. 516, 120–126 (2019). Article  CAS  PubMed  Google Scholar  Guo, N. et al. Seasonal dynamics of diet-gut microbiota interaction in adaptation of yaks to life at high altitude. NPJ Biofilms Microbiomes 7, 38 (2021)….

Continue Reading Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta)

Mirusviruses link herpesviruses to giant viruses

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

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Mutation-induced infections of phage-plasmids | Nature Communications

Media The minimal marine media, MBL media, was used for serial dilution growth of Tritonibacter mobilis A3R06. It contained 10 mM NH4Cl, 10 mM Na2HPO4, 1 mM Na2SO4, 50 mM HEPES buffer (pH 8.2), NaCl (20 g/liter), MgCl2*6H2O (3 g/l), CaCl2*2H2O (0.15 g/l), and KCl (0.5 g/l). Glucose was added as the only carbon source at a…

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Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Philippi M, Kitzinger K, Berg JS, Tschitschko B, Kidane AT, Littmann S, et al. Purple sulfur bacteria fix N2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue. Nat Commun. 2021;12:4774. Article  CAS  PubMed  PubMed Central  Google Scholar  Xiong Y, Guilbaud R, Peacock CL, Cox RP, Canfield DE, Krom MD,…

Continue Reading Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno

Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting

Handa IT, Aerts R, Berendse F, Berg MP, Bruder A, Butenschoen O, et al. Consequences of biodiversity loss for litter decomposition across biomes. Nature. 2014;509:218–21. Article  CAS  PubMed  Google Scholar  Roux S, Adriaenssens EM, Dutilh BE, Koonin EV, Kropinski AM, Krupovic M, et al. Minimum information about an uncultivated virus…

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Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method

Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI….

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Toxins | Free Full-Text | Metagenome Analysis Identifies Microbial Shifts upon Deoxynivalenol Exposure and Post-Exposure Recovery in the Mouse Gut

1. Introduction Fusarium fungi are world-wide producers of a range of mycotoxins. Deoxynivalenol (DON) belonging to the group B trichothecenes, is one of the most prevalent food-associated mycotoxins mainly produced by Fusarium graminearum and Fusarium culmorum, and frequently contaminates cereals and cereal products [1,2]. Almost half of a total of…

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rna seq – RNAseq: Why would using a more complete scaffold reduce DEGs?

Fungi, ain’t a kingdom most of us will know much about. The only thing I can guess at is that in bacteria there has resurgence in methods for de novo assembly specifically aimed at reducing the total number of contigs in an assembly. The ‘new wave’ is summarised in this…

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How to analize multiple letters codes in COG IDs?

How to analize multiple letters codes in COG IDs? 1 Hi Biostars, I’m trying to analize undescribed genes by their functional categories (eggnog) and it would be very helpful to receive suggestions regarding how to deal with these “chimeric” codes such as ‘IQ’, ‘ET’, and ‘EGIPQ’. I’ve read that researchers…

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A phylogenomic analysis of Limosilactobacillus reuteri reveals ancient and stable evolutionary relationships with rodents and birds and zoonotic transmission to humans | BMC Biology

Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, et al. Evolution of mammals and their gut microbes. Science. 2008;320:1647–51. Article  CAS  PubMed  PubMed Central  Google Scholar  Ochman H, Worobey M, Kuo CH, Ndjango JB, Peeters M, Hahn BH, et al. Evolutionary relationships of wild hominids recapitulated…

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Parser EggNOG-mapper annotation output using pythom

Hello Biostars, I used to use python but I’m not good at it thus I need your help. I’m trying parsing a tab file resulting from the functional annotation using EggNOG-mapper. here. I want to explore all the essential information and make some plots from this data. what I did…

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A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes

Inagaki, F., Takai, K., Kobayashi, H., Nealson, K. H. & Horikoshi, K. Sulfurimonas autotrophica gen. nov., sp. nov., a novel sulfur-oxidizing e-proteobacterium isolated from hydrothermal sediments in the Mid-Okinawa Trough. Int. J. Syst. Evol. Microbiol. 53, 1801–1805 (2003). Article  CAS  PubMed  Google Scholar  Timmer-Ten Hoor, A. A new type of…

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Gene Enrichment analysis with EggNog output

Gene Enrichment analysis with EggNog output 0 Hi everyone! I want to perform a gene set enrichment analysis of differently expressed host genes during virus infection. I performed Gene Ontology (GO) annotation with eggnog for the whole host genome and got one .tsv file, an excel file, and two .orthologs…

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Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars

Zhang J, Liu Y, Zhang N, Hu B, Jin T, Xu H, et al. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nat Biotechnol. 2019;37:676–84. Article  CAS  PubMed  Google Scholar  Philippot L, Raaijmakers JM, Lemanceau P, van der Putten WH. Going back to the roots:…

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What to do if hundreds or genes have no functional domain!

Forum:What to do if hundreds or genes have no functional domain! 0 Hi! I did functional annotation (using KEGG, eggNOG, TRAPID, NR,Uniprot, and Mercator) of 5 cultivars (plants) to do my analysis. Long story short I identified genes that are private to each cultivar. Almost 70% genes in every cultivar…

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Gene names/ids on annotated protein files

Gene names/ids on annotated protein files 0 Hello all, I have annotated around 276 protein files using EggNog. The protein files have the following headers (example from one of the species): head Spodoptera_frugiperda.fa file_1_file_1_g22553.t1 gene=file_1_file_1_g22553 MNRLGMIVDLSHVGENTTRAAIKLSRAPVVFTHSSVYSLCNHKRNVPDDIIHSLKENGGIIMVNFFPDFVKCAPNATISDVAEHFHYIKRMVGADYVGIGGDFDGVNRVPRGLEDVSRYPELFAELLRSGQWTVQELKNLAGLNMLRVMRQVEKVRDEMRTNGVEPEEHPDSPNDNGNCTSNAFYTEYV The annotation file from EggNog has the following: head Spodoptera_frugiperda.softmasked.prot.fa.emapper.annotations file_1_file_1_g22553.t1 13037.EHJ66618 2.39e-121 357.0…

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metagenome – eggNOG: DNA-DNA or protein-protein orthologue identification?

I’m trying to work out is how reliable/accurate my eggNOG metagenomic outputs are. Critical for this is how its identifying orthologues. Background eggNOG is commonly used in metagenomics gene identification. Take a sample, randomly sequence all the DNA therein, then “annotate” via eggNOG. It identifies the putative gene function against…

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Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:….

Functional annotation results with Eggnog mapper, For a same query several COGs, several GO:…. 0 Hello, pleaaaase I need help !!! I performed a fonctionnal annotation for 2 set of transcriptomes with eggnogmapper, the problem is that I don’t really know how to exploit this results .. For example for…

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Genomic analysis of an ultrasmall freshwater green alga, Medakamo hakoo

Materials Medakamo hakoo 311 was obtained from the personal aquarium of Prof. Kuroiwa (Kagurazaka, Tokyo, Japan)4. The M. hakoo strain was cultured in 0.05% HYPONeX (HYPONeX Japan Corp., Ltd., Osaka, Japan) liquid medium and on 0.05% HYPONeX gellan gum-based solid medium in plates. Cyanidioschyzon merolae 10D (Toda et al. 1995)…

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The genus Serratia revisited by genomics

Merlino, C. P. Bartolomeo Bizio’s letter to the most eminent priest, Angelo Bellani, concerning the phenomenon of the red-colored polenta [translated from the Italian]. J. Bacteriol. 9, 527–543 (1924). Grimont, P. A. D. & Dulong de Rosnay, H. L. C. Numerical study of 60 strains of Serratia. J. Gen. Microbiol….

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The evolutionary origin of host association in the Rickettsiales

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

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Frontiers | Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation

Introduction The study of the microbial environments has benefited from the sequencing revolution, where technology improvement decreased the DNA sequencing cost and increased the number of sequenced nucleic bases. For approximately 20 years (depending on how we define the term metagenomics), it has allowed the decryption of the microbial composition…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Bioinformatics script using Python/Biopython/Clustalw using stdout to iterate over a directory of proteins

What exactly is the error you are seeing? You shouldn’t set sys.sterr and sys.stdout to string values (the clustalw_cline() function returns the clustal stderr and stdout as strings), as you won’t be able to write anything to stdout from python. I tried to clean up and correct your code below….

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Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions

1. Oh, J. et al. Biogeography and individuality shape function in the human skin metagenome. Nature 514, 59–64 (2014). 2. Byrd, A. L., Belkaid, Y. & Segre, J. A. The human skin microbiome. Nat. Rev. Microbiol. 16, 143–155 (2018). CAS  PubMed  Google Scholar  3. Oh, J. et al. Temporal stability…

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Towards the biogeography of prokaryotic genes

1. Sunagawa, S. et al. Structure and function of the global ocean microbiome. Science 348, 1261359 (2015). PubMed  Google Scholar  2. Zou, Y. et al. 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. Nat. Biotechnol. 37, 179–185 (2019). CAS  PubMed  PubMed Central  Google Scholar  3. Mohammad,…

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What is the best tool to recover nitrogen cycling genes from an annotated assembly?

What is the best tool to recover nitrogen cycling genes from an annotated assembly? 0 I have annotated metagenomic assemblies and am wanting to recover genes involved in the nitrogen cycle. I have identified three tools to help me do this but I unsure how to go about selecting them…

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Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

1. Szathmáry E, Smith JM. The major evolutionary transitions. Nature 1995;374:227–32. PubMed  Google Scholar  2. West SA, Fisher RM, Gardner A, Kiers ET. Major evolutionary transitions in individuality. Proc Natl Acad Sci USA. 2015;112:10112–9. CAS  PubMed  PubMed Central  Google Scholar  3. Moran NA. The coevolution of bacterial endosymbionts and phloem-feeding…

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Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis

1. Hackstein JH, Stumm CK. Methane production in terrestrial arthropods. Proc Natl Acad Sci USA. 1994;91:5441–5. CAS  PubMed  PubMed Central  Article  Google Scholar  2. Hackstein JHP, van Alen TA. Fecal methanogens and vertebrate evolution. Evolution. 1996;50:559–72. PubMed  Article  PubMed Central  Google Scholar  3. Borrel G, McCann A, Deane J, Neto…

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