Tag: MAFFT

Sperm-specific histone H1 in highly condensed sperm nucleus of Sargassum horneri

Cho, C. et al. Haploinsufficiency of protamine-1 or-2 causes infertility in mice. Nat. Genet. 28, 82–86 (2001). Article  CAS  PubMed  Google Scholar  Oliva, R. Protamines and male infertility. Hum. Reprod. Update 12, 417–435 (2006). Article  CAS  PubMed  Google Scholar  Balhorn, R. The protamine family of sperm nuclear proteins. Genome Biol….

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Domestic pigs are susceptible to experimental infection with non-human primate-derived Reston virus without the need for adaptation

Ethics and animal welfare statement All infectious work with RESTV, including sample inactivation, was performed in the Containment Level 4 laboratory (CL4) in accordance with the policies and protocols outlined by the Canadian Science Centre for Human and Animal Health Institutional Biosafety Committee. All animal work was performed in strict…

Continue Reading Domestic pigs are susceptible to experimental infection with non-human primate-derived Reston virus without the need for adaptation

Obtain satellite DNA monomer from dot plot

Obtain satellite DNA monomer from dot plot 1 I have come across numerous articles in which researchers extract monomers of satellite DNA, creating dot plots from contigs that contain this satellite. For instance, in the article linked doi: 10.3390/ijms22116052 the process is described as follows: ‘For each candidate cluster, we…

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First complete mitogenome of Massarineae and its contribution to phylogenetic implications in Pleosporales

Crous, P. W. et al. Fungal Planet description sheets: 214–280. Persoonia 32, 184–306 (2014). Article  PubMed  PubMed Central  Google Scholar  Zhang, Y. et al. Multi-locus phylogeny of Pleosporales: A taxonomic, ecological and evolutionary re-evaluation. Stud. Mycol. 64, 85–105 (2009). Article  PubMed  PubMed Central  Google Scholar  Schoch, C. L. et al….

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Diversity and dissemination of viruses in pathogenic protozoa

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

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Maternal dominance contributes to subgenome differentiation in allopolyploid fishes

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

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Unravelling the effect of New Year’s Eve celebrations on SARS-CoV-2 transmission

Setting The study was conducted in the setting of a dedicated testing and contact tracing program targeting around 50,000 higher education students at KU Leuven Association in Leuven, Belgium. A test and trace program was implemented, specifically targeting this student population. Students could attend for a PCR test at no…

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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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Analysis of geometric morphometrics and molecular phylogeny for Anopheles species in the Republic of Korea

World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar  Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…

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Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Wang, W. T. Revision of Adonis (Ranunculaceae). Bull. Bot. Res. 14, 1–31 (1994). Google Scholar  Gao, T. et al. Evaluating the feasibility of using candidate DNA Barcodes in discriminating species of the large Asteraceae family. BMC Evol. Biol. 10, 324 (2016). Article  Google Scholar  Conti, F. et al. Adonis fucensis…

Continue Reading Insight into chloroplast genome structural variation of the Mongolian endemic species Adonis mongolica (Ranunculaceae) in the Adonideae tribe

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

Continue Reading Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution

FAO, ITPS, GSBI, CBD & EC. State of knowledge of soil biodiversity – Status, challenges and potentialities, Report 2020. (FAO). doi.org/10.4060/cb1928en. 2020. Potapov, A. M. et al. Feeding habits and multifunctional classification of soil-associated consumers from protists to vertebrates. Biol. Rev. 97, 1057–1117 (2022). Article  PubMed  Google Scholar  García-Palacios, P.,…

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A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Jiao, Y. N. et al. Ancestral polyploidy in seed plants and angiosperms. Nature 473, 97–100 (2011). Article  PubMed  Google Scholar  Levin, D. A. Polyploidy and novelty in flowering plants. Am. Nat. 122, 1–25 (1983). Article  Google Scholar  Soltis, P. S. & Soltis, D. E. Ancient WGD events as drivers of…

Continue Reading A genome assembly for Orinus kokonorica provides insights into the origin, adaptive evolution and further diversification of two closely related grass genera

Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Honegger, R. The lichen symbiosis: What is so spectacular about it?. Lichenologist 30, 193–212 (1998). Article  Google Scholar  Grube, M. & Berg, G. Microbial consortia of bacteria and fungi with focus on the lichen symbiosis. Fung. Biol. Rev. 23, 72–85 (2009). Article  Google Scholar  Spribille, T. et al. Basidiomycete yeasts…

Continue Reading Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses

Human microbiota dysbiosis after SARS-CoV-2 infection have the potential to predict disease prognosis | BMC Infectious Diseases

Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020;323(13):1239–42. Article  CAS  PubMed  Google Scholar  Kesheh MM, Hosseini P, Soltani S, Zandi M. An…

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Phylogenomic assessment of 23 equid alphaherpesvirus 1 isolates obtained from USA-based equids | Virology Journal

Damiani AM, de Vries M, Reimers G, Winkler S, Osterrieder N. A severe equine herpesvirus type 1 (EHV-1) abortion outbreak caused by a neuropathogenic strain at a breeding farm in northern Germany. Vet Microbiol. 2014;172(3–4):555–62. Article  PubMed  Google Scholar  Negussie H, Gizaw D, Tessema TS, Nauwynck HJ. Equine herpesvirus-1 myeloencephalopathy,…

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Pairwise Alignment, Multiple Alignment, and BLAST

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410 CrossRef  CAS  PubMed  Google Scholar  Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database…

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Ancient diversity in host-parasite interaction genes in a model parasitic nematode

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

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Anopheles gambiae on remote islands in the Indian Ocean: origins and prospects for malaria elimination by genetic modification of extant populations

Irish, S. R., Kyalo, D., Snow, R. W. & Coetzee, M. Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands. Zootaxa 4747(3), 401–449. doi.org/10.1646/zootaxa.4747.3.1 (2020). Article  Google Scholar  Jacques, B. Les moustiques de l’archipel Comores. Série Entomologie Médicale et Parasitologie 15(2), 153–170 (1977)….

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Development and evaluation of specific polymerase chain reaction assays for detecting Theileria equi genotypes | Parasites & Vectors

Knowles DP, Kappmeyer LS, Stiller D, Hennager SG, Perryman LE. Antibody to a recombinant merozoite protein epitope identifies horses infected with Babesia equi. J Clin Microbiol. 1992;30:3122–6. CAS  PubMed  PubMed Central  Google Scholar  Ueti MW, Palmer GH, Kappmeyer LS, Statdfield M, Scoles GA, Knowles DP. Ability of the vector tick…

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Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Soltis, D. E. et al. Polyploidy and angiosperm diversification. Am. J. Bot. 96, 336–348 (2009). Article  PubMed  Google Scholar  Van de Peer, Y., Mizrachi, E. & Marchal, K. The evolutionary significance of polyploidy. Nat. Rev. Genet. 18, 411–424 (2017). Article  PubMed  Google Scholar  Amborella Genome Project et al. The Amborella…

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The Mla system of diderm Firmicute Veillonella parvula reveals an ancestral transenvelope bridge for phospholipid trafficking

Bacterial strains and growth conditions Veillonella parvula SKV38 was grown in SK medium (10 g/L tryptone [Difco], 10 g/L yeast extract [Difco], 0.4 g/L disodium phosphate, 2 g/L sodium chloride, and 10 ml/L 60% [wt/vol] sodium DL-lactate; described in ref. 51. Cultures were incubated at 37 °C in anaerobic conditions, either in anaerobic bags (GENbag anaero;…

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Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins | Parasites & Vectors

Yabsley MJ, Shock BC. Natural history of zoonotic Babesia: role of wildlife reservoirs. Int J Parasitol Parasit Wildl. 2013;2:18–31. Article  Google Scholar  Hersh MH, Tibbetts M, Strauss M, Ostfeld RS, Keesing F. Reservoir competence of wildlife host species for Babesia microti. Emerg Infect Dis. 2012;18:1951–7. Article  PubMed  PubMed Central  Google…

Continue Reading Detection of a novel Babesia sp. in Amblyomma javanense, an ectoparasite of Sunda pangolins | Parasites & Vectors

A DNA barcode library for woody plants in tropical and subtropical China

Hebert, P. D. N., Cywinska, A., Ball, S. L. & deWaard, J. R. Biological identifications through DNA barcodes. Proc Biol Sci 270, 313–321 (2003). Article  CAS  PubMed  PubMed Central  Google Scholar  Huang, X., Ci, X., Conran, J. G. & Li, J. Application of DNA barcodes in Asian tropical trees –…

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Bacteria can maintain rRNA operons solely on plasmids for hundreds of millions of years

Egan, E. S., Fogel, M. A. & Waldor, M. K. Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes. Mol. Microbiol. 56, 1129–1138 (2005). Article  CAS  PubMed  Google Scholar  Harrison, P. W., Lower, R. P., Kim, N. K. & Young, J. P. Introducing the bacterial ‘chromid’: not a…

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Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae

Sheridan, P. O. et al. Gene duplication drives genome expansion in a major lineage of Thaumarchaeota. Nat. Commun. 11, 1–12 (2020). Article  Google Scholar  Sheridan, P. O., Meng, Y., Williams, T. A. & Gubry-Rangin, C. Recovery of Lutacidiplasmatales archaeal order genomes suggests convergent evolution in Thermoplasmatota. Nat. Commun. 13, 1–13…

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Chromosome-level genomes of three key Allium crops and their trait evolution

Chase, M. W. et al. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Bot. J. Linn. Soc. 181, 1–20 (2016). Article  Google Scholar  Jones, M. G. et al. Biosynthesis of the flavour precursors of onion and garlic. J. Exp. Bot….

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The evolutionary innovation of root suberin lamellae contributed to the rise of seed plants

Fich, E. A., Segerson, N. A. & Rose, J. K. C. The plant polyester cutin: biosynthesis, structure, and biological roles. Annu. Rev. Plant Biol. 67, 207–233 (2016). Article  CAS  PubMed  Google Scholar  Geldner, N. The endodermis. Annu. Rev. Plant Biol. 64, 531–558 (2013). Article  CAS  PubMed  Google Scholar  Calvo-Polanco, M….

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sequence alignment – I can’t make mafft run inside my program

This is easy because MAFFT is installed via Conda, but you have not activated that Conda environment, thus it will not give you access to the program. If you type … conda activate labinf mafft This will now work. To activate this inside a shell script you simply include the…

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Single-cell transcriptomics reveals the brain evolution of web-building spiders

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

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Catalytically inactive long prokaryotic Argonaute systems employ distinct effectors to confer immunity via abortive infection

Bacterial strains and phages Escherichia coli DH5a was routinely grown in Lysogeny broth (LB) medium and used for plasmid cloning, while E. coli BL21 (DE3) was used for protein production and the in vivo assays. E. coli phages T5, T7 and Lambda-vir are gifts from Shi Chen lab (Wuhan University,…

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Dryad | Data — MtDNA genomes from Ranis individuals aligned with previously published ancient & modern humans

The Middle to Upper Palaeolithic transition in Europe is associated with the regional disappearance of Neanderthals and the spread of Homo sapiens. Archaeological evidence indicates the presence of technocomplexes at the interface of this transition, complicating our understanding of the period and the association of those with specific hominin groups….

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Inferring bacterial transmission dynamics using deep sequencing genomic surveillance data

Study design Experiments were performed in accordance with the New Zealand Animal Welfare Act (1999) and institutional guidelines provided by the University of Auckland Animal Ethics Committee, which reviewed and approved these experiments under application R1003. We did not use any specific randomisation process to allocate animals to a particular…

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Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand

Hayes, E. B. Zika virus outside Africa. Emerg. Infect. Dis. 15(9), 1347–1350. doi.org/10.3201/eid1509.090442 (2009). Article  PubMed  PubMed Central  Google Scholar  Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20th century. PLoS Negl. Trop. Dis. 8(1), e2636. doi.org/10.1371/journal.pntd.0002636 (2014). Article  CAS  PubMed  PubMed Central  Google…

Continue Reading Genetic diversity and phylogenetic analyses of Asian lineage Zika virus whole genome sequences derived from Culex quinquefasciatus mosquitoes and urine of patients during the 2020 epidemic in Thailand

Mycobacterium tuberculosis Sub Lineage 4.2.2/SIT149 as DR

Introduction Antimicrobial resistance is a hidden global pandemic that shattered over 4.9 million people in 2019 alone, and the burden is highest, mainly in low-resource settings.1 Drug-resistant tuberculosis (DR-TB) caused by Mycobacterium tuberculosis (Mtb) complex (MTBC), which is resistant to one or more anti-TB drugs, is a leading global public…

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Invasive Californian death caps develop mushrooms unisexually and bisexually

Mushroom collecting Sporocarps were collected from various herbaria and during three expeditions to Point Reyes National Seashore (PRNS), California in 2004, 2014 and 2015, and in 2015 from three sites in Portugal. A total of 86 sporocarps were collected: 67 Californian sporocarps (one early herbarium sample dates to 1993), 11…

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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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Common loss of far-red light photoacclimation in cyanobacteria from hot and cold deserts: a case study in the Chroococcidiopsidales

Quesada A, Vincent WF. Strategies of adaptation by antarctic cyanobacteria to ultraviolet radiation. Eur J Phycol. 1997;32:335–42. Article  Google Scholar  Genuário DB, Corrêa DM, Komárek J, Fiore MF. Characterization of freshwater benthic biofilm-forming Hydrocoryne (Cyanobacteria) isolates from Antarctica. J Phycol. 2013;49:1142–53. Article  PubMed  Google Scholar  Makhalanyane TP, Valverde A, Gunnigle…

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How To Install mafft on Debian 10

Learn how to install mafft on Debian 10 with this tutorial. mafft is Multiple alignment program for amino acid or nucleotide sequences Introduction In this tutorial we learn how to install mafft on Debian 10. What is mafft mafft is: MAFFT is a multiple sequence alignment program which offers three…

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Plastid-localized xanthorhodopsin increases diatom biomass and ecosystem productivity in iron-limited surface oceans

Protein sequence and prediction analysis The amino acid sequence of FcR was deduced from the F. cylindrus genome sequence33. Protein alignments with characterized microbial rhodopsins were performed using the MUSCLE algorithm implemented in Geneious (v.5.6)69. Predictions of subcellular location were performed with SignalP v.4.0 and TargetP (v.1.1)70. Putative transmembrane domains…

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Index of /~psgendb/birchhomedir/local/pkg/ugene/data/cmdline

Name Last modified Size Description Parent Directory   –   align-clustalo.uwl 2019-09-24 01:05 3.0K   align-clustalw.uwl 2019-09-24 01:05 5.1K   align-kalign.uwl 2019-09-24 01:05 2.8K   align-mafft.uwl 2019-09-24 01:05 2.7K   align-tcoffee.uwl 2019-09-24 01:05 3.1K   align-to-reference.uwl 2019-09-24 01:05 3.1K   align.uwl 2019-09-24 01:05 2.7K   convert-msa.uwl 2019-09-24 01:05 1.4K  …

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Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

Genes coding for endo-chitinases (EC 3.2.1.14), the enzymes that cleave chitin polymers into oligomers [16], were found on 32 of 42 Endozoicomonadaceae genomes (Fig. 1 and Table S1), including representatives of all formally described genera and all Candidatus Gorgonimonas MAGs. Several genomes harbored more than one endo-chitinase encoding gene, resulting in…

Continue Reading Widespread occurrence of chitinase-encoding genes suggests the Endozoicomonadaceae family as a key player in chitin processing in the marine benthos

Generation of quality-controled SARS-CoV-2 variant stocks

World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at covid19.who.int/ (2023). de Vries, M. et al. A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19. J. Virol. 95, e01819-20 (2021). Article  PubMed  PubMed Central  Google Scholar  FDA. Emergency Use Authorization (Eua) of…

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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,…

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Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Anderson, P. K. et al. Emerging infectious diseases of plants: Pathogen pollution, climate change and agrotechnology drivers. Trends Ecol. Evol. 19, 535–544. doi.org/10.1016/j.tree.2004.07.021 (2004). Article  PubMed  Google Scholar  Fisher, M. C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). Article  ADS  CAS  PubMed …

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Phylogenomics reveals the history of host use in mosquitoes

Taxon sampling and specimen collection All samples were collected legally following local requirements and our research complies with all relevant ethical regulations. Insect specimens were received at NC State University’s Insect Museum, pursuant to CITES permit 08US827653 (GRSCICOLL URI: grbio.org/cool/ij62-iybb). Our dataset contains representatives of 268 species from nine tribes,…

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Permission error-hoc – User Support

kulandai1 (Balamurugan) October 5, 2023, 9:21am 1 HiI am running qiime in hpc with pbs script, I got error as Traceback (most recent call last):File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/q2cli/commands.py”, line 473, in callresults = action(**arguments)File “”, line 2, in align_to_tree_mafft_fasttreeFile “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/action.py”, line 411, in parsl_wrappersetup_parallel()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”, line 69, in setup_parallelconfig_fp = _get_vendored_config()File “/home/dell_emc/easybuild/software/QIIME2/2023.5/lib/python3.8/site-packages/qiime2/sdk/parallel_config.py”,…

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Transposon-encoded nucleases use guide RNAs to promote their selfish spread

Siguier, P., Gourbeyre, E., Varani, A., Ton-Hoang, B. & Chandler, M. Everyman’s guide to bacterial insertion sequences. Microbiol. Spectr. 3, MDNA3-0030-2014 (2015). Article  PubMed  Google Scholar  He, S. et al. The IS200/IS605 family and “peel and paste” single-strand transposition mechanism. Microbiol. Spectr. 3, MDNA3-0039-2014 (2015). Article  ADS  Google Scholar  Kapitonov,…

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Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago

Nutman, P. S. Centenary lecture. Phil. Trans. R. Soc. B 317, 69–106 (1987). Google Scholar  Kelly, S., Radutoiu, S. & Stougaard, J. Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr. Opin. Plant Biol. 39, 152–158 (2017). Article  CAS  PubMed  Google Scholar  Roy, S. et al. Celebrating 20 years of…

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Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast

Rubin, S., Parr, T., Da Costa, L. & Friston, K. Future climates: Markov blankets and active inference in the biosphere. J. R. Soc. Interface 17, 20200503 (2020). Article  CAS  PubMed  PubMed Central  Google Scholar  Cantonati, M. et al. Characteristics, main impacts, and stewardship of natural and artificial freshwater environments: Consequences…

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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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Characterization and organelle genome sequencing of Pyropia species from Myanmar

Yang, L. E. et al. Redefining Pyropia (Bangiales, Rhodophyta): Four new genera, resurrection of Porphyrella and description of Calidia pseudolobata sp. Nov. from China. J. Phycol. 56, 862–879 (2020). Article  CAS  PubMed  Google Scholar  Mumford Jr, T. F. Porphyra as Food: Cultivation and Economics in Algae and Human Affairs (ed….

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Polish gulls harbor new coronavirus strains, spotlighting avian role in viral evolution

In a recent article published in the journal Scientific Reports, researchers characterize five strains of gammacoronaviruses (gCoV) and deltacoronaviruses (dCoV) that were detected in black-headed gulls (Chroicocephalus ridibundus) and common gulls (Larus canus) in Poland. Study: Gulls as a host for both gamma and deltacoronaviruses. Image Credit: Nataliya Dorokhina / Shutterstock.com Background The Orthocoronavirinae subfamily consists…

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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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Error: Alpha rarefaction curve after merging the data of two different runs – Technical Support

Hi!I am facing a problem in alpha rarefaction curve plotting. In this study my samples were sequenced in two different runs “under same conditions” using Illumina Platform- MiSeq. For that reason I have merged the data from both the runs using same filtering parameters and following DADA2. Till “phylogeny align-to-tree-mafft-fasttree”…

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Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae

Brocks, J. J. et al. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578–581 (2017). Article  ADS  CAS  PubMed  Google Scholar  Leliaert, F. Green algae: Chlorophyta and Streptophyta. In Encyclopedia of microbiology 457–468 (Academic Press, 2019). Zhang, Z. et al. Origin and evolution of…

Continue Reading Phylotranscriptomics unveil a Paleoproterozoic-Mesoproterozoic origin and deep relationships of the Viridiplantae

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

Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing | BMC Infectious Diseases

Mboowa G, Sserwadda I, Bulafu D, Chaplain D, Wewedru I, Seni J, et al. Transmission Dynamics of Antimicrobial Resistance at a National Referral Hospital in Uganda. Am J Trop Med Hyg. 2021;105(2):498–506. Article  CAS  PubMed  PubMed Central  Google Scholar  Rossolini GM, Arena F, Pecile P. Pollini SJCoip. Update on the…

Continue Reading Unraveling virulence determinants in extended-spectrum beta-lactamase-producing Escherichia coli from East Africa using whole-genome sequencing | BMC Infectious Diseases

Genomic and transcriptomic analysis of camptothecin producing novel fungal endophyte: Alternaria burnsii NCIM 1409

Atanasov, A. G. et al. Discovery and resupply of pharmacologically active plant-derived natural products: A review. Biotechnol. Adv. 33, 1582–1614 (2015). Article  CAS  PubMed  PubMed Central  Google Scholar  Swamy, M. K. et al. Biotechnology of camptothecin production in Nothapodytes nimmoniana, Ophiorrhiza sp. and Camptotheca acuminata. Appl. Microbiol. Biotechnol. 105, 9089–9102…

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What programs allow you to find the mutation rate of many sequences without needing to calculate by hand?

What programs allow you to find the mutation rate of many sequences without needing to calculate by hand? 0 Many methodologies require extensive calculation to determine mutation rate, but I am looking for a program (MAFFT, MEGA 11, BEAST, Arlequin, etc.) that has a feature that allows for the calculation…

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Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade

Cryan JF, O’Riordan KJ, Cowan CSM, Sandhu KV, Bastiaanssen TFS, Boehme M, et al. The microbiota-gut-brain axis. Physiol Rev. 2019;99:1877–2013. Article  CAS  PubMed  Google Scholar  Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog. 2013;5:e23. Article  Google Scholar  Collins…

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Regulation of gene editing using T-DNA concatenation

Gelvin, S. B. Integration of Agrobacterium T-DNA into the plant genome. Annu. Rev. Genet. 51, 195–217 (2017). Article  CAS  PubMed  Google Scholar  Gelvin, S. B. Plant DNA repair and Agrobacterium T-DNA integration. Int. J. Mol. Sci. doi.org/10.3390/ijms22168458 (2021). Jupe, F. et al. The complex architecture and epigenomic impact of plant…

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Course on Phylogenomics

Dear all, We are excited to announce our upcoming online course on Phylogenomics, focused on Phylogenetic Inference and Divergence-Time Estimation with Genomic Data Sets. This course aims to provide researchers with the necessary tools and techniques to harness the power of genomic data for understanding evolutionary relationships and divergence times….

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Interrogating the viral dark matter of the rumen ecosystem with a global virome database

Gregory, A. C. et al. Marine DNA viral macro-and microdiversity from pole to pole. Cell 177, 1109–1123.e1114 (2019). Article  CAS  PubMed  PubMed Central  Google Scholar  Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016). Article  CAS  PubMed  Google Scholar  Camarillo-Guerrero, L….

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Neighborhood socioeconomic status is associated with low diversity gut microbiomes and multi-drug resistant microorganism colonization

Buettgens, M., Blavin, F. & Pan, C. The affordable care act reduced income inequality in the US. Health Aff. 40, 121–129 (2021). Article  Google Scholar  Chen, E. & Miller, G. E. Socioeconomic status and health: mediating and moderating factors. Annu. Rev. Clin. Psychol. 9, 723–749 (2013). Article  PubMed  Google Scholar …

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Accelerated evolution of SARS-CoV-2 in free-ranging white-tailed deer

Sample collection Previously, we collected nasal samples from WTD in northeastern Ohio focusing on metropolitan area parks11. In the present study, we expanded geographical study area by approximately 1000-fold to target the entire state of Ohio. We collected 1522 nasal swabs from WTD across 83 of Ohio’s 88 counties from…

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Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors

Miterpáková M, Trbolová A, Hurníková Z, Balicka A, Čabanová V, Valentová D, et al. Thelazia callipaeda in Slovakia—from sporadic cases to endemic areas. Parasitol Int. 2022;87:102495. doi.org/10.1016/j.parint.2021.102495. Article  PubMed  Google Scholar  Gama A, Pires I, Canado M, Coutinho T, Lopes AP, Latrofa MS, et al. First report of Thelazia callipaeda…

Continue Reading Occurrence of Thelazia callipaeda and its vector Phortica variegata in Austria and South Tyrol, Italy, and a global comparison by phylogenetic network analysis | Parasites & Vectors

Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Porubsky, D. et al. Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders. Cell 185, 1986–2005 (2022). Article …

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Time-dependent variations in BK polyomavirus genome from kidney transplant recipients with persistent viremia

Garcia, G. G., Harden, P. & Chapman, J. The global role of kidney transplantation. Kidney Blood Press. Res. 35(5), 299–304 (2012). Article  PubMed  Google Scholar  Tonelli, M. et al. Systematic review: Kidney transplantation compared with dialysis in clinically relevant outcomes. Am. J. Transplant. 11(10), 2093–2109 (2011). Article  CAS  PubMed  Google…

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Genome mining shows that retroviruses are pervasively invading vertebrate genomes

Johnson, W. E. Origins and evolutionary consequences of ancient endogenous retroviruses. Nat. Rev. Microbiol 17, 355–370 (2019). Article  CAS  PubMed  Google Scholar  Stoye, J. P. Studies of endogenous retroviruses reveal a continuing evolutionary saga. Nat. Rev. Microbiol 10, 395–406 (2012). Article  CAS  PubMed  Google Scholar  Zheng, J., Wei, Y. &…

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Align raw Nanopore reads (amplicon, long PCR)

long PCR, 6000 bp, long indels (>100bp), multicopy gene = multiple amplicons from same PCR but only differ in indel meaning minimal substitutions: variance~1%, 2000 reads per sample, homopolymers (12bp) and tandem repeats (up to 55 fold, length 12-250bp), no reference available I want to de-noise my amplicons and generate…

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Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle

Bond PL, Hugenholtz P, Keller J, Blackall LL. Bacterial community structures of phosphate-removing and non-phosphate-removing activated sludges from sequencing batch reactors. Appl Environ Microbiol. 1995;61:1910–6. Article  CAS  PubMed  PubMed Central  Google Scholar  Wang Z, Guo F, Liu L, Zhang T. Evidence of carbon fixation pathway in a bacterium from candidate…

Continue Reading Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle

Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing | BMC Infectious Diseases

Pappas G, Papadimitriou P, Akritidis N, Christou L, Tsianos EV. The new global map of human brucellosis. Lancet Infect Dis. 2006;6(2):91–9. Article  PubMed  Google Scholar  Pappas G. The changing Brucella ecology: novel reservoirs, new threats. Int J Antimicrob Agents. 2010;36(Suppl 1):8–11. Article  Google Scholar  Wyatt HV. Lessons from the history…

Continue Reading Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing | BMC Infectious Diseases

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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Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors

Zumpt F. Myiasis in man and animals in the old world. A textbook for physicians, veterinarians and zoologists. London: Butterworth; 1965. Google Scholar  Stevens JR, Wall R. Genetic variation in populations of the blowflies Lucilia cuprina and Lucilia sericata (Diptera: Calliphoridae). Random amplified polymorphic DNA analysis and mitochondrial DNA sequences….

Continue Reading Mitochondrial genomic investigation reveals a clear association between species and genotypes of Lucilia and geographic origin in Australia | Parasites & Vectors

The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors

Cowie RH. Annotated catalogue of species of Angiostrongylus and the related genera Gallegostrongylus, Rodentocaulus and Stefanskostrongylus (Nematoda: Metastrongyloidea, Angiostrongylidae). J Helminthol. 2019;93:389–423. Article  PubMed  Google Scholar  de Almeida LR, de Souza JGR, Santos HA, Torres EJL, Vilela R, do V, Cruz OMS, et al. Angiostrongylus minasensis n. sp.: new species…

Continue Reading The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses | Parasites & Vectors

Phylogenetic tree differ between including and excluding other species bacteria within same genus

Phylogenetic tree differ between including and excluding other species bacteria within same genus 0 Hello, I am new microbiology researcher currently researching bacteria using whole genome sequencing and currently doing analysis. I intend to create bacteria phylogenetic tree using BV-BRC services. The tree was succesfully created using MAFFT program with…

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Vertical and horizontal gene transfer shaped plant colonization and biomass degradation in the fungal genus Armillaria

Baumgartner, K., Coetzee, M. P. A. & Hoffmeister, D. Secrets of the subterranean pathosystem of Armillaria: subterranean pathosystem of Armillaria. Mol. Plant Pathol. 12, 515–534 (2011). Article  PubMed  PubMed Central  Google Scholar  Heinzelmann, R. et al. Latest advances and future perspectives in Armillaria research. Can. J. Plant. Pathol. 41, 1–23…

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Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction

Simberloff, D. et al. Impacts of biological invasions: What’s what and the way forward. Trends Ecol. Evol. 28, 58–66 (2013). Article  PubMed  Google Scholar  Bellard, C., Cassey, P. & Blackburn, T. M. Alien species as a driver of recent extinctions. Biol. Lett. doi.org/10.1098/rsbl.2015.0623 (2016). Article  PubMed  PubMed Central  Google Scholar …

Continue Reading Invasion success of a Lessepsian symbiont-bearing foraminifera linked to high dispersal ability, preadaptation and suppression of sexual reproduction

Multiple sequence aligment orientation

Multiple sequence aligment orientation 1 I’m seeking assistance with aligning multiple sequences using MAFFT. I’ve encountered a challenge as some of the sequences are on the forward strand, while others are on the reverse strand. I understand that for a successful multiple sequence alignment, all sequences need to have the…

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Sample ID in feature table and meta data not in order – Other Bioinformatics Tools

A. I got this error (below) for this code physeq <- qza_to_phyloseq( features = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/dada2_table_16S.qza”, tree = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/phylogeny-align-to-tree-mafft-fasttree/rooted_tree.qza”, taxonomy = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/taxonomy.qza”, metadata = “/Users/parikramasapkota/Desktop/CedricWind/durp_unpooled_rhizosphere/metadata16S.tsv” )Error in validObject(.Object) : invalid class “phyloseq” object:Component sample names do not match.Try sample_names() As I was trying to look into detail, this was the error,…

Continue Reading Sample ID in feature table and meta data not in order – Other Bioinformatics Tools

Enzyme stabilization and thermotolerance function of the intrinsically disordered LEA2 proteins from date palm

Hernández-Sánchez, et al. LEAfing through literature: Late embryogenesis abundant proteins coming of age-achievements and perspectives. J. Exp. Bot. 73, 6525–6546 (2020). Article  Google Scholar  Graether, S. P. Proteins involved in plant dehydration protection: The late embryogenesis abundant family. Biomolecules 12, 1380 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Dure,…

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Plugin error from phylogeny: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’ returned non-zero exit status 1. – Technical Support

Hello, I am experiencing the following error (below) when running the following command (below). I tried this command on multiple cloud instances with high specs, and I have tried running the artifact on the latest version of QIIME 2 after initially trying this on version QIIME2_2019.10. I even tried filtering…

Continue Reading Plugin error from phylogeny: Command ‘[‘mafft’, ‘–preservecase’, ‘–inputorder’, ‘–thread’, ‘1’ returned non-zero exit status 1. – Technical Support

Increased interregional virus exchange and nucleotide diversity outline the expansion of chikungunya virus in Brazil

Mourad, O., Makhani, L. & Chen, L. H. Chikungunya: an emerging public health concern. Curr. Infect. Dis. Rep. 24, 217–228 (2022). Article  PubMed  PubMed Central  Google Scholar  Chala, B. & Hamde, F. Emerging and re-emerging vector-borne infectious diseases and the challenges for control: a review. Front. Public Health 9, 715759…

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CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don)

Christenhusz, M. J. M. et al. A new classification and linear sequence of extant gymnosperms. Phytotaxa 19, 55–70 (2011). Article  Google Scholar  Forestry Agency. Statistical Handbook of Forest and Forestry. (Japan Forest Foundation, 2017) (in Japanese). Forestry Agency. Annual Report on Forest and Forestry in Japan. Fiscal Year 2018 (Summary)….

Continue Reading CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don)

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

Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs

Floudas, D. et al. The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science 336, 1715–1719 (2012). Article  ADS  CAS  PubMed  Google Scholar  Bissaro, B., Várnai, A., Røhr, Å. K. & Eijsink, V. G. H. Oxidoreductases and reactive oxygen species in conversion of lignocellulosic biomass. Microbiol. Mol…

Continue Reading Insights into peculiar fungal LPMO family members holding a short C-terminal sequence reminiscent of phosphate binding motifs

A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes)

Formenti, G. et al. The era of reference genomes in conservation genomics. Trends Ecol. Evol. 37, 197–202 (2022). Article  CAS  PubMed  Google Scholar  Lee, H. et al. Third-generation sequencing and the future of genomics. bioRxiv, 048603 (2016). Irestedt, M. et al. A guide to avian museomics: Insights gained from resequencing…

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Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support

Subject: Need help with Qiime2 installation: ResolvePackageNotFound error Dear Qiime2 Community, I hope this message finds you well. I am currently facing an issue during the installation of Qiime2 and would greatly appreciate your assistance in resolving it. During the installation process, after following the Qiime2 instructions, I encountered the…

Continue Reading Subject:[QIIME2.2023.5] Need help with Qiime2 installation: ResolvePackageNotFound error – Technical Support

The genome of the glasshouse plant noble rhubarb (Rheum nobile) provides a window into alpine adaptation

Billings, W. Adaptations and origins of alpine plants. Arct. Alp. Res. 6, 129–142 (1974). Article  Google Scholar  Agakhanjanz, O. & Breckle, W. Origin and evolution of the mountain flora in middle Asia and neighbouring mountain regions. in Arctic and Apine Biodiversity: Patterns, Causes and Ecosystem Consequences (eds. Chapin, F. &…

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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

Is it possible to get a pairwise distance matrix from a mafft alignment?

Is it possible to get a pairwise distance matrix from a mafft alignment? 1 I’ve googled around a bit. From reading the publications and software documentation, its clear that there is a distance matrix being used but it doesnt seem possible to obtain. There is rumor of a –distout flag…

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Mitochondrial DNA is a target of HBV integration

Patients Tumour tissues from seven HBsAg-positive patients (6 men, 1 woman; mean age 66.7 ± 8 years) with HBV-related HCC and paired adjacent non-tumour tissues from six of them were studied. The clinical, histological, and virologic characteristics of the patients are summarised in Table 1. Two normal liver samples from HBV-negative patients who…

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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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Evolutionary mining and functional characterization of TnpB nucleases identify efficient miniature genome editors

Cong, L. et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339, 819–823 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823–826 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Zetsche, B. et al. Cpf1 is a single…

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BTN3A3 evasion promotes the zoonotic potential of influenza A viruses

Lipsitch, M. et al. Viral factors in influenza pandemic risk assessment. eLife doi.org/10.7554/eLife.18491 (2016). Afrache, H., Gouret, P., Ainouche, S., Pontarotti, P. & Olive, D. The butyrophilin (BTN) gene family: from milk fat to the regulation of the immune response. Immunogenetics 64, 781–794 (2012). Article  CAS  PubMed  Google Scholar  Ye,…

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Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential

Sample collection Sampling kits were sent out to various bat rehabilitators in the UK, as described previously56, for the collection of faeces from bats. These faecal samples (0.02–1 g) were immediately stored in 5 ml of RNAlater solution to prevent degradation of RNA. The geographical locations and collection dates for all samples…

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phylogenetics – Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of the codon sequences are at half length. If average is X then some sequences are X/2. This is choking IQ-Tree….

Continue Reading phylogenetics – Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

Universal whole-genome Oxford nanopore sequencing of SARS-CoV-2 using tiled amplicons

Clinical RNA SARS-CoV-2 isolate For surveillance studies, a set of residual nasopharyngeal swab specimens positive for SARS-CoV-2 qRT-PCR from the Republican Diagnostic Centre (RDC) (umc.org.kz/en/) and private laboratory KDL “Olymp” (www.kdlolymp.kz/) were collected across the Republic of Kazakhstan between 2020 and 2022. 341 sequences that passed quality control are deposited…

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Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average. 0 I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine… except some of…

Continue Reading Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average.