Tag: Phylum

Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

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Continue Reading Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

Significance The DPANN superphylum is a grouping of symbiotic microorganisms categorized based on their genomic contents and a few examples of cultivation experiments. Although the genome information of DPANN archaea is increasing year by year, most of them have remained uncultivated, limiting our knowledge of these organisms. Herein, a thermoacidophilic…

Continue Reading Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses

combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

This is to the part of the question “replace actual sequences with OTU ids (Phyloseq/dada2)?” I contacted the phyloseq/dada2 developers and based on Susan Holmes’ reply (github.com/joey711/phyloseq/issues/1030) I came up with this piece of code to replace the amplicon sequences with a numbered OTU header. Further discussion can be found…

Continue Reading combine OTU and tax table and replace actual sequences with OTU ids (Phyloseq/dada2)

Network plot using NetCoMi and igraph

Hi, I am trying to plot the Network plot as suggested here (github.com/stefpeschel/NetCoMi#single-association-network-on-genus-level) by using igraph and NetCoMi. But I am not getting the network plot as expected- I just want to label the hub genera and phyla. and want the network plot in spherical layout. # Agglomerate to genus…

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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…

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

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…

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