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Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastro
Microorganisms play crucial roles in water recycling, pollution removal and resource recovery in the wastewater industry. The structure of these microbial communities is increasingly understood based on 16S rRNA amplicon sequencing data. However, such da
Methane (CH4) has a strong global warming potential and the process by which it is produced (methanogenesis) is a key process underlying climate change [1]. Methanogenesis is largely constrained to a group of anaerobic methanogenic archaea that belong to the archaeal phylum Euryarchaeota, while sev...
We also generated NCBI taxonomy annotations for each species-level genome on the basis of its placement in the GTDB tree, using the ‘gtdb_to_ncbi_majority_vote.py’ script available in the GTDB-Tk repository (https://github.com/Ecogenomics/GTDBTk/). Maximum-likelihood trees were generated ...
The lamins are the major architectural proteins of the animal cell nucleus. Lamins line the inside of the nuclear membrane, where they provide a platform for the binding of proteins and chromatin and confer mechanical stability. They have been implicated
In some of our groups, the phylogenetic trees could not be fully resolved. This could be due to either very similar or very distant sequences. In both cases the phylogenetic signal is too weak to resolve the tree [29]. Several receptors (for example, TM7SF1, DUFF, GPR, GPRM, GPR75...
All trees recovered five basic clades corresponding to the subgroups 1–5. The results indicate that pARTs of subgroups 1 and 2 are more closely related (sistergroups) to one another than to members of the other subgroups. A similar relationship is seen for pARTs of subgroups 3 and 4. Note...
The former tree is corroborated by a recent phylotranscriptomic analysis of 1,090 viri- diplant species in which the placement of three Palmophyllophyceae was unstable in ASTRAL trees but resolved as the basal divergence of Viridiplantae in concatenated trees29. Previous plastome phylog- enies ...
a maximum-likelihood phylogenetic tree was constructed for each single-copy orthogroup. We then used ASTRAL to combine all single-copy gene trees into a species tree with the multi-species coalescent model. Finally, we compared and summarized phylogenetic trees using different methods or different da...