The colonization of low-light environments exerts selective pressure to enhance non-visual senses while relaxing selection on vision, often leading to opsi

A place for bioinformatics software that has been abandoned - Bioinformatics Orphanage

At Davos, Canadian Prime Minister Mark Carney set fire to liberal platitudes. His actual politics, however, do quite the opposite.

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Archaeal extrachromosomal elements (ECEs) are arguably the least well understood of all genetic elements, and few have > 200 kbp ("jumbo") genomes. Here, we report circular, jumbo ECEs with genomes of up to 535 kbp in length that associate with anaerobic methane-oxidizing Methanoperedens archaea. Notably, a 409-kbp genome related to jumbo ECEs is integrated into a subset of the ~4.2 Mbp Methanoperedens chromosomes at the tRNA-Asp genes. This represents the largest integrative element in Archaea and supports the jumbo ECE - host association. Multiple genome alignment and phylogenetic analyses suggest that the large sizes were developed by extensive DNA acquisition from Methanoperedens. The newly identified ECEs encode, and in some cases express, metabolic genes such as tetrahydromethanopterin S-methyltransferase exclusively involved in methane oxidation, and genes for nitrogen and sulfur compound transformations. Also encoded are defense systems, some of which are absent in hosts, such as hybrid Type I/Type III-A CRISPR-Cas systems. In contrast to viruses and plasmids, they have host-like replication machinery and occur at stable copy ratios of 1.44 ± 0.24 : 1 to the host. Overall, our results reveal a spectrum of jumbo ECEs of Methanoperedens, ranging from plasmid-like to minichromosome-like. ### Competing Interest Statement J.F.B. is a co-founder of Metagenomi. The remaining authors declare no competing interests. Emerson Collective (United States)

Abstract. Polyploidization has been recognized as a major force in plant evolution. With the continuous progress in sequencing technologies and genome asse

Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

TnPedia provides a curated framework for understanding prokaryotic transposable elements (TEs), including general and historical information and basic concepts, while integrating mechanistic insights,...

Eukaryotic genomes are ubiquitously occupied by mobile genetic elements termed transposons, which are silenced via a specialized class of small RNA called piRNA. The small RNA is produced from the transposons themselves when they occupy specialized regions of the genome termed piRNA clusters. The formation of these specialized regions, or their evolution over time, is not well understood. Recent work has suggested that they are extremely variable even within a single species such as Drosophila melanogaster. We were interested in taking a comparative approach to piRNA cluster evolution to ask the question - what processes are unique to D.melanogaster and which are shared? Shared phenomena are more likely to be fundamental aspects of piRNA formation and evolution compared to those that are more labile. Using five high-quality long-read genome assemblies and five genotype-specific piRNA libraries, we approach this question from a population genetics standpoint. We annotate piRNA clusters, transposons, and structural variants in each of these five genomes. We found extensive variation in piRNA clusters across strains, with smaller piRNA clusters more likely to be limited to a single genotype. By and large, our results are consistent with a model of piRNA cluster evolution in which piRNA clusters are rapidly formed and lost, with a small subset increasing in frequency and length over time. However, we find that the TEs which nucleate the formation of small piRNA clusters are entirely distinct in D.simulans compared to D.melanogaster, and likely reflect its invasion history rather than any inherent property of the transposon to nucleate clusters. Therefore, while large common clusters can act as 'traps' as has been posited for piRNA clusters, there are also numerous small clusters that are born and lost rapidly within a species. ### Competing Interest Statement The authors have declared no competing interest. National Science Foundation, NSF-EPSCoR-1826834, NSF-EPSCoR-2032756 National Institutes of Health, R35GM155272