Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115635118. doi: 10.1073/pnas.2115635118. NO ABSTRACT PMID:35042800 | DOI:10.1073/pnas.2115635118
January 2022 archive
Jan 19
Why sequence all eukaryotes?
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115636118. doi: 10.1073/pnas.2115636118. ABSTRACT Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How have these innovations come about and what constraints are there …
Jan 19
Standards recommendations for the Earth BioGenome Project
Proc Natl Acad Sci U S A. 2022 Jan 25;119(4):e2115639118. doi: 10.1073/pnas.2115639118. ABSTRACT A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer …
Jan 18
Microbiome differential abundance methods produce different results across 38 datasets
Nat Commun. 2022 Jan 17;13(1):342. doi: 10.1038/s41467-022-28034-z. ABSTRACT Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. …
Jan 17
First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)
Dinoflagellates are a large group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in…
Jan 17
First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae)
Dinoflagellates are a large group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in…
Jan 15
Unveiling the genomic structures and evolutionary events of the saxitoxin biosynthetic gene sxtA in the marine toxic dinoflagellate Alexandrium
Marine dinoflagellates Alexandriumare known to produce saxitoxin (STX) and cause paralytic shellfish poisoning (PSP) which can result in mortality in human. SxtA is considered a core gene for the biosynthesis of STX. However, its gene coding structure and evolutionary history have yet to be fully elucidated. Here, we determined the full-length sequences of sxtA cDNA and genomic coding regions from two toxic dinoflagellates, Alexandrium catenella (LIMS-PS-2645 and LIMS-PS-2647) andA. pacificum…
Jan 14
Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional…
Jan 14
Site-and-branch-heterogeneous analyses of an expanded dataset favour mitochondria as sister to known Alphaproteobacteria
Determining the phylogenetic origin of mitochondria is key to understanding the ancestral mitochondrial symbiosis and its role in eukaryogenesis. However, the precise evolutionary relationship between mitochondria and their closest bacterial relatives remains hotly debated. The reasons include pervasive phylogenetic artefacts as well as limited protein and taxon sampling. Here we developed a new model of protein evolution that accommodates both across-site and across-branch compositional…
Jan 13
Microbiota of Crassostrea virginica larvae during a hatchery crash and under normal production: Amplicon sequence data
Data Brief. 2021 Dec 23;40:107755. doi: 10.1016/j.dib.2021.107755. eCollection 2022 Feb. ABSTRACT We present oyster larval microbiota from two feeding studies, in which wild type and low-salinity tolerant lines were either fed or starved. In one study, all larvae unexpectedly died, which was concurrent with an event in which all larvae in an adjoining oyster hatchery …
- 1
- 2
Recent Comments