Genomics and Phylogenetic Studies

Divergent NUMT mimicking functional coding region of the mitochondrial genome

The paper identifies a divergent NUMT in a sawfly species that mimics mitochondrial coding regions and suggests it may result from recent mitochondrial introgression.

Guide-tree bias of whole genome alignment can mislead phylogenomic analyses

The paper shows guide-tree bias in whole-genome alignment can mislead phylogenomic analyses and proposes a consensus alignment strategy to reduce this bias.

Transcript quantification using context-aware MAPQ modeling

CALMeR improves transcript quantification by context-aware MAPQ modeling, recovering more spike-in transcripts and better matching known concentrations.

Twenty-five new microsporidian genomes: Insights into ploidy, reproduction, and the group's pangenome

The paper presents 25 new microsporidian genomes, revealing extreme pangenome diversity and novel tetraploid structures in some species.

DGM Is Dead; Long Live DGM-Star! A Quantization-Theoretic Approach to Gamma Rate Discretization

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

Complete genome sequence and metabolic features of Vreelandella zhaodongensis BS253: A new isolate from hypersaline lakes from Brazilian Pantanal

This paper reports the complete genome sequence and metabolic features of a new extremophile isolate, Vreelandella zhaodongensis BS253, from a hypersaline lake, highlighting its potential for biotechnological applications in carbon capture and sustainable processes.