Genomics and Phylogenetic Studies

PREMISE: Tulips are one of the best-known geophytes, but their taxonomy remains convoluted and their evolutionary history poorly understood. Here, we used plastid genomes to identify some issues with current classification, understand the diversification history of the genus, and identify potential species linked to h…

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The genus Silene (Caryophyllaceae) is one of the most species-rich groups in Türkiye, with 180 recognized taxa, 63 of which are endemic. Despite their ecological and conservation importance, the phylogenetic relationships of many endemic and threatened taxa remain unresolved. Here, we investigated twelve Turkish Silen…

ABSTRACT Accurate multiple sequence alignment (MSA) is central to understanding protein evolution, structure, and function. We present BioMatics 1.0, a novel MSA algorithm that applies optimal transport principles through the Wasserstein first‐order distance function to align amino acid distributions across positions,…

This technical report, developed under the scope of the Biodiversa+ WOLFNESS project (WP3, Comparative population genomics), details the generation and quality assessment of whole-genome sequencing data from 108 canids, including 105 wolves and recently admixed wolf-dog individuals, and three domestic dogs. The datase…

This technical report, developed under the scope of the Biodiversa+ WOLFNESS project (WP3, Comparative population genomics), details the generation and quality assessment of whole-genome sequencing data from 108 canids, including 105 wolves and recently admixed wolf-dog individuals, and three domestic dogs. The datase…

Abstract Pangenomics quantifies the conserved and variable gene repertoire among genomes, but popular implementations ignore gene synteny. Graph-based approaches incorporate both gene homology and synteny, but become difficult to interpret due to pervasive rearrangements. Here we present network-pruning and graph-layo…

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This article formally describes Craticula vanensis sp. nov., a new species of diatom from Lake Van, the largest soda lake in the world, and the fifth new species identified in the lake following an 81-years gap in investigations. A genomic approach based on short reads allowed the complete cluster of nuclear rRNA gene…

BACKGROUND: Ajuga is currently known to include approximately 69 species, with a combined distribution extending throughout Eurasia, Africa, and Australia. Its popularity and significance are largely based on an extensive history of medicinal and horticultural use. It is divided into two sections based on morphologica…

Abstract Hypericum (Hypericaceae) is a large genus of flowering plants that contains approximately 500 species. In China, Hypericum is comprised of 13 sections, 76 species, and 9 subspecies, with at least 30 species that are used in traditional Chinese medicine. Despite its medicinal importance, only a few studies hav…

Hypericum is the largest genus in Hypericaceae and is widely recognized for its medicinal importance. To investigate the evolutionary dynamics of the genus, we assembled and annotated the first mitochondrial genomes of H. ascyron (411,519 bp) and H. perforatum (485,128 bp). Both genomes were recovered as circular stru…