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RNA sequencing (RNA-seq) is a highly sensitive method for transcriptome analysis that allows simultaneous assessment of expression of thousands of genes and identification of expression patterns under various conditions. The existing variety of RNA-seq data …
Read PDFEggplant is one of the most important vegetables worldwide, with some varieties displaying prickles. These prickles, present on the leaves, stems, and fruit calyxes, posing challenges during cultivation, harvesting, and transportation, making them an undesirable …
Read PDFMedicinal plants synthesize structurally diverse pharmacologically active natural products through conserved precursor pathways, which are further diversified by lineage-specific tailoring enzymes. Although the biosynthetic pathways of well-studied compounds (e.g., berberine, paclitaxel, and ginsenosides) have been …
Read PDFBACKGROUND: Niemann-Pick type C2 (NPC2) proteins have been proposed as soluble carriers for semiochemicals in arthropods, serving as putative functional substitutes for the canonical odorant-binding proteins (OBPs) largely absent in arachnids. However, the evolutionary mechanisms …
Read PDFLilies are popular ornamental and medicinal plants with gigantic genomes. Due to the challenge of assembling complex giga-genomes, our understanding of the genetic architecture, epigenetic regulation and evolution of large-genome plants such as lily remains …
Read PDFChronic pulmonary aspergillosis involves the formation of a fungal ball (aspergilloma) in lung cavities. Pseudomonas aeruginosa commonly co-colonizes these lesions; however, the in vivo mechanisms underlying its persistence are unknown. Using a multi-omics approach on …
Read PDF<h4>Background</h4>The protist family Trypanosomatidae includes parasites of insects, vertebrates, plants, and even other unicellular eukaryotes. The genomes of these species harbor clues to the evolution of parasitism, adaptation to new hosts, and infection of mammals. …
Read PDFXenacoelomorpha are mostly microscopic, morphologically simple worms, lacking many structures typical of other bilaterians. Xenacoelomorphs-which include three main groups, namely Acoela, Nemertodermatida, and Xenoturbella-have been proposed to be an early diverging Bilateria, sister to protostomes …
Read PDF<h4>Introduction</h4>The taxonomy of Euphorbiaceae is extremely difficult, especially the phylogeny of closely related genera. In <i>Ricinus</i>, which embraces an important non-food oil-seed crop worldwide, <i>Discocleidion</i> and <i>Speranskia</i> are closely related genera based on molecular evidence …
Read PDFPhylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights …
Read PDFBees are important global pollinators that play a vital role in maintaining ecosystems and supporting global food production. They also exhibit a diversity of social organization, making them ideal model organisms for studying the evolution …
Read PDFEukaryotic diversity is largely microbial, with macroscopic lineages (plants, animals, and fungi) nesting among a plethora of diverse protists. Our understanding of the evolutionary relationships among eukaryotes is rapidly advancing through 'omics analyses, but phylogenomic …
Read PDFThe 2025 Tutzing Workshop, held at the Evangelische Akademie on the shores of Lake Starnberg, continued a long tradition of highly integrative meetings focused on the biology and evolution of basal metazoans. The meeting was …
Read PDFAnaerobic gut fungi (AGF, <i>Neocallimastigomycota</i>) represent a phylum of zoospore-producing fungi inhabiting the gastrointestinal tracts of herbivores. Twenty mammalian-affiliated genera (M-AGF) and two tortoise-affiliated genera (T-AGF) have been described so far. Here, we report on …
Read PDF<h4>Background</h4>Cercozoa are single-celled eukaryotes (protists) and are part of the supergroup Rhizaria. Cercozoans have vastly different morphologies and are defined by their phylogenetic affinity. While the group includes some well-known and well-researched taxa, like the …
Read PDFPlant phylogenetics has been revolutionised in the genomic era, with target capture acting as the primary workhorse of most recent research in the new field of phylogenomics. Target capture (aka Hyb-Seq) allows researchers to sequence …
Read PDF<h4>Premise</h4>Advances in new next-generation sequencing (NGS) methods have revolutionized phylogenetics, yet challenges remain in effectively utilizing data from a wide range of sources. A well-resolved and broadly sampled phylogeny for Sonerileae, the second-largest tribe in …
Read PDF<h4>Premise</h4>Conflicting phylogenetic signals are common in plant phylogenomics and often reflect evolutionary histories shaped by processes like hybridization, incomplete lineage sorting, and whole-genome duplication (WGD). We aimed to identify and assess these complex processes in …
Read PDF<h4>Premise</h4>Current phylogenies of Amaranthaceae sensu stricto (s.s.) are inadequately sampled and resolved to reflect the entire evolutionary history of the lineage, which is likely complex due to at least three whole-genome duplication events, occasionally followed …
Read PDFRecent advances in high-throughput sequencing have exponentially increased the number of genomic data available for animals (Metazoa) in the last decades, with high-quality chromosome-level genomes being published almost daily. Nevertheless, generating a new genome is …
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