Unraveling the genetic basis of Rhizobium rhizogenes-mediated transformation and hairy root formation in rose using a genome-wide association study

P Rüter, T Debener, T Winkelmann - Plant Cell Reports, 2024 - Springer
Understanding genetic mechanisms of plant transformation remains crucial for
biotechnology. This is particularly relevant for roses and other woody ornamentals that …

Populating a continent: phylogenomics reveal the timing of australian frog diversification

IG Brennan, AR Lemmon, E Moriarty Lemmon… - Systematic …, 2024 - academic.oup.com
The Australian continent's size and isolation make it an ideal place for studying the
accumulation and evolution of biodiversity. Long separated from the ancient supercontinent …

PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals

S Wang, Y Di, Y Yang, B Salovska, W Li, L Hu, J Yin… - Cell Reports …, 2024 - cell.com
To support PTM proteomic analysis and annotation in different species, we developed
PTMoreR, a user-friendly tool that considers the surrounding amino acid sequences of PTM …

Australia's hidden radiation: Phylogenomics analysis reveals rapid Miocene radiation of blindsnakes

S Tiatragul, IG Brennan, ES Broady… - Molecular Phylogenetics …, 2023 - Elsevier
Snakes represent one of the most successful vertebrates groups with a global radiation of∼
4000 extant species (McDiarmid et al., 1999, Uetz et al., 2021). Recent advances in …

The Low-Copy-Number Satellite DNAs of the Model Beetle Tribolium castaneum

T Gržan, M Dombi, E Despot-Slade, D Veseljak… - Genes, 2023 - mdpi.com
The red flour beetle Tribolium castaneum is an important pest of stored agricultural products
and the first beetle whose genome was sequenced. So far, one high-copy-number and ten …

Long-read genome assembly of the insect model organism Tribolium castaneum reveals spread of satellite DNA in gene-rich regions by recurrent burst events

M Volarić, E Despot-Slade, D Veseljak… - Genome …, 2024 - genome.cshlp.org
Eukaryotic genomes are replete with satellite DNAs (satDNAs), large stretches of tandemly
repeated sequences that are mostly underrepresented in genome assemblies. Here we …

Portable BLAST-like algorithm library and its implementations for command line, Python, and R

S Schmid, A Jeevannavar, TR Julian, M Tamminen - Plos one, 2023 - journals.plos.org
Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence
analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches …

Reference-Guided De Novo Genome Assembly of the Flour Beetle Tribolium freemani

M Volarić, E Despot-Slade, D Veseljak… - International journal of …, 2022 - mdpi.com
The flour beetle Tribolium freemani is a sibling species of the model organism and important
pest Tribolium castaneum. The two species are so closely related that they can produce …

The Genome Organization of 5S rRNA Genes in the Model Organism Tribolium castaneum and Its Sibling Species Tribolium freemani

M Volarić, E Despot-Slade, D Veseljak, M Pavlek… - Genes, 2024 - mdpi.com
5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in
genome assemblies. In the present study, we performed a global and in-depth analysis of …

Phylogenetic relationships in the Eugongylini (Squamata: Scincidae): generic limits and biogeography

DG Chapple, SNJ Chapple, SA Smith… - Australian Journal of …, 2023 - CSIRO Publishing
Skinks (Family Scincidae) are the most diverse family of lizards (~ 1745 described species
worldwide), and the Australasian region (Australia, New Caledonia, New Zealand) is a …