BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

L Gabriel, T Brůna, KJ Hoff, M Ebel… - Genome …, 2024 - genome.cshlp.org
Gene prediction has remained an active area of bioinformatics research for a long time. Still,
gene prediction in large eukaryotic genomes presents a challenge that must be addressed …

Northern light reviews–Application of orthology and network biology to infer gene functions in non‐model plants

K Vandepoele, S Thierens, M Van Bel - Physiologia Plantarum, 2024 - Wiley Online Library
Approximately 60% of the genes and gene products in the model species Arabidopsis
thaliana have been functionally characterized. In non‐model plant species, the functional …

Tiberius: end-to-end deep learning with an HMM for gene prediction

L Gabriel, F Becker, KJ Hoff, M Stanke - Bioinformatics, 2024 - academic.oup.com
Motivation For more than 25 years, learning-based eukaryotic gene predictors were driven
by hidden Markov models (HMMs), which were directly inputted a DNA sequence. Recently …

Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization

C Gardner, J Chen, C Hadfield, Z Lu… - Genome …, 2024 - genome.cshlp.org
Interspecies hybridization is prevalent in various eukaryotic lineages and plays important
roles in phenotypic diversification, adaptation, and speciation. To better understand the …

New insights into the phylogeny of Neogastropoda aided by draft genome sequencing of a volutid snail

H Wang, X He, C Chen, K Gao, Y Dai… - Zoologica Scripta, 2024 - Wiley Online Library
Neogastropoda is a large order of predominantly marine gastropod molluscs, typically
predatory or parasitic on other animals. It includes over 16,000 species representing a large …

Chromosome-level subgenome-aware de novo assembly of Saccharomyces bayanus provides insight into genome divergence after hybridization

C Gardner, J Chen, C Hadfield, Z Lu… - Genome …, 2024 - genome.cshlp.org
Interspecies hybridization is prevalent in various eukaryotic lineages and plays important
roles in phenotypic diversification, adaptation, and speciation. To better understand the …

Chromosome-level genome assembly of the sacoglossan sea slug Elysia timida (Risso, 1818)

L Männer, T Schell, J Spies, C Galià-Camps… - BMC genomics, 2024 - Springer
Background Sequencing and annotating genomes of non-model organisms helps to
understand genome architecture, the genetic processes underlying species traits, and how …

Newly sequenced genomes reveal patterns of gene family expansion in select Dragonflies (Odonata: Anisoptera)

ER Tolman, CD Beatty, PB Frandsen, J Bush… - bioRxiv, 2023 - biorxiv.org
As in many other lineages, the dragonflies, or anisoptera (Insecta: Odonata), contain a
myriad of life history and diversification patterns. Two families within anisoptera highlight the …

The genomes of Dahlia pinnata, Cosmos bipinnatus, and Bidens alba in tribe Coreopsideae provide insights into polyploid evolution and inulin biosynthesis

H Wang, D Xu, F Jiang, S Wang, A Wang, H Liu… - …, 2024 - academic.oup.com
Abstract Background The Coreopsideae tribe, a subset of the Asteraceae family,
encompasses economically vital genera like Dahlia, Cosmos, and Bidens, which are widely …

A chromosome-scale genome assembly of the pioneer plant Stylosanthes angustifolia: insights into genome evolution and drought adaptation

C Liu, J Zhang, R Xu, J Lv, Z Qiao, M Bai, S Zhao… - …, 2025 - academic.oup.com
Background Drought is a major limiting factor for plant survival and crop productivity.
Stylosanthes angustifolia, a pioneer plant, exhibits remarkable drought tolerance, yet the …