Genome evolution in plants and the origins of innovation

JW Clark - New Phytologist, 2023 - Wiley Online Library
Plant evolution has been characterised by a series of major novelties in their vegetative and
reproductive traits that have led to greater complexity. Underpinning this diversification has …

Reconstructing the last common ancestor of all eukaryotes

TA Richards, L Eme, JM Archibald, G Leonard… - PLoS …, 2024 - journals.plos.org
Understanding the origin of eukaryotic cells is one of the most difficult problems in all of
biology. A key challenge relevant to the question of eukaryogenesis is reconstructing the …

A transcriptomic hourglass in brown algae

JS Lotharukpong, M Zheng, R Luthringer, D Liesner… - Nature, 2024 - nature.com
Complex multicellularity has emerged independently across a few eukaryotic lineages and
is often associated with the rise of elaborate, tightly coordinated developmental processes …

Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution

GE Larue, SW Roy - Nucleic Acids Research, 2023 - academic.oup.com
Spliceosomal introns are gene segments removed from RNA transcripts by
ribonucleoprotein machineries called spliceosomes. In some eukaryotes a second …

pLM-BLAST: distant homology detection based on direct comparison of sequence representations from protein language models

K Kaminski, J Ludwiczak, K Pawlicki, V Alva… - …, 2023 - academic.oup.com
Motivation The detection of homology through sequence comparison is a typical first step in
the study of protein function and evolution. In this work, we explore the applicability of …

Single-cell atlases of two lophotrochozoan larvae highlight their complex evolutionary histories

L Piovani, DJ Leite, LA Yañez Guerra, F Simpson… - Science …, 2023 - science.org
Pelagic larval stages are widespread across animals, yet it is unclear whether larvae were
present in the last common ancestor of animals or whether they evolved multiple times due …

A highly contiguous genome assembly reveals sources of genomic novelty in the symbiotic fungus Rhizophagus irregularis

BF Manley, JS Lotharukpong… - G3: Genes …, 2023 - academic.oup.com
The root systems of most plant species are aided by the soil-foraging capacities of symbiotic
arbuscular mycorrhizal (AM) fungi of the Glomeromycotina subphylum. Despite recent …

De Novo Emerged Gene Search in Eukaryotes with DENSE

P Roginski, A Grandchamp, C Quignot… - Genome Biology and …, 2024 - academic.oup.com
The discovery of de novo emerged genes, originating from previously noncoding DNA
regions, challenges traditional views of species evolution. Indeed, the hypothesis of …

The brittle star genome illuminates the genetic basis of animal appendage regeneration

E Parey, O Ortega-Martinez, J Delroisse… - Nature Ecology & …, 2024 - nature.com
Species within nearly all extant animal lineages are capable of regenerating body parts.
However, it remains unclear whether the gene expression programme controlling …

Evolutionary assembly of the plant terrestrialization toolkit from protein domains

A Dhabalia Ashok, S de Vries, T Darienko… - …, 2024 - royalsocietypublishing.org
Land plants (embryophytes) came about in a momentous evolutionary singularity: plant
terrestrialization. This event marks not only the conquest of land by plants but also the …