Papadopulos, A. | Search bioRxiv

bioRxiv2024

Chromosome-scale genome assembly and linkage map for Silene uniflora reveal the recombination landscape in a rapidly evolving plant species

The genus Silene is an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly for S. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination with ab initio gene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two other Silene species with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggesting Silene may be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation. Significance statementPlant species in the genus Silene (campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genus Silene and the family Caryophyllaceae more generally.

evolutionary biology↗

bioRxiv2018

Actomyosin-II facilitates long-range retrograde transport of large cargoes by controlling axonal radial contractility

Most mammalian neurons have a narrow axon, which constrains the passage of large cargoes such as autophagosomes that can be larger than the axon diameter. Radial axonal expansion must therefore occur to ensure efficient axonal trafficking. In this study we consistently find that the trafficking speed of various large axonal cargoes is significantly slower than that of small ones, and reveal that the transit of diverse-sized cargoes causes an acute, albeit transient axonal radial expansion, which is immediately restored by constitutive contractility. Using live super-resolution microscopy, we demonstrate that actomyosin-II controls axonal radial contractility and local expansion, and that NM-II filaments associate with periodic F-actin rings via their head domains. Pharmacological inhibition of NM-II activity, significantly increases axon diameter by detaching the NM-II from F-actin, and impacts the trafficking speed, directionality, and overall efficiency of long-range retrograde trafficking. Consequently, prolonged disruption of NM-II activity leads to disruption of periodic actin rings and formation of focal axonal swellings, a hallmark of axonal degeneration.\n\nSummaryAxonal radial contractility and local expansion control the retrograde trafficking of large cargoes. The periodic actomyosin-II network comprises of NM-II filaments and F-actin rings. Loss of actomyosin-II-mediated radial contractility causes defects in axonal trafficking and stability, leading to degeneration.

neuroscience↗