Percy, D. | bioRxiv Science

bioRxiv2025

A haplotype-phased male genome sequence of the stinging nettle, Urtica dioica ssp. dioica

Stinging nettle (Urtica dioica L.) is a widespread weed of economic significance with a dioecious mating system. Previously, we generated a high-quality genome assembly of a diploid female plant, which showed extreme levels of structural variation between haplotypes. Here, we present a chromosome-level, haplotype-resolved sequence of a diploid male plant; since the male is believed to be the heterogametic sex in Urtica dioica, this assembly represents a first step towards elucidating the control of sex determination in this species. This completely independently assembled genome also allows confirmation of previously reported features of the nettle genome, including (1) a high degree of structural variation between haplotypes, including large inversions, (2) the likely existence of polycentric centromeres, and (3) the presence of urticaceous "pain peptide" sequences. Chromosome 8 stands out for its multiple large, nested inversions and high levels of repetitive sequences, features that are often associated with sex determining regions (SDRs). This chromosome is therefore a candidate for further investigations to characterize the sex determination in nettle.

genomics↗

bioRxiv2024

Deciphering the patterns and timing of diversification of the genus Melanastera (Hemiptera: Psylloidea: Liviidae) in the Neotropics

Even after decades of research on diversification in the Neotropics, our understanding of the evolutionary processes shaping Neotropical clades is still incomplete. In the current study, we used different divergence times and likelihood-based methods to investigate the influence of biogeography and host associations on the diversification of the most species-rich Neotropical psyllid genus Melanastera (Liviidae) using molecular phylogenetic data from seven gene fragments (four mitochondrial and three nuclear). The putatively monophyletic group of Neotropical Melanastera species has an estimated crown node age of 20.2 Ma (ML, CI 20.2-30.6) or 23.2 Ma (BI, 95% HPD 16.6-32.6), with diversification occurring mainly in the Upper Miocene, although some species groups diversified in the Pliocene and Pleistocene. Biogeographic analysis suggests that the Neotropical Melanastera originated from the Pacific region of South and Central America. We detected a shift in diversification rates that likely occurred either at the time of origin of Melanastera or during the main colonisation of the Atlantic and Amazon Forests, followed by a subsequent slowdown in speciation rates. State-dependent speciation and extinction models revealed a significant relationship between this diversification shift and the shift of Melanastera to the plant families Melastomataceae and Annonaceae, reflecting the impact of host switching on speciation rates in this group. This period also coincides with several independent dispersal events from the Atlantic and Amazon Forests to other parts of the Neotropics. Taken together, the results of the current study suggest that diversification of Melanastera was facilitated by major shifts to new host families, which may have promoted the dispersal of Melanastera into new adaptive zones with subsequent processes of local speciation.

evolutionary biology↗