Utteridge, T. | bioRxiv Science

bioRxiv2025

Expanding Ventilago to incorporate Smythea: new combinations in Ventilagineae (Rhamnaceae) based on novel sequence data and phylogenetic analysis

Ventilagineae (Rhamnaceae) is a tribe of palaeotropical climbing plants, comprising two genera: Smythea and Ventilago. Previous studies have established the monophyly of the tribe, but the relationships within it remain unclear. This research includes six species of Smythea and seven species of Ventilago in a molecular phylogeny using the Angiosperms353 probe set. The results show that Ventilago is paraphyletic, with Smythea nested within it. To resolve this issue, we propose to merge Smythea into Ventilago. To achieve this, we make seven new combinations in Ventilago as well as resurrecting five names previously published in Ventilago but subsequently transferred to Smythea. In addition, we typify Ventilago.

evolutionary biology↗

bioRxiv2022

Herbarium Specimen Sequencing Allows Precise Datation of Xanthomonas citri pv. citri Diversification History

Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.

evolutionary biology↗