Reconstructing the evolutionary history of the Raveneliaceae (Basidiomycota: Pucciniales) using hyRAD sequencing, and revision of their taxonomy
Final Report Abstract
This project aimed to clarify the phylogeny and systematics of the tropical rust fungus family Raveneliaceae and to establish a protocol for analyzing historical DNA in rust fungi. The originally planned hyRAD method was replaced with the more flexible hybSeq approach for practical advantages, and the taxonomic focus was expanded to the suborder Raveneliineae. The hybSeq method was restricted to mitochondrial genes to enhance success rates, generate robust data, and achieve publishable results. A total of 56 samples from three herbaria were analyzed and complemented with fresh collections. Sequencing via Illumina MiSeq provided high-quality data, with paralogous genes identified through sequencing depth and phylogenetic analyses, and contaminants filtered using a local BLAST database. Combined phylogenetic analyses of hybSeq and PCR-based data offered novel insights into the evolution of the Raveneliineae. Although results confirmed that the Raveneliaceae do not form a monophyletic group, phylogenetic groups of yet unresolved taxonomic rank were identified by integrating many newly sequenced taxa. Initial findings led to the introduction of new genera such as Raveneliopsis and Cerradopsora and are expected to facilitate the reclassification of various taxa, including economically important species like the cotton rust (Phakopsora gossypii) and eucalyptus rust (P. myrtacearum). Morphological traits traditionally used for genus delimitation, such as teliospore form and structure, were found to be mostly phylogenetically insignificant, as even closely related species exhibited significant morphological differences. Additionally, the presence of long branch lengths in the phylogenies suggests underrepresented diversity, further complicating a comprehensive taxonomic reorganization. The hybSeq method proved to be highly robust and well-suited for analyzing historical fungal specimens, even when starting material was limited or severely degraded. Its flexibility enables targeted adaptation to specific research questions and holds great potential for exploring the diversity of historical rust fungus collections. It will help close taxonomic sampling gaps in future studies. The establishment of hybSeq complements efforts to make the immense biodiversity archived in museums and herbaria across Germany and worldwide more accessible. Many of these collections, often centuries old, include species that are extinct or otherwise difficult to access today. Focusing on plant-parasitic fungi, for example, opens avenues to study evolutionary mechanisms and adaptation processes over time. Such research could contribute to addressing challenges in agriculture, forestry, and biodiversity conservation in the face of climate change.
Publications
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Cerradopsora , a new genus of neotropical rust fungi. Mycologia, 115(6), 802-812.
Ebinghaus, Malte; Martins, João M. T.; Dos Santos, Maria D. M.; Tonelli, Guilherme S. S. S.; Macagnan, Dirceu; Pinho, Danilo B. & Dianese, Jose C.
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Raveneliopsis , a new genus of ravenelioid rust fungi on Cenostigma (Caesalpinioideae) from the Brazilian Cerrado and Caatinga. Mycologia, 115(2), 263-276.
Ebinghaus, Malte; dos Santos, Maria D. M.; Tonelli, Guilherme S. S. S.; Macagnan, Dirceu; Carvalho, Eudes Arruda & Dianese, Jose C.
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Establishing the HybSeq approach for historic specimens of rust fungi - A case study on the tropical Raveneliineae. Post IMC 12
Ebinghaus M., Duong T., Ono Y., Martins J.M.T., dos Santos M.D.M., Pinho D.B., Wood A., Rajchenberg M. & Dianese J.C.
