Revisiting the phylogeny of Melastomataceae in the era of genomics

• Applicants: Professorin Dr. Gudrun Kadereit; Dr. Marie Claire Veranso-Libalah, Ph.D.
• Subject Area: Evolution and Systematics of Plants and Fungi
• Term: since 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 441541553

Melastomataceae range among the ten most diverse angiosperm families in the world with c. 3500 New World and c. 1600 Old World species. The only family-wide molecular phylogenetic treatment by Clausing and Renner (2001), was based on Sanger sequencing using only chloroplast DNA sequences with only 54 (~1%) species included. The level of variation across these few sampled plastid markers is unsatisfactory, and even sequencing of whole cp genomes showed no deep phylogenetic insight and progress in resolving the molecular trees in melastomes. Lack of robust and resolved phylogenies and lack of phylogenomic tools in this family hampers evolutionary and ecological studies although it shows a number of highly interesting features e.g. the conspicuous predominance of buzz-pollination, various forms of ant-plant interactions, an enormous diversity of growth forms, and is an ubiquitous element of tropical vegetation which makes it an ideal group to study the evolution of tropical vegetation.Over the past few years, several genome-partitioning strategies to sequence selected subsets of the genome, have emerged as powerful tools in plant phylogenomics, resolving species relationships by making use of vast sequence data and potentially alleviating previous problems of phylogenetics that resulted from limitation of sampling few genes by expanding the number of characters and gene trees. In this project we have chosen two methods: (1) Hyb-Seq, which combines target enrichment of low-copy nuclear genes and genome skimming, the use of low-coverage shotgun sequencing to assemble high-copy genomic targets. Using the recently published angiosperm-wide probes for HybSeq together with melastome customized probes, our aim is to generate a family-wide phylogenetic tree of Melastomataceae in cooperation with our American and Brazilian colleagues, all currently working in the family. While all labs will share and use the same protocols and probe sets, our lab will concentrates on the Old World melastomes and our partners on the NW taxa. We aim to sample c. 350 species representing all OW genera, albeit with a special focus on Dissochaeteae. (2) HyRAD which improves loci coverage and allows sequencing of orthologous loci from highly degraded DNA samples, opening the possibility to use museum collections. Using a modified HyRAD-protocol we will generate long, informative loci suitable for species tree calculation at low taxonomic levels. We aim to resolve two species rich clades within Dissochaeteae, the Madagascan Medinilla (c. 70 spp.) and the South East Asian scrambling shrubs clade (ca. 98 spp.) as case studies. Both molecular tools as well as the backbone phylogeny based on genomic data will promote systematic, taxonomic studies and subsequently boost evolutionary and ecological research in the family.

• DFG Programme: Research Grants