Genomic and phylogenomic of groups of red algae little studied of the subclass Nemaliophycidae (Rhodophyta): orders Acrochaetiales, Balliales, Colaconematales, Corynodactylales, Entwisleales, Ottiales and Rhodachlyales

• Grant number: 24/08953-1
• Support Opportunities: Regular Research Grants
• Start date: March 01, 2025
• End date: February 29, 2028
• Field of knowledge: Biological Sciences - Botany - Plant Taxonomy
• Principal Investigator: Orlando Necchi Junior
• Grantee: Orlando Necchi Junior
• Host Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil

Abstract

The vast majority of red algae species are found in the class Florideophyceae, which contains five subclasses (Hildenbrandiophycidae, Nemaliophycidae, Corallinophycidae, Ahnfeltiophycidae and Rhodymeniophycidae). Nemaliophycidae is one of the most taxonomically diverse and represents an ideal group to study the evolution of red algae. It is the only subclass that comprises orders with exclusively continental taxa (Balbianiales, Batrachospermales, Ottales and Thoreales) or with marine and freshwater occurrence (Acrochaetiales). Recent studies have demonstrated that the four freshwater orders are relatively distant phylogenetically and only one clade that grouped some orders had high support, whereas the phylogenetic relationships between all other orders were poorly resolved. Among the twelve orders of Nemaliophycidade, five (Balbianiales, Batrachospermales, Nemaliales, Palmariales and Thoreales) are relatively well studied based on the number of genomes available in relation to the number of species in these groups. The focus of the project will be on seven orders that are still little studied or have no published genomes: Acrochaetiales, Balliales, Colaconematales, Corynodactylales, Entwisleales, Ottiales and Rhodachlyales. This project is a broad phylogenomic approach with emphasis on the five little or not yet studied orders of the Nemaliophycidade subclass based on organellar genomes (plastid and mitochondrial) involving a representative number of species for each order. The results generated will allow us to test the following hypotheses: 1) Considering that the taxonomic groups to be studied are quite diverse and relatively distant phylogenetically within the Nemaliophycidae, the comparative analysis of genomic characteristics should reveal large differences and wide variations in relation to the genomes already described for the other orders (Balbianiales, Batrachospermales, Nemaliales, Palmariales and Thoreales). 2) Phylogenomic analyzes will allow us to infer robust phylogenies between orders and elucidate currently unresolved relationships between the various clades. The phylogenetic tree obtained based on these analyzes will be robust, highlighting clades with high support and will clearly show the relationships between them. These analyzes will allow the proposition of a solid classification system for the subclass. 3) Comparative genomics and phylogenomic analyzes based on data from all orders of Nemaliophycidae will elucidate aspects of the transition from marine to continental environments of the exclusively freshwater orders (Balbianiales, Batrachospermales, Ottiales and Thoreales). The analyses will demonstrate that the emergence and subsequent radiation of these four lineages represented independent events within the evolutionary history of the subclass. To test these hypotheses, the following objectives are proposed: a) describe the characteristics of plastid and mitochondrial genomes (size, position, total number of genes and coding genes, GC content, number of introns, among others) of representative species of the orders Acrochaetiales, Balliales, Colaconematales, Corynodactylales, Entwisleales and Rhodachlyales; b) carry out phylogenomic analysis aiming to infer the phylogenetic relationships between all orders to elucidate their positioning within Nemaliophycidae; c) apply the data to raise possible explanations in the process of transition from marine to freshwater environments. The proposed project comprises aspects of great relevance, namely: i) this is the broadest and most representative genomic investigation for the subclass Nemaliophycidae; ii) will provide valuable information for phylogenomic and comparative genomic analyzes in relation to members of the other subclasses of Florideophyceae; iii) will provide a robust set of data for all orders, which will allow a general assessment of the transition from marine to freshwater environments. (AU)