RedToL: Phylogenetic and Genomic Approaches to Reconstructing the Red Algal Tree of Life

Background

Rhodophyta (red algae) is one of the most ancient and successful eukaryotic phyla with fossil evidence stretching back 1.2 billion years. Red algae are not only key members of aquatic environments but they are sources for important human foods such as dulse and sushi wrap and have a multitude of pharmaceutical and industrial uses (e.g., agarose and carrageenans). Perhaps most importantly is the role red algae played in the evolution of our planet through secondary endosymbiosis. A red alga was the ancient (>1 billion years ago) donor of the plastid in chlorophyll−c containing algae (chromalveolates) that rose to prominence in marine ecosystems after the end Permian with groups such as diatoms currently providing ca. 20% of global fixed carbon. In spite of its obvious importance, the Rhodophyta is under−studied and missing from the Assembling the Tree of Life (AToL) portfolio.

Here, we aim to correct this omission to ultimately achieve Charles Darwin´s dream of a "very fairly true genealogical trees of each great kingdom of Nature".

Specific Aims

To accomplish the aims of RedToL, we propose to do the following:

1. Reconstruct a robust phylogeny of 471 red algal species using a concatenated dataset of two nuclear, four plastid and two mitochondrial encoded gene markers.

2. Sequence plastid genomes and generate transcriptome databases for 16 key taxa that represent the phylogenetic (e.g., class− and order−level) breadth of the red algae

3. Make freely available the red algal multi−gene and genome data via release to GenBank and the project website. The 471 chosen species from 294 genera represent the diversity of ca. 6000 red algal species (i.e., ca. 35% of all red algal genera will be included, which represent all extant orders).

Expected Outcomes

The robust phylogenetic framework resulting from our study will be the basis for a comprehensive taxonomic revision of the red algae and provide the basis for interpreting key innovations during red algal evolution. Because our marker genes are shared across different AToL projects, it will provide a common framework for a future comprehensive eukaryotic tree.

Complete plastid genome and transcriptome data from 16 major red algal taxa will provide a genome inventory to facilitate understanding of red algal evolution, as well as provide the basis for phylogenetic analyses using a rich set (i.e., 100s) of vertically inherited genes. We will use the genome data specifically to test the relationships among the major classes and orders of red algae. The RedToL team includes the most prominent active national and international red algal specialists from different generations who use different methods (taxonomy vs. genomics) to enhance our understanding of red algal biology. Team members come from eight institutions including two foreign collaborators and 15 advisory board members. The proposed research is being addressed by recognized experts in the field and has the potential to revolutionize phycology/plant science and bring into question or clarify theories and perspectives about the evolution of red algae and their place in the Tree of Life (ToL).

Broader Impacts

• Student Training:

  1. Four post−doctoral researchers, two graduate students and several undergraduate students will be trained from this project.

  2. Summer Workshops on the Red Algae: Five−day workshops on the red algae are planned at the end of the first and third years at Bigelow Lab for Ocean Sciences (BLOS). All PIs and personnel from the RedToL team and external participants will be trained in the biology of red algae.

  3. Undergraduate and Graduate Education: Several undergraduate studentes will be trained through the REU program. Three international graduate students (Sung Min Boo and Gary Saunders labs) will visit BLOS for two months each summer. Students will receive significant mentoring in being a scientist and in graduate school/workforce preparation.

  4. Morgan L. Vis−Chiasson, Juan Lopez−Bautista, and Debashish Bhattacharya will integrate the RedToL project into the classes at their institutions.

• Outreach:

  1. Phytoplankton Culturing Techniques Class at BLOS: Hwan Su Yoon will present lectures to participants from around world who are actively working on algae.

  2. Café Scientifique, a lecture series to the public: BLOS is committed to promoting public engagement with science and to making science accountable to the general public during the summer tourist season. Hwan Su Yoon will present the RedToL story via this lecture series.

• Mentoring Activities for Postdoctoral Associates:

  PIs will commit to train post−doctoral associates with each having a personalized training plan. By the end of the grant, all four post−docs will be independent systematists and algal genome researchers who have experience in molecular and morphological research, high−throughput genomics as well as institutional governance. This extensive experience should better prepare the person for a future position as a faculty member or research scientist.