COMPARATIVE GENOMICS REVEALS ACELERATED DIVERSIFICATION OF THE OCHROPHYTA PLASTOME FROM SECONDARY ENDOSYMBIOSIS OF A BASAL GROUP OF RHODOPHYTA

Luís Gustavo Araújo Garcia; Hiago Rodrigues Martins; Ayrton Breno Pimenta Lisboa; Paula Luize Camargos Fonseca; Luiz Eduardo Vieira Del Bem

Paper Title

Authors

Luís Gustavo Araújo Garcia
Hiago Rodrigues Martins
Ayrton Breno Pimenta Lisboa
Paula Luize Camargos Fonseca
Luiz Eduardo Vieira Del Bem

Modality

Poster

Subject area

Phylogeny and Evolution

Publishing Date

08/11/2023

Country of Publishing

Brazil | Brasil

Language of Publishing

Inglês

Paper Page

https://www.even3.com.br/anais/xmeeting2023/639525-comparative-genomics-reveals-acelerated-diversification-of-the-ochrophyta-plastome-from-secondary-endosymbiosis-o

ISBN

978-65-272-0061-1

Keywords

Chloroplasts, Evolution, Algae, Comparative Genomics

Summary

Chloroplasts are vital organelles for oxygenic photosynthesis, the fundamental process underlying life on Earth. This process generates oxygen, which supports the basic metabolism of most organisms and produces glucose, the primary food source of the food chain. Photosynthesis involves using light energy to convert carbon dioxide and water into organic molecules, releasing molecular oxygen into the atmosphere. Chloroplasts evolved from cyanobacteria through primary endosymbiosis, which gave rise to Rhodophyta (red algae) and Viridiplantae (green algae and land plants). Subsequently, Rhodophyta plastids led to the formation of Ochrophyta (brown algae) plastids through secondary endosymbiosis. While the plastome (plastid genome) has undergone severe genome reduction in all cases, discrepancies exist in its genome structure, content, and gene variation. However, the evolutionary patterns of these changes in algae plastomes are yet to be determined. Therefore the main objective is to identify the evolutionary patterns of general plastome evolution. We obtained plastome data from the NCBI database using batch entrez for all relevant organisms. We analyzed general information, such as genome size, GC content, number of coding sequences (CDS), and non-coding regions. We used violin and correlation plots for statistical analysis and visualization of the three populations (Rhodophyta, Ochrophyta, and Viridiplantae). We performed a dN/dS analysis of the photosystem genes in Rhodophyta and Ochrophyta using DNAsp. We employed OGdraw to generate plastome maps. We aligned 178 genes of the plastome, which BLAST determined to be at least 50% present in Rhodophyta, using MAFFT. We used Trimal to trim sequences and Pal2nal to translate amino acids to nucleotides. The resulting aligned sequences were concatenated with FASconCAT-G to generate a supermatrix for phylogenetic analysis using IQTree 1.6.12 with ModelFinder enabled. We identified inverted repeats (IRs) using BLAST2seq by querying the FASTA file containing the plastome DNA with itself. We used InterProScan for gene function and gene duplication analysis, categorizing the results using GO terms. Our phylogenetic analysis suggests a single event of secondary endosymbiosis gave rise to the origin of the plastid in Ochrophyta, and the common ancestor was most likely closer to the Cyanidiophyceae, an extremophile unicellular organism family in Rhodophyta. Our dN/dS analysis on the photosystem genes indicates a higher synonymous rate of change in Ochrophyta than in Rhodophyta. Our general data analysis shows difference in size, GC content, CDS number, and non-coding DNA content of Rhodophyta, Ochrophyta, and Viridiplantae. The reduction in size and CDS number in Ochrophyta presents a positive correlation, indicating that the size reduction in these organisms was driven by the loss of CDS genes. Our functional gene analysis indicates a loss of genes in Ochrophyta related to pigmentation and fatty acid biosynthesis, as well as a slight reduction in photosystem and ribosomal proteins. The IRs region of Ochrophyta is highly unstable, with differences in size and gene content between each family. In conclusion, our work shows different trends of plastome evolution, with Ochrophyta experiencing the most significant changes compared to Rhodophyta origin. Further investigation is required to observer whether this changes have a functional impact on the photosynthesis process.

Title of the Event: X-Meeting / BSB 2023
City of the Event: Curitiba
Title of the Proceedings of the event: X-Meeting presentations
Name of the Publisher: Even3
Means of Dissemination: Meio Digital

How to cite

GARCIA, Luís Gustavo Araújo et al.. COMPARATIVE GENOMICS REVEALS ACELERATED DIVERSIFICATION OF THE OCHROPHYTA PLASTOME FROM SECONDARY ENDOSYMBIOSIS OF A BASAL GROUP OF RHODOPHYTA.. In: X-Meeting presentations. Anais...Curitiba(PR) Campus da indústria, 2023. Available in: https//www.even3.com.br/anais/xmeeting2023/639525-COMPARATIVE-GENOMICS-REVEALS-ACELERATED-DIVERSIFICATION-OF-THE-OCHROPHYTA-PLASTOME-FROM-SECONDARY-ENDOSYMBIOSIS-O. Access in: 07/05/2025