Phylogenetic Analysis of a Cryptic Microscopic Red Alga

Author

Katelyn Wadland, University of Rhode IslandFollow

Date of Award

2016

Degree Type

Thesis

Degree Name

Master of Science in Biological and Environmental Sciences (MSBES)

Department

Biological Sciences

First Advisor

Christopher Lane

Abstract

Red algae demonstrate significant phenotypic plasticity and convergent evolution, making morphological species identification difficult. Microscopic members of this lineage further complicate identification by their limited number of morphological features. An unidentified red algal epiphyte (minute in size and composed of a few cells) was discovered growing on another red alga (Camontagnea oxyclada) collected in Stanley, Tasmania, Australia. This organism was originally detected as contamination during routine DNA barcoding surveys. Genetic data facilitates the discrimination between morphologically similar red algae, including this unique sample of Camontagnea oxyclada with its unknown red algal epiphyte. The objective of this research was to sequence commonly used phylogenetic markers (cox1, cob, rbcL, psaB, psaA, psbA) from both the host and epiphyte to place them in a wider red algal phylogenetic context, and to annotate the organellar genome contigs of the host and epiphyte.

DNA was extracted for the combined red algal host and epiphyte using a microphenol- chloroform method and sequenced on the Illumina Miseq platform. The phylogenetic markers for each organism were then located and aligned within a concatenated data set. Phylogenetic placement of the organisms was determined using Bayesian and maximum-likelihood methods. The robust placement of the host, Camontagnea oxyclada, as a sister genus to Rhodothamniella in the Palmariales, Nemaliophycidae, was confirmed. The epiphyte, on the other hand, was firmly allied as a sister to the genus Ballia, Balliales, also within the Nemaliophycidae, but at a large genetic distance. A new florideophyte order will be created to classify the novel alga.

The organellar genome contigs of the host and epiphyte were annotated, after de novo assembly, from the Miseq data, referencing currently available Florideophycean genomes from Genbank. The majority of the mitochondrion (mtDNA) and plastid (ptDNA) genomes were recovered as several contigs, for both the host and the epiphyte. A total of 25 protein encoding genes and 20 transfer RNAs (tRNAs) were recovered for the host mitochondrion genome. The epiphyte had 12 protein encoding genes and 14 tRNAs recovered. The unique arrangement of the cox1 gene is conserved across the host and epiphyte in the mtDNA. Additionally, 178 protein coding genes and 29 tRNAs were recovered for the host plastid genome, and 161 protein coding genes and 25 tRNAs were recovered for the epiphyte plastid genome. For both the host and epiphyte ptDNA the segment of DNA from the chlL-chlN genes through the ycf60-rps6 genes, just before the ribosomal RNAs, was inverted when compared to the Calliarthron tuberculosum plastid genome.

The phylogenetic placement of this new epiphyte in the red algal tree of life has helped to uncover a potentially new order and further clarify red algal diversity. The mitochondrion and plastid contigs of the host and epiphyte provide insight into organellar genome evolution in red algae as a whole and specifically within the Nemaliophycidae where both organisms group phylogenetically.

Recommended Citation

Wadland, Katelyn, "Phylogenetic Analysis of a Cryptic Microscopic Red Alga" (2016). Open Access Master's Theses. Paper 851.
https://digitalcommons.uri.edu/theses/851