Eun Chan Yang

Publications of Eun Chan Yang

• Supermatrix data highlight the phylogenetic relationships of photosynthetic stramenopiles.

  Authors: Eun Chan Yang, Ga Hun Boo, Hee Jeong Kim, Sung Mi Cho, Sung Min Boo, Robert A Andersen, Hwan Su Yoon

  Protist. 03/2012; 163(2):217-31.

  Molecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlierMolecular data had consistently recovered monophyletic classes for the heterokont algae, however, the relationships among the classes had remained only partially resolved. Furthermore, earlier studies did not include representatives from all taxonomic classes. We used a five-gene (nuclear encoded SSU rRNA; plastid encoded rbcL, psaA, psbA, psbC) analysis with a subset of 89 taxa representing all 16 heterokont classes to infer a phylogenetic tree. There were three major clades. The Aurearenophyceae, Chrysomerophyceae, Phaeophyceae, Phaeothamniophyceae, Raphidophyceae, Schizocladiophyceae and Xanthophyceae formed the SI clade. The Chrysophyceae, Eustigmatophyceae, Pinguiophyceae, Synchromophyceae and Synurophyceae formed the SII clade. The Bacillariophyceae, Bolidophyceae, Dictyochophyceae and Pelagophyceae formed the SIII clade. These three clades were also found in a ten-gene analysis. The approximately unbiased test rejected alternative hypotheses that forced each class into either of the other two clades. Morphological and biochemical data were not available for all 89 taxa, however, existing data were consistent with the molecular phylogenetic tree, especially for the SIII clade.

• Single cell genome analysis supports a link between phagotrophy and primary plastid endosymbiosis.

  Authors: Debashish Bhattacharya, Dana C Price, Hwan Su Yoon, Eun Chan Yang, Nicole J Poulton, Robert A Andersen, Sushma Parankush Das

  Scientific reports. 01/2012; 2:356.

  Two cases of primary plastid endosymbiosis are known. The first occurred ca. 1.6 billion years ago and putatively gave rise to the canonical plastid in algae and plants. The second is restricted to aTwo cases of primary plastid endosymbiosis are known. The first occurred ca. 1.6 billion years ago and putatively gave rise to the canonical plastid in algae and plants. The second is restricted to a genus of rhizarian amoebae that includes Paulinella chromatophora. Photosynthetic Paulinella species gained their plastid from an α-cyanobacterial source and are sister to plastid-lacking phagotrophs such as Paulinella ovalis that ingest cyanobacteria. To study the role of feeding behavior in plastid origin, we analyzed single-cell genome assemblies from six P. ovalis-like cells isolated from Chesapeake Bay, USA. Dozens of contigs in these cell assemblies were derived from prey DNA of α-cyanobacterial origin and associated cyanophages. We found two examples of horizontal gene transfer (HGT) in P. ovalis-like nuclear DNA from cyanobacterial sources. This work suggests the first evidence of a link between feeding behavior in wild-caught cells, HGT, and plastid primary endosymbiosis in the monophyletic Paulinella lineage.

• Single-cell genomics reveals organismal interactions in uncultivated marine protists.

  Authors: Hwan Su Yoon, Dana C Price, Ramunas Stepanauskas, Veeran D Rajah, Michael E Sieracki, William H Wilson, Eun Chan Yang, Siobain Duffy, Debashish Bhattacharya

  Science (New York, N.Y.). 05/2011; 332(6030):714-7.

  Whole-genome shotgun sequence data from three individual cells isolated from seawater, followed by analysis of ribosomal DNA, indicated that the cells represented three divergent clades ofWhole-genome shotgun sequence data from three individual cells isolated from seawater, followed by analysis of ribosomal DNA, indicated that the cells represented three divergent clades of picobiliphytes. In contrast with the recent description of this phylum, we found no evidence of plastid DNA nor of nuclear-encoded plastid-targeted proteins, which suggests that these picobiliphytes are heterotrophs. Genome data from one cell were dominated by sequences from a widespread single-stranded DNA virus. This virus was absent from the other two cells, both of which contained non-eukaryote DNA derived from marine Bacteroidetes and large DNA viruses. By using shotgun sequencing of uncultured marine picobiliphytes, we revealed the distinct interactions of individual cells.

• Red and green algal monophyly and extensive gene sharing found in a rich repertoire of red algal genes.

  Authors: Cheong Xin Chan, Eun Chan Yang, Titas Banerjee, Hwan Su Yoon, Patrick T Martone, José M Estevez, Debashish Bhattacharya

  Current biology : CB. 02/2011; 21(4):328-33.

  The Plantae comprising red, green (including land plants), and glaucophyte algae are postulated to have a single common ancestor that is the founding lineage of photosynthetic eukaryotes. However,The Plantae comprising red, green (including land plants), and glaucophyte algae are postulated to have a single common ancestor that is the founding lineage of photosynthetic eukaryotes. However, recent multiprotein phylogenies provide little or no support for this hypothesis. This may reflect limited complete genome data available for red algae, currently only the highly reduced genome of Cyanidioschyzon merolae, a reticulate gene ancestry, or variable gene divergence rates that mislead phylogenetic inference. Here, using novel genome data from the mesophilic Porphyridium cruentum and Calliarthron tuberculosum, we analyze 60,000 novel red algal genes to test the monophyly of red + green (RG) algae and their extent of gene sharing with other lineages. Using a gene-by-gene approach, we find an emerging signal of RG monophyly (supported by ∼50% of the examined protein phylogenies) that increases with the number of distinct phyla and terminal taxa in the analysis. A total of 1,808 phylogenies show evidence of gene sharing between Plantae and other lineages. We demonstrate that a rich mesophilic red algal gene repertoire is crucial for testing controversial issues in eukaryote evolution and for understanding the complex patterns of gene inheritance in protists.

• Differential gene retention in plastids of common recent origin.

  Authors: Adrian Reyes-Prieto, Hwan Su Yoon, Ahmed Moustafa, Eun Chan Yang, Robert A Andersen, Sung Min Boo, Takuro Nakayama, Ken-ichiro Ishida, Debashish Bhattacharya

  Molecular biology and evolution. 07/2010; 27(7):1530-7.

  The cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely onThe cyanobacterium-derived plastids of algae and plants have supported the diversification of much of extant eukaryotic life. Inferences about early events in plastid evolution must rely on reconstructing events that occurred over a billion years ago. In contrast, the photosynthetic amoeba Paulinella chromatophora provides an exceptional model to study organelle evolution in a prokaryote-eukaryote (primary) endosymbiosis that occurred approximately 60 mya. Here we sequenced the plastid genome (0.977 Mb) from the recently described Paulinella FK01 and compared the sequence with the existing data from the sister taxon Paulinella M0880/a. Alignment of the two plastid genomes shows significant conservation of gene order and only a handful of minor gene rearrangements. Analysis of gene content reveals 66 differential gene losses that appear to be outright gene deletions rather than endosymbiotic gene transfers to the host nuclear genome. Phylogenomic analysis validates the plastid ancestor as a member of the Synechococcus-Prochlorococcus group, and the cyanobacterial provenance of all plastid genes suggests that these organelles were not targets of interphylum gene transfers after endosymbiosis. Inspection of 681 DNA alignments of protein-encoding genes shows that the vast majority have dN/dS ratios <1, providing evidence for purifying selection. Our study demonstrates that plastid genomes in sister taxa are strongly constrained by selection but follow distinct trajectories during the earlier phases of organelle evolution.

• Evidence for two independent lineages of Griffithsia (Ceramiaceae, Rhodophyta) based on plastid protein-coding psaA, psbA, and rbcL gene sequences.

  Authors: Eun Chan Yang, Sung Min Boo

  Molecular phylogenetics and evolution. 06/2004; 31(2):680-8.

  The ceramiaceous red algal genus Griffithsia has characteristic large vegetative cells visible to the unaided eye and thousands of nuclei in a single cell at maturity. Its members often occurThe ceramiaceous red algal genus Griffithsia has characteristic large vegetative cells visible to the unaided eye and thousands of nuclei in a single cell at maturity. Its members often occur intertidally along temperate to tropical coasts. Although previous morphological studies indicated that Griffithsia is subdivided into four groups, there is no molecular phylogeny for the genus. We present the multigene phylogeny of the genus based on plastid protein-coding psaA, psbA, and rbcL genes from ten samples of eight Griffithsia species, eight samples of five putative relatives, such as Anotrichium and Halurus, and three outgroup taxa. Saturation plots for each of the three datasets showed no evidence of saturation at any codon position. The partition homogeneity test indicated that none of the individual datasets resulted in significantly incongruent trees. All the analyses of individual and concatenated datasets separated Griffithsia into two well-defined lineages: Lineage 1 was composed of Griffithsia corallinoides, Griffithsia pacifica, and Griffithsia tomo-yamadae, while lineage 2 encompassed Griffithsia antarctica, Griffithsia japonica, Griffithsia teges, Griffithsia traversii, and Griffithsia sp. Our results support the monophyly of the four Anotrichium species and cast a question on the autonomy of Halurus. The monophyly of the tribe Griffithsieae is well resolved, although interrelationships among Griffithsia, Anotrichium, and Halurus were unclear. Our study indicates that the psaA and psbA genes are powerful new tools for the genus-level phylogeny of red algal groups, such as Griffithsia. This is the first report on the multigene phylogeny of the Ceramiales algae based on three protein-coding plastid genes.