Analysis of alexandrium tamarense (dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote

Cheong Xin Chan, Marcelo B. Soares, Maria F. Bonaldo, Jennifer H. Wisecaver, Jeremiah Hackett, Donald M. Anderson, Deana L. Erdner, Debashish Bhattacharya

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Microbial eukaryotes may extinguish much of their nuclear phylogenetic history due to endosymbiotic/horizontal gene transfer (E/HGT). We studied E/HGT in 32,110 contigs of expressed sequence tags (ESTs) from the dinoflagellate Alexandrium tamarense (Dinophyceae) using a conservative phylogenomic approach. The vast majority of predicted proteins (86.4%) in this alga are novel or dinoflagellate-specific. We searched for putative homologs of these predicted proteins against a taxonomically broadly sampled protein database that includes all currently available data from algae and protists, and reconstructed a phylogeny from each of the putative homologous protein sets. Of the 2,523 resulting phylogenies, 14%-17% are potentially impacted by E/HGT involving both prokaryote and eukaryote lineages, with 2%-4% showing clear evidence of reticulate evolution. The complex evolutionary histories of the remaining proteins, many of which may also have been affected by E/HGT, cannot be interpreted using our approach with currently available gene data. We present empirical evidence of reticulate genome evolution that combined with inadequate or highly complex phylogenetic signal in many proteins may impede genome-wide approaches to infer the tree of microbial eukaryotes.

Original languageEnglish (US)
Pages (from-to)1130-1142
Number of pages13
JournalJournal of Phycology
Volume48
Issue number5
DOIs
StatePublished - Oct 2012

Fingerprint

Alexandrium
eukaryote
Dinophyceae
eukaryotic cells
gene transfer
algae
history
protein
gene
genes
proteins
phylogeny
dinoflagellate
genome
alga
phylogenetics
protist
prokaryote
prokaryotic cells
expressed sequence tags

Keywords

  • Dinoflagellates
  • Endosymbiosis
  • Eukaryote evolution
  • Horizontal gene transfer
  • Phylogenomics

ASJC Scopus subject areas

  • Aquatic Science
  • Plant Science

Cite this

Analysis of alexandrium tamarense (dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. / Chan, Cheong Xin; Soares, Marcelo B.; Bonaldo, Maria F.; Wisecaver, Jennifer H.; Hackett, Jeremiah; Anderson, Donald M.; Erdner, Deana L.; Bhattacharya, Debashish.

In: Journal of Phycology, Vol. 48, No. 5, 10.2012, p. 1130-1142.

Research output: Contribution to journalArticle

Chan, CX, Soares, MB, Bonaldo, MF, Wisecaver, JH, Hackett, J, Anderson, DM, Erdner, DL & Bhattacharya, D 2012, 'Analysis of alexandrium tamarense (dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote', Journal of Phycology, vol. 48, no. 5, pp. 1130-1142. https://doi.org/10.1111/j.1529-8817.2012.01194.x
Chan, Cheong Xin ; Soares, Marcelo B. ; Bonaldo, Maria F. ; Wisecaver, Jennifer H. ; Hackett, Jeremiah ; Anderson, Donald M. ; Erdner, Deana L. ; Bhattacharya, Debashish. / Analysis of alexandrium tamarense (dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. In: Journal of Phycology. 2012 ; Vol. 48, No. 5. pp. 1130-1142.
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