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 D., Anderson, Donald M., Erdner, Deana L. and Bhattacharya, Debashish (2012) Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote. Journal of Phycology, 48 5: 1130-1142.


Author Chan, Cheong Xin
Soares, Marcelo B.
Bonaldo, Maria F.
Wisecaver, Jennifer H.
Hackett, Jeremiah D.
Anderson, Donald M.
Erdner, Deana L.
Bhattacharya, Debashish
Title Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote
Formatted title Analysis of Alexandrium tamarense (Dinophyceae) genes reveals the complex evolutionary history of a microbial eukaryote
Journal name Journal of Phycology   Check publisher's open access policy
ISSN 0022-3646
1529-8817
Publication date 2012-10
Sub-type Article (original research)
DOI 10.1111/j.1529-8817.2012.01194.x
Volume 48
Issue 5
Start page 1130
End page 1142
Total pages 13
Place of publication Hoboken, NJ, United States
Publisher Wiley-Blackwell Publishing
Collection year 2013
Language eng
Formatted 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.
Keyword Dinoflagellates
Endosymbiosis
Eukaryote evolution
Horizontal gene transfer
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2013 Collection
School of Chemistry and Molecular Biosciences
 
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Created: Mon, 08 Oct 2012, 15:50:33 EST by Cheong Xin Chan on behalf of School of Chemistry & Molecular Biosciences