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.
journal_name
J Phycoljournal_title
Journal of phycologyauthors
Chan CX,Soares MB,Bonaldo MF,Wisecaver JH,Hackett JD,Anderson DM,Erdner DL,Bhattacharya Ddoi
10.1111/j.1529-8817.2012.01194.xsubject
Has Abstractpub_date
2012-10-01 00:00:00pages
1130-1142issue
5eissn
0022-3646issn
1529-8817journal_volume
48pub_type
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