Publication Date:
2022-05-26
Description:
© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
Description:
The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
Description:
J.H.W. was supported by the NSF IGERT
Program in Comparative Genomics at the University of
Arizona (grant number DGE-0654435). This work was supported
by grants from the National Science Foundation (grant
numbers OCE-0723498, EF-0732440) and funding provided
by the BIO5 Institute at the University of Arizona to J.D.H.
Keywords:
Gene innovation
;
Alexandrium tamarense Group IV
;
Phylogenetic profile
;
Phylogenomics
;
De novo transcriptome assembly
;
Mitochondrial metabolism
Repository Name:
Woods Hole Open Access Server
Type:
Article
Format:
application/pdf
Format:
application/vnd.ms-excel
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