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Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida

by 1,2,3,†, 2,3,4,†, 1,2,3,†, 2,3,5, 2,3,4, 1,2,3, 1,2, 2,3, 2,4, 6, 2,3,4, 2,4,7,* and 2,4,7,*
1
Beijing Genomics Institute (BGI) Education Center, University of Chinese Academy of Sciences, Beijing 100049, China
2
Beijing Genomics Institute (BGI) Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
3
China National Gene Bank, Institute of New Agricultural Resources, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
4
State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute (BGI) Shenzhen, Shenzhen 518083, China
5
School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
6
Botanical Institute, Cologne Biocenter, University of Cologne, D-50674 Cologne, Germany
7
Department of Biology, University of Copenhagen, DK-1165 Copenhagen, Denmark
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(12), 3020; https://doi.org/10.3390/ijms20123020
Received: 5 May 2019 / Revised: 18 June 2019 / Accepted: 18 June 2019 / Published: 20 June 2019
(This article belongs to the Section Molecular Genetics and Genomics)
Selenoproteins that contain selenocysteine (Sec) are found in all kingdoms of life. Although they constitute a small proportion of the proteome, selenoproteins play essential roles in many organisms. In photosynthetic eukaryotes, selenoproteins have been found in algae but are missing in land plants (embryophytes). In this study, we explored the evolutionary dynamics of Sec incorporation by conveying a genomic search for the Sec machinery and selenoproteins across Archaeplastida. We identified a complete Sec machinery and variable sizes of selenoproteomes in the main algal lineages. However, the entire Sec machinery was missing in the Bangiophyceae-Florideophyceae clade (BV) of Rhodoplantae (red algae) and only partial machinery was found in three species of Archaeplastida, indicating parallel loss of Sec incorporation in different groups of algae. Further analysis of genome and transcriptome data suggests that all major lineages of streptophyte algae display a complete Sec machinery, although the number of selenoproteins is low in this group, especially in subaerial taxa. We conclude that selenoproteins tend to be lost in Archaeplastida upon adaptation to a subaerial or acidic environment. The high number of redox-active selenoproteins found in some bloom-forming marine microalgae may be related to defense against viral infections. Some of the selenoproteins in these organisms may have been gained by horizontal gene transfer from bacteria. View Full-Text
Keywords: evolution; horizontal gene transfer; phylogenomics; selenoproteins; selenocysteine; Sec machinery evolution; horizontal gene transfer; phylogenomics; selenoproteins; selenocysteine; Sec machinery
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Liang, H.; Wei, T.; Xu, Y.; Li, L.; Kumar Sahu, S.; Wang, H.; Li, H.; Fu, X.; Zhang, G.; Melkonian, M.; Liu, X.; Wang, S.; Liu, H. Phylogenomics Provides New Insights into Gains and Losses of Selenoproteins among Archaeplastida. Int. J. Mol. Sci. 2019, 20, 3020.

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