ArticleProceedings of the National Academy of Sciences of the United States of America2016
Protein networks identify novel symbiogenetic genes resulting from plastid endosymbiosis.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 48 citations in OpenAlex.
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- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Why is primary endosymbiosis so rare?The New phytologist · 2021Review
- Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Paulinella, a model for understanding plastid primary endosymbiosis.Journal of phycology · 2020Review
- Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal.Scientific reports · 2020Article
- Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study.Genome biology and evolution · 2020Article
- Horizontal and endosymbiotic gene transfer in early plastid evolution.The New phytologist · 2019Review
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- Two divergent Symbiodinium genomes reveal conservation of a gene cluster for sunscreen biosynthesis and recently lost genes.BMC genomics · 2018Article
- Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution.Genome biology · 2018Article
- Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.BMC biology · 2018Review
- Tracking the Rules of Transmission and Introgression with Networks.Microbiology spectrum · 2018Review
- Bipartite Network Analysis of Gene Sharings in the Microbial World.Molecular biology and evolution · 2018Article
- Integrative analysis of large scale transcriptome data draws a comprehensive landscape of Phaeodactylum tricornutum genome and evolutionary origin of diatoms.Scientific reports · 2018Article
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- Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing.Biotechnology for biofuels · 2018Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The integration of foreign genetic information is central to the evolution of eukaryotes, as has been demonstrated for the origin of the Calvin cycle and of the heme and carotenoid biosynthesis pathways in algae and plants. For photosynthetic lineages, this coordination involved three genomes of divergent phylogenetic origins (the nucleus, plastid, and mitochondrion). Major hurdles overcome by the ancestor of these lineages were harnessing the oxygen-evolving organelle, optimizing the use of light, and stabilizing the partnership between the plastid endosymbiont and host through retargeting of proteins to the nascent organelle. Here we used protein similarity networks that can disentangle reticulate gene histories to explore how these significant challenges were met. We discovered a previously hidden component of algal and plant nuclear genomes that originated from the plastid endosymbiont: symbiogenetic genes (S genes). These composite proteins, exclusive to photosynthetic eukaryotes, encode a cyanobacterium-derived domain fused to one of cyanobacterial or another prokaryotic origin and have emerged multiple, independent times during evolution. Transcriptome data demonstrate the existence and expression of S genes across a wide swath of algae and plants, and functional data indicate their involvement in tolerance to oxidative stress, phototropism, and adaptation to nitrogen limitation. Our research demonstrates the "recycling" of genetic information by photosynthetic eukaryotes to generate novel composite genes, many of which function in plastid maintenance.
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