Summary
Algae are characterized by the presence of plastids (chloroplasts), which are organelles of cyanobacterial origin. Plastids have their own genome, machineries for replication, transcription and translation, and are the site of photosynthesis (except in secondarily non-photosynthetic species) and a variety of other biological functions. Algae are subdivided into those whose plastids can be traced back to a common cyanobacterial endosymbiont (algae with primary plastids), and others in which plastids are second-hand acquisitions that were introduced by eukaryote-eukaryote endosymbioses.
Only a fraction of plastid components is encoded in plastid DNA; the majority of genes coding for plastid proteins are in the nucleus, many of which originated through transfers (in some cases still ongoing) from the organelle to the nuclear genome. Despite the broad phylogenetic affiliation of algae, most plastid genomes are fairly homogenous, coding for about 100–250 genes, except in non-photosynthetic algae that rapidly lose genes involved in photosynthesis. The most gene-rich and cyanobacteria-like plastid genomes are in red algae, followed by glaucophyte and green algae. Genomes in secondary or higher-order plastids usually have a reduced gene count, compared to their primary photosynthetic donors. In this chapter, we provide an overview on the evolutionary history, organization and coding properties of algal plastid genomes, for which complete (or almost complete) sequences are publicly available.
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Abbreviations
- aa –:
-
Amino acid;
- CASH –:
-
Cryptophyta Alveolata, Stramenopila plus Haptophyta their plastids are of red algal origin and pt genomes are closely related (which is incompatible with respective nuclear genome phylogenies).
- CW –:
-
‘Clockwise’ arrangement of flagellar basal bodies in Chlamydomonadales;
- DO –:
-
‘Directly opposed’ arrangement of flagellar basal bodies in Sphaeropleales;
- IR –:
-
Inverted genomic repeat region occurs in a large number of ptDNAs;
- LBA –:
-
Long Branch Attraction phylogenetic artifact that leads to the incorrect grouping of fast-evolving species or attraction to distant outgroups, due to evolutionary model violations and under-estimation of repeated sequence change;
- mtDNA –:
-
Mitochondrial DNA protists – eukaryotes other than fungi animals and plants;
- pt –:
-
Plastid (chloroplast);
- ptDNA –:
-
Plastid DNA;
- SC –:
-
Single-copy regions separating large inverted repeats in ptDNAs;
- tmRNA –:
-
Transfer mRNA occurs in bacterial some plastid and jakobid mitochondrial genomes typically contains a tRNA-like and a protein-coding domain involved in releasing ribosomes that are stalled by degraded mRNAs without in-frame stop codons
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Acknowledgments
We are grateful to Dr. G. Burger (Université de Montréal, Montreal, Canada) for insightful discussion and comments on the manuscript. This work was supported by the Canadian Research Chair Program and the Natural Sciences and Engineering Research Council (NSERC; 194560–2011) of Canada.
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Lang, B.F., Nedelcu, A.M. (2012). Plastid Genomes of Algae. In: Bock, R., Knoop, V. (eds) Genomics of Chloroplasts and Mitochondria. Advances in Photosynthesis and Respiration, vol 35. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2920-9_3
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