Journal Article

The Complete Plastid Genome Sequence of the Secondarily Nonphotosynthetic Alga <i>Cryptomonas paramecium</i>: Reduction, Compaction, and Accelerated Evolutionary Rate

Natalie Donaher, Goro Tanifuji, Naoko T. Onodera, Stephanie A. Malfatti, Patrick S. G. Chain, Yoshiaki Hara and John M. Archibald

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 1, issue , pages 439-448
Published in print January 2009 |
Published online November 2009 | e-ISSN: 1759-6653 | DOI: https://dx.doi.org/10.1093/gbe/evp047

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The cryptomonads are a group of unicellular algae that acquired photosynthesis through the engulfment of a red algal cell, a process called secondary endosymbiosis. Here, we present the complete plastid genome sequence of the secondarily nonphotosynthetic species Cryptomonas paramecium CCAP977/2a. The ∼78 kilobase pair (Kbp) C. paramecium genome contains 82 predicted protein genes, 29 transfer RNA genes, and a single pseudogene (atpF). The C. paramecium plastid genome is approximately 50 Kbp smaller than those of the photosynthetic cryptomonads Guillardia theta and Rhodomonas salina; 71 genes present in the G. theta and/or R. salina plastid genomes are missing in C. paramecium. The pet, psa, and psb photosynthetic gene families are almost entirely absent. Interestingly, the ribosomal RNA operon, present as inverted repeats in most plastid genomes (including G. theta and R. salina), exists as a single copy in C. paramecium. The G + C content (38%) is higher in C. paramecium than in other cryptomonad plastid genomes, and C. paramecium plastid genes are characterized by significantly different codon usage patterns and increased evolutionary rates. The content and structure of the C. paramecium plastid genome provides insight into the changes associated with recent loss of photosynthesis in a predominantly photosynthetic group of algae and reveals features shared with the plastid genomes of other secondarily nonphotosynthetic eukaryotes.

Keywords: cryptomonads; plastids; genome reduction; photosynthesis; secondary endosymbiosis

Journal Article.  6897 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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