Original Paper

Molecular Genetics and Genomics

, Volume 276, Issue 5, pp 464-477

First online:

Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum

  • Anne-Sophie BélangerAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval
  • , Jean-Simon BrouardAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval
  • , Patrick CharleboisAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval
  • , Christian OtisAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval
  • , Claude LemieuxAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval
  • , Monique TurmelAffiliated withDépartement de biochimie et de microbiologie, Pavillon Charles-Eugène Marchand, Université Laval Email author 

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Abstract

The chloroplast genome has experienced many architectural changes during the evolution of chlorophyte green algae, with the class Chlorophyceae displaying the lowest degree of ancestral traits. We have previously shown that the completely sequenced chloroplast DNAs (cpDNAs) of Chamydomonas reinhardtii (Chlamydomonadales) and Scenedesmus obliquus (Sphaeropleales) are highly scrambled in gene order relative to one another. Here, we report the complete cpDNA sequence of Stigeoclonium helveticum (Chaetophorales), a member of a third chlorophycean lineage. This genome, which encodes 97 genes and contains 21 introns (including four putatively trans-spliced group II introns inserted at novel sites), is remarkably rich in derived features and extremely rearranged relative to its chlorophycean counterparts. At 223,902 bp, Stigeoclonium cpDNA is the largest chloroplast genome sequenced thus far, and in contrast to those of Chlamydomonas and Scenedesmus, features no large inverted repeat. Interestingly, the pattern of gene distribution between the DNA strands and the bias in base composition along each strand suggest that the Stigeoclonium genome replicates bidirectionally from a single origin. Unlike most known trans-spliced group II introns, those of Stigeoclonium exhibit breaks in domains I and II. By placing our comparative genome analyses in a phylogenetic framework, we inferred an evolutionary scenario of the mutational events that led to changes in genome architecture in the Chlorophyceae.

Keywords

Chlorophyta Plastid genome evolution Gene order Origin of replication Group II introns Repeated sequences