Large Diversity of Nonstandard Genes and Dynamic Evolution of Chloroplast Genomes in Siphonous Green Algae (Bryopsidales, Chlorophyta)

Ma Chiela M. Cremen, Frederik Leliaert, Vanessa R. Marcelino, Heroen Verbruggen

Research output: Contribution to journalArticleResearchpeer-review

14 Citations (Scopus)

Abstract

Chloroplast genomes have undergone tremendous alterations through the evolutionary history of the green algae (Chloroplastida). This study focuses on the evolution of chloroplast genomes in the siphonous green algae (order Bryopsidales).We present five new chloroplast genomes, which along with existing sequences, yield a data set representing all but one families of the order. Using comparative phylogeneticmethods, we investigated the evolutionary dynamics of genomic features in the order. Our results show extensive variation in chloroplast genome architecture and intron content. Variation in genome size is accounted for by the amount of intergenic space and freestanding open reading frames that do not show significant homology to standard plastid genes. We show the diversity of these nonstandard genes based on their conserved protein domains, which are often associated with mobile functions (reverse transcriptase/intron maturase, integrases, phage- or plasmid-DNA primases, transposases, integrases, ligases). Investigation of the introns showed proliferation of group II introns in the early evolution of the order and their subsequent loss in the core Halimedineae, possibly through RT-mediated intron loss.

Original languageEnglish
Pages (from-to)1048-1061
Number of pages14
JournalGenome Biology and Evolution
Volume10
Issue number4
DOIs
Publication statusPublished - Apr 2018
Externally publishedYes

Keywords

  • Bryopsidales
  • Chlrorophyta
  • freestanding ORFs
  • genome evolution
  • mobile elements

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