Chloroplast genome evolution in early diverged leptosporangiate ferns

Hyoung Tae Kim, Myong Gi Chung, Ki Joong Kim

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

In this study, the chloroplast (cp) genome sequences from three early diverged leptosporangiate ferns were completed and analyzed in order to understand the evolution of the genome of the fern lineages. The complete cp genome sequence of Osmunda cinnamomea (Osmundales) was 142,812 base pairs (bp). The cp genome structure was similar to that of eusporangiate ferns. The gene/intron losses that frequently occurred in the cp genome of leptosporangiate ferns were not found in the cp genome of O. cinnamomea. In addition, putative RNA editing sites in the cp genome were rare in O. cinnamomea, even though the sites were frequently predicted to be present in leptosporangiate ferns. The complete cp genome sequence of Diplopterygium glaucum (Gleicheniales) was 151,007 bp and has a 9.7 kb inversion between the trnL-CAA and trnV-GCA genes when compared to O. cinnamomea. Several repeated sequences were detected around the inversion break points. The complete cp genome sequence of Lygodium japonicum (Schizaeales) was 157,142 bp and a deletion of the rpoC1 intron was detected. This intron loss was shared by all of the studied species of the genus Lygodium. The GC contents and the effective numbers of codons (ENCs) in ferns varied significantly when compared to seed plants. The ENC values of the early diverged leptosporangiate ferns showed intermediate levels between eusporangiate and core leptosporangiate ferns. However, our phylogenetic tree based on all of the cp gene sequences clearly indicated that the cp genome similarity between O. cinnamomea (Osmundales) and eusporangiate ferns are symplesiomorphies, rather than synapomorphies. Therefore, our data is in agreement with the view that Osmundales is a distinct early diverged lineage in the leptosporangiate ferns.

Original languageEnglish
Pages (from-to)372-382
Number of pages11
JournalMolecules and cells
Volume37
Issue number5
DOIs
Publication statusPublished - 2014 May

Keywords

  • Chloroplast genomes
  • Diplopterygium glaucum
  • Early diverged leptosporangiate ferns
  • Inversion mutations
  • Lygodium japonicum
  • Osmunda cinnamomea
  • rpoC1 intron loss

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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