Plant Molecular Biology

, Volume 29, Issue 1, pp 63–80 | Cite as

Two copies of a DNA element, ‘Wendy’, in the chloroplast chromosome of Chlamydomonas reinhardtii between rearranged gene clusters

  • Wen-Hua Fan
  • Mark A. Woelfle
  • Gisela Mosig
Research Article

Abstract

We have characterized two copies of a 2.4 kb DNA element that we call ‘Wendy’, in the chloroplast chromosome of Chlamydomonas reinhardtii. The two copies of Wendy reside in different single-copy regions at opposite positions in the chloroplast genome. Like many mobile DNA elements, both copies of Wendy are bordered by inverted repeats and contain several additional degenerate copies of these repeat sequences in direct or inverted orientation. In addition, four basepairs are repeated in direct orientation. Two major open reading frames (ORFs) are predicted from the DNA sequence of Wendy I. These ORFs are co-transcribed from a promoter inside the element. The deduced amino acid sequence of the larger of these ORFs shares some weak similarities with sequence motifs of transposases and integrases of other mobile elements. Wendy II appears to be altered relative to Wendy I by point mutations and small deletions and insertions which destroy the ORFs. The leader sequence of the Wendy transcript is nearly identical with the leader sequence of the rbcL transcript of C. reinhardtii, but not of C. moewusii (where the complete Wendy was also undetectable). Furthermore, both copies of Wendy are bracketed by gene clusters that are separated in C. reinhardtii but are contiguous in C. moewusii where they exist in an inverted orientation compared with C. reinhardtii. Wendy was not found in any of the completely sequenced chloroplast genomes of rice, tobacco, pine, Euglena or Marchantia, nor in any other GenBank entry. Our results suggest that Wendy has invaded C. reinhardtii after divergence from other species. Subsequent Wendy-dependent illegitimate homologous or site-specific recombination events or both may have contributed to scrambling of the C. reinhardtii chloroplast genome relative to genomes of other species.

Key words

evolution Chlamydomonas reinhardtii chloroplast site-specific recombination transcription transposition 

Abbreviations

ORF

open reading frame

nt

nucleotide

LIR

large inverted repeat of the chloroplast genome

TIR

terminal inverted repeats of Wendy

TIRL

the TIR near the 5′ end of Wendy

TIRR

the TIR near the 3′ end of Wendy I

DR

direct repeats bordering Wendy

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Copyright information

© Kluwer Academic Publishers 1995

Authors and Affiliations

  • Wen-Hua Fan
    • 1
  • Mark A. Woelfle
    • 1
  • Gisela Mosig
    • 1
  1. 1.Department of Molecular BiologyVanderbilt UniversityNashvilleUSA

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