Gene content, organization and molecular evolution of plant organellar genomes and sex chromosomes: insights from the case of the liverwort Marchantia polymorpha

Abstract

The complete nucleotide sequence of chloroplast DNA (121,025 base pairs, bp) from a liverwort, Marchantia polymorpha, has made clear the entire gene organization of the chloroplast genome. Quite a few genes encoding components of photosynthesis and protein synthesis machinery have been identified by comparative computer analysis. We also determined the complete nucleotide sequence of the liverwort mitochondrial DNA and deduced 96 possible genes in the sequence of 186,608 bp. The complete chloroplast genome encodes twenty introns (19 group II and 1 group I) in 18 different genes. One of the chloroplast group II introns separates a ribosomal protein gene in a trans-position. The mitochondrial genome contains thirty-two introns (25 group II and 7 group I) in the coding regions of 17 genes. From the evolutionary point of view, we describe the origin of organellar introns and give evidence for vertical and horizontal intron transfers and their intragenomic propagation. Furthermore, we describe the gene organization of the Y chromosome in the dioecious liverwort M. polymorpha, the first detailed view of a Y chromosome in a haploid organism. On the 10 megabase (Mb) Y chromosome, 64 genes are identified, 14 of which are detected only in the male genome. These 14 genes are expressed in reproductive organs but not in vegetative thalli, suggesting their participation in male reproductive functions. These findings indicate that the Y and X chromosomes share the same ancestral autosome and support the prediction that in a haploid organism essential genes on sex chromosomes are more likely to persist than in a diploid organism.

Fig. 1

Revised genetic map of the chloroplast genome of the liverwort Marchantia polymorpha. IRa, IRb, SSC and LSC on the inner circle indicate the inverted repeat regions, the small single-copy region and the large single-copy region, respectively. Genes shown inside the map are transcribed clockwise, and those outside are transcribed anticlockwise. Asterisks indicate genes with introns. Genes for tRNAs are indicated by the one-letter amino acid code with the unmodified anticodon. Identified protein genes and rRNA genes are indicated by gene symbols, and the remaining open boxes represent unidentified ORFs. Red arrows indicate the sites of the rps12 trans-splicing gene. Genes are color coded according to their functions: Photosynthesis and electron transport (rbc, psa, psb, pet, ndh, atp, frx); Transcription (rpo); Translation (rpl, rps, rrn, trn); Miscelleaneous (mbp, chl, clp); Unidentified ORF.^–

Fig. 2

Transcriptional regulation by the formation of double stranded RNA. (A) The psbN gene is found on the opposite DNA strand from the psbB gene. (B) In the dark, transcription occurs from the psbB gene to the petD gene (left). In the light, transcription of the psbN gene is induced and its transcripts can form a double stranded RNA with the mRNAs of the psbB operon, resulting in the inhibition of transcription from the psbH gene to the petD gene. Closed boxes and hatched boxes are exons and introns, respectively. ⇧ A region of double strand RNA formation.

Fig. 3

Gene organization of the mitochondrial genome from the liverwort Marchantia polymorpha. Genes shown inside the map are transcribed clockwise, those outside are transcribed anticlockwise. Asterisks indicate genes with introns. Genes for tRNAs are indicated by the one-letter amino acid code with the unmodified anticodon. Identified protein genes and rRNA genes are indicated by gene symbols. The remaining open boxes represent unassigned ORFs. Genes are color coded according to their functions: Respiration (cox, cob, nad, atp); Translation (rpl, rps, rrn, trn); Miscelleaneous (sdh, ccb, mtt); Unidentified ORF.^,

Fig. 4

Trans-splicing of the gene for ribosomal protein S12. (A) The 5′-upstream region and 3′-downstream region of the rps12 gene are coded on opposite DNA strands and transcribed independently. (B) Intron 1 (trans) is spliced as a split lariat intron. Intron 2 (cis) is spliced as a normal lariat intron and a single mature mRNA is formed.

Fig. 5

Schematic alignments of cox1 genes with the same insertion sites of introns from M. polymorpha(L), P. anserina(P), S. cerevisiae(Y), S. pombe(S), and N. crassa(N). Arrows indicate introns inserted at identical sites in the mitochondrial genomes of the different species. Open and filled triangles indicate group I and group II introns, respectively.

Fig. 6

No RNA editing in the liverwort mitochondrial genome. (A) RNA editing is not seen in the regions of the liverwort mitochondrial mRNA of the atp9 gene where RNA editing was demonstrated in the wheat atp9 gene. Boxed residues are RNA editing sites (C to U conversions) in the wheat atp9 gene. The corresponding sites in the liverwort atp9 gene are not required to be edited because T residues are encoded in the genomic sequence. (B) RNA/cDNA sequence analyses of the liverwort cob gene demonstrated the lack of RNA editing at any potential RNA editing site in the liverwort cob gene where RNA editing has been reported in higher plants. Boxed residues demonstrate RNA editing sites in Oenothera cob gene.

Fig. 7

(A) FISH analysis of unique repeated sequences in the Y chromosome from male M. polymorpha. (a) Giemsa-stained prometaphase chromosomes are shown with the Y chromosome indicated by an arrowhead. (b) The false color image of the DAPI stain (red) is superimposed onto the FITC image of the biotin-labeled PAC clone pMM4G7 (yellow). The magnified Y chromosome is presented in the lower left. (B) Schematic illustration of the M. polymorpha Y chromosome and alignment of the sequenced PAC clones. (C) Overview of YR2. The linear arrangements of Contig-A and Contig-B are shown with pertinent features indicated by the following letters: G, putative gene; P, pseudogene or EST homolog; O, organellar DNA insertion; T, transposable element; R, repeat. Arrowheads under the letters indicate their orientation.

Fig. 8

Molecular evolution of the liverwort sex chromosomes. During evolution of the X and Y chromosomes the genes essential for the maintenance of each sex were sustained or degenerated as required in each sex. In parallel, repeats specific for each sex chromosome accumulated.^, Both X and Y chromosomes retained the genes coding for essential metabolic or regulatory functions required for normal growth and development.