Chloroplast DNA from the fern Osmunda cinnamomea: physical organization, gene localization and comparison to angiosperm

Chloroplast genome evolution in early diverged leptosporangiate ferns

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 trnVGCA 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.

The localization and orientation of specific genes in the chloroplast chromosome of Vicia faba

The genes for six chloroplast polypeptides have been localized on the map of Vicia faba chloroplast DNA using heterologous probes. These include the three subunits (α, β, ε) of CF1 of ATP synthase, subunit III of CF0 from ATP synthase, the 32 kilodalton thylakoidal membrane protein of photosystem II and cytochrome f of the electron transport chain. The direction of transcription has been determined for the three subunits of CF1 and the 32 kilodalton thylakoidal protein. The physical map of the chloroplast DNA has also been expanded to include Sma1 sites in addition to previously mapped restriction enzyme sites. Finally, the genetic arrangement of Vicia faba chloroplast DNA was compared to other known genetic maps.

Characterization of inverted repeat sequences and ribosomal RNA genes of chloroplast DNA from Chlorella ellipsoidea

Chloroplast DNA isolated from a green alga Chlorella was shown by agarose gel electrophoresis and electron microscopy to contain a pair of large inverted repeat sequences of ca. 23 kbp. Electron microscopy revealed that the repeats were separated from each other by a small single strand loop of 29.5 kbp and a large single strand region of 98.5 kbp.Digestion with the restriction endonucleases Kpnl, Sstl, and Xhol, and hybridization with (32)P-labelled tobacco rDNAs revealed that the genes for 16S and 23S rRNAs are present in the repeated sequences. From the hybridization pattern, a restriction map around the sequences were constructed, and the rRNA genes were found to be on the 10.8 kbp SstI fragment. This location was supported by electron microscopy (R-loop formation).Unlike Chlamydomonas reinhardii, Chlorella lacks a large intron in its 23S rRNA gene, and the 16S-23S spacer region is considerably long; the organization of rRNA operon is similar to that of higher plants.

Complete plastome sequences of Equisetum arvense and Isoetes flaccida: implications for phylogeny and plastid genome evolution of early land plant lineages

Background

Despite considerable progress in our understanding of land plant phylogeny, several nodes in the green tree of life remain poorly resolved. Furthermore, the bulk of currently available data come from only a subset of major land plant clades. Here we examine early land plant evolution using complete plastome sequences including two previously unexamined and phylogenetically critical lineages. To better understand the evolution of land plants and their plastomes, we examined aligned nucleotide sequences, indels, gene and nucleotide composition, inversions, and gene order at the boundaries of the inverted repeats.

Results

We present the plastome sequences of Equisetum arvense, a horsetail, and of Isoetes flaccida, a heterosporous lycophyte. Phylogenetic analysis of aligned nucleotides from 49 plastome genes from 43 taxa supported monophyly for the following clades: embryophytes (land plants), lycophytes, monilophytes (leptosporangiate ferns + Angiopteris evecta + Psilotum nudum + Equisetum arvense), and seed plants. Resolution among the four monilophyte lineages remained moderate, although nucleotide analyses suggested that P. nudum and E. arvense form a clade sister to A. evecta + leptosporangiate ferns. Results from phylogenetic analyses of nucleotides were consistent with the distribution of plastome gene rearrangements and with analysis of sequence gaps resulting from insertions and deletions (indels). We found one new indel and an inversion of a block of genes that unites the monilophytes.

Conclusions

Monophyly of monilophytes has been disputed on the basis of morphological and fossil evidence. In the context of a broad sampling of land plant data we find several new pieces of evidence for monilophyte monophyly. Results from this study demonstrate resolution among the four monilophytes lineages, albeit with moderate support; we posit a clade consisting of Equisetaceae and Psilotaceae that is sister to the "true ferns," including Marattiaceae.

Unusual characteristics of Codium fragile chloroplast DNA revealed by physical and gene mapping

A complete physical map of the Codium fragile chloroplast genome was constructed and the locations of a number of chloroplast genes were determined. Several features of this circular genome are unusual. At 89 kb in size, it is the smallest chloroplast genome known. Unlike most chloroplast genomes it lacks any large repeat elements. The 8 kb spacer region between the 16S and 23S rRNA genes is the largest such spacer characterized to date in chloroplast DNA. This spacer region is also unusual in that it contains the rps12 gene or at least a portion thereof. Three regions polymorphic for size are present in the Codium chloroplast genome. The psbA and psbC genes map closely to one of these regions, another region is in the spacer between the 16S and 23S rRNA genes and the third is very close to or possibly within the 16S rRNA gene. The gene order in the Codium genome bears no marked resemblance to either the "consensus" vascular plant order or to that of any green algal or bryophyte genome.

Organization and nucleotide sequence of genes at both junctions between the two inverted repeats and the large single-copy region in the rice chloroplast genome

We describe the isolation and organization, at the nucleotide sequence level, of genes located at the two junctions of the large single-copy region (LSCR) and the two inverted repeats (IRA and IRB) in the rice chloroplast genome. This is the first example where the two junctions are precisely located in a monocot. In rice, a ribosomal protein gene cluster, rpl23-rpl2-rps19, which codes for the ribosomal proteins L23 (rpl23), L2 (rpl2) and S19 (rps19), lies at the ends of the two IRs near the LSCR. The inverted repeats end 45 bp from the translation stop codon of rps19. The gene for the 32-kDa photosystem II protein, psbA, is located at the extremity of the LSCR near IRA, and transcribed towards IRA. The translation stop codon of psbA is 68 bp from the right-hand junction (JLA). Thus, JLA is located within the intergenic sequence of the two genes, rps19 and psbA. Around the left-hand junction (JLB), there is a typical ribosomal protein gene cluster, rpl23-rpl2-rps19-rpl22 (rpl22 for the ribosomal protein L22). The translation start codon of rpl22 is located in the LSCR 25 bp from JLB. Therefore, JLB is located within the intergenic sequence between rps19 and rpl22.

A fern spore storage protein is genetically similar to the 1.7 S seed storage protein of Brassica napus

The ostrich fern, Matteuccia struthiopteris L., contains two globulin spore storage proteins of 2.2 S and 11.3 S, with physical characteristics similar to those of seed storage proteins of Brassica napus (rapeseed) and Raphanus sativus (radish). By the use of a cloned cDNA that encodes the 1.7 S B. napus storage protein (napin), gene sequences that hybridized with napin were detected in fern nuclear DNA, and a 900-nucleotide homologous mRNA was detected in developing spores. In vitro translation of this fern mRNA produced a 22-kD polypeptide comparable in size to the 21-kD precursor polypeptide identified in Brassica. No hybridizations were observed between the Brassica 12 S clone and either fern DNA or developing spore mRNA.

Polymorphism and gene arrangement among plastomes of ten Epilobium species

Plastid DNAs of ten different Epilobium species from four continents have been analysed using the restriction endonucleases BamHI, BglI, BglII, EcoRI, PstI, PvuII and SalI. With respect to the position of cleavage sites of those enzymes, each species has a specific plastome. Fragment patterns of different species from the same continent show a higher degree of similarity than those from different continents. Physical maps of the circular plastid DNA molecule have been constructed for each of the ten species by localising the cleavage sites of the enzymes BglI, PvuII and SalI. As in most other higher plants, the plastid DNA of Epilobium is segmentally organized into two inverted repeats separated by a large and a small single copy region. In heterologous hybridization experiments using radioactively labelled gene probes, the positions of structural genes coding for the rRNAs and for seven polypeptides have been determined. In contrast to its closest relative, Oenothera, the gene arrangement of Epilobium plastomes has the same order as in spinach. This indicates that changes in gene arrangement may be genus-specific and not the result of one or several events affecting all members of a plant family.

The sequence of the chloroplast atpB gene and its flanking regions in Chlamydomonas reinhardtii

The chloroplast (cp)-encoded CF1 ATPase beta-subunit gene (atpB) of Chlamydomonas reinhardtii and its flanking regions have been sequenced. The derived amino acid (aa) sequence is highly homologous to that of the beta-subunit gene in Escherichia coli, bovine heart mitochondria, and higher plant cp. In contrast to all other cp genomes, the CF1 epsilon subunit gene (atpE) does not lie at the 3' end of the atpB gene but maps to a position 92 kb away in the other single-copy region. Northern blots confirm that the beta subunit is not encoded as part of a dicistronic message as it is in higher plants. The region just upstream from the atpB gene in C. reinhardtii contains two small open reading frames (ORFs) and not the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase as is found in cp genomes of higher plants. No transcripts for either ORF were detected, but the codon usage in these ORFs as well as in the atpB gene follows the unique pattern of codon usage previously seen in other cp genes in C. reinhardtii.

The plastome of a brown alga,Dictyota dichotoma : I. Physical properties and the Bam HI/Sal I/Bgl II cleavage site map

Plastids of the brown algaDictyota dichotoma contain a single homogeneous DNA species which bands at a buoyant density of 1.693 g/cm(3) in neutral CsCl equilibrium density gradients. The corresponding nuclear DNA has a density of 1.715 g/cm(3). The molecular size of the plastid DNA is 123 kbp as calculated by both electron microscopy of spread intact circular molecules and gel electrophoresis following single and double digestions with various restriction enzymes. A restriction map has been constructed using the endonucleases Sal I, Bam HI, and Bgl II which cleave theDictyota plastome into 6, 12, and 17 fragments, respectively. No large repeated regions, as found in chlorophycean andEuglena plastid DNAs, were detected.Dictyota dichotoma is the first member from the chlorophyll c-line of the algal pedigree for which a physical map of plastid DNA has been established.

A 21 kilobase-pair deletion/addition difference in the inverted repeat sequence of chloroplast DNA from Chlamydomonas eugametos and C. moewusii

Our recent physical mapping of chloroplast DNA (cpDNA) from Chlamydomonas moewusii, a unicellular green alga which is interfertile with Chlamydomonas eugametos, has revealed a two-fold size difference between the inverted repeat sequences of these algae. With a size of 42 kbp, the inverted repeat of C. moewusii is the largest yet identified in any chloroplast genome. Here we have compared the arrangement of conserved sequences within the two algal inverted repeats by hybridizing cloned restriction fragments representing over 90% of these repeats to Southern blots of cpDNA digests from the two algae. We found that the size difference between the two algal inverted repeats is due to the presence of an extra DNA segment of 21 kilobase pairs (kbp) in C. moewusii. Except for this sequence, the C. moewusii inverted repeat is highly homologous to the entire C. eugametos repeat and the arrangement of conserved sequences in the two repeats is identical. Southern hybridizations with specific gene probes revealed that the conserved sequences include the rDNA region and the genes coding for the large subunit of ribulose 1,5 bisphosphate carboxylase-oxygenase (rbcL) and for the '32 kilodalton' thylakoid membrane protein (psbA). With respect to the conserved sequences, the extra 21 kbp DNA segment of C. moewusii lies in the region of psbA, most probably slightly downstream from this gene.

Mapping of transfer RNA genes on tobacco chloroplast DNA

Tobacco chloroplast tRNAs have been purified by two-dimensional polyacrylamide gel electrophoresis, identified by aminoacylation, labelled at their 3'-end and hybridized to tobacco chloroplast DNA restriction fragments, in order to establish a tRNA gene map. These hybridization studies have revealed the localization of at least seven genes in each inverted repeat region, a minimum of 22 tRNA genes in the large single copy region and one tRNA gene in the small single copy region. Comparison of the tobacco chloroplast tRNA gene map to that of maize shows many similarities, but also some differences suggesting that DNA sequence rearrangements have occurred in the chloroplast genome during evolution.