Diana B. Stein

Conservation of chloroplast genome structure among vascular plants

SummaryWe have constructed the first physical map of a gymnosperm chloroplast genome and compared its organization with those of a fern and several angiosperms by heterologous filter hybridization. The chloroplast genome of the gymnosperm Ginkgo biloba consists of a 158 kb circular chromosome that contains a ribosomal RNA-encoding inverted repeat approximately 17 kb in size. Gene mapping experiments demonstrate a remarkable similarity in the linear order and absolute positions of the ribosomal RNA genes and of 17 protein genes in the cpDNAs of Ginkgo biloba, the fern Osmunda cinnamomea and the angiosperm Spinacia oleracea. Moreover, filter hybridizations using as probes cloned fragments that cover the entirety of the angiosperm chloroplast genome reveal a virtually colinear arrangement of homologous sequence elements in these genomes representing three divisions of vascular plants that diverged some 200–400 million years ago. The only major difference in chloroplast genome structure among these vascular plants involves the size of the rRNA-encoding inverted repeat, which is only 10 kb in Osmunda, 17 kb in Ginkgo, and about 25 kb in most angiosperms. This size variation appears to be the result of spreading of the repeat through previously single copy sequences, or the reverse process of shrinkage, unaccompanied by any overall change in genome complexity.

Structural evolution and flip-flop recombination of chloroplast DNA in the fern genus Osmunda

SummaryThe evolution and recombination of chloroplast genome structure in the fern genus Osmunda were studied by comparative restriction site mapping and filter hybridization of chloroplast DNAs (cpDNAs) from three species — 0. cinnamomea, 0. claytoniana and 0. regalis. The three 144 kb circular genomes were found to be colinear in organization, indicating that no major inversions or transpositions had occurred during the approximately 70 million years since their radiation from a common ancestor. Although overall size and sequence arrangement are highly conserved in the three genomes, they differ by an extensive series of small deletions and insertions, ranging in size from 50 bp to 350 by and scattered more or less at random throughout the circular chromosomes. All three chloroplast genomes contain a large inverted repeat of approximately 10 kb in size. However, hybridizations using cloned fragments from the 0. cinnamomea and 0. regalis genomes revealed the absence of any dispersed repeats in at least 50% of the genome. Analysis with restriction enzymes that fail to cleave the 10 kb inverted repeat indicated that each of the three fern chloroplast genomes exists as an equimolar population of two isomeric circles differing only in the relative orientation of their two single copy regions. These two inversion isomers are inferred to result from high frequency intramolecular recombination between paired inverted repeat segments. In all aspects of their general organization, recombinational heterogeneity, and extent of structural rearrangement and length mutation, these fern chloroplast genomes resemble very closely the chloroplast genomes of most angiosperms.

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

SummaryChloroplast DNA from the fern Osmunda einnamomea was isolated by a sucrose gradient procedure utilizing PEG to stabilize chloroplasts. Analysis with the restriction endonucleases PvuII, Sacl and BstEII indicates a chloroplast genome size of 144 kb. A physical map of the fragments produced by these three enzymes was constructed by filter hybridizations using purified PvuII fragments as hybridization probes. The Osmunda chloroplast genome is circular and contains an inverted repeat 8–13 kb in size.Gene probes from tobacco, corn and spinach were used to map the positions of six genes on the Osmunda chloroplast chromosome. The 16S and 23S ribosomal RNAs are encoded by duplicate genes which lie within the inverted repeat. Genes for the large subunit of ribulose-1,5-bisphosphate carboxylase, a photosystem II polypeptide, and the alpha and beta subunits of chloroplast coupling factor are located in three different segments of the large single copy region.The Osmunda chloroplast genome is remarkably similar in size, conformation, physical organization, and map positions of known genes, to chloroplast DNA from a number of angiosperms. The major difference between chloroplast DNA from this fern and angiosperms is that the inverted repeat is smaller in Osmunda (8–13 kb) than in angiosperms (22–25 kb).

The relationships of the Papuasian Cyatheaceae to new world tree ferns

Phylogenetic hypotheses about the Cyatheaceae have been based largely on either New World or Old World species. In this study we examine molecular data for species from both hemispheres. Chloroplast DNA restriction site variation has been compared among 23 species of Cyatheaceae from Papuasia and the Pacific and 61 species from the New World. Parsimony anal- ysis of the variation documented supports the existence of three major clades, and reveals a cor- relation between phylogenetic relationship and biogeography. Species from the Neotropics appear derived with respect to those from the Paleotropics in the Alsophila clade; in this clade species from Papua New Guinea and Lord Howe Island are basal to those from the American tropics. A similar relationship is tentatively suggested for the Cyathea clade, where the sole Old World representative, (C. howeana) from Lord Howe Island, is basal to the remainder of the clade. This finding extends the worldwide distribution of the Cyathea clade across the Pacific. No clear cor- relation between phylogeny and biogeography of the Sphaeropteris clade was observed based on current data. These results suggest that additional sampling from other regions in the Old World tropics may further elucidate the evolutionary history of this group of plants.

The chlL (frxC)* gene: phylogenetic distribution in vascular plants and DNA sequence from Polystichum acrostichoides (Pteridophyta) and Synechococcus sp. 7002 ( Cyanobacteria)

We examinedchlL (frxC) gene evolution using several approaches. Sequences from the chloroplast genome of the fernPolystichum acrostichoides and from the cyanobacteriumSynechococcus sp. 7002 were determined and found to be highly conserved. A complete physical map of the fern chloroplast genome and partial maps of other vascular plant taxa show thatchlL is located primarily in the small single copy region as inMarchantia polymorpha. A survey of a wide variety of non-angiospermous vascular plant DNAs shows thatchlL is widely distributed but has been lost in the pteridophytePsilotum and (presumably independently) within the Gnetalean gymnosperms.

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 ofBrassica napus (rapeseed) andRaphanus sativus (radish). By the use of a cloned cDNA that encodes the 1.7 SB. 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 inBrassica. No hybridizations were observed between theBrassica 12 S clone and either fern DNA or developing spore mRNA.

Chloroplast DNA evolution and phylogeny of some polystichoid ferns

Restriction site mutations in the chloroplast DNAs from members of the fern genus, Phanerophlebia, and some representatives of Cyrtomium and Polystichum were used to elucidate phylogenetic relationships within and between these groups. Evidence is presented against the hypothesis that Phanerophlebia was derived from Cyrtomium; rather the two genera appear to be convergent segregate genera that arose independently from Polystichum. The chloroplast DNA mutations also provide information on the maternal parentage of several tetraploid species