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PubMed2004

Conservation and diversity in flower land.

During the past decade, enormous progress has been made in understanding the molecular regulation of flower development. In particular, homeotic genes that determine the identity of the floral organs have been characterised from different flowering plants, revealing considerable conservation among angiosperm species. On the other hand, evolutionary diversification has led to enormous variation in flower morphology. Increasing numbers of reports have described differences in the regulation, redundancy and function of homeotic genes from various species. These fundamentals of floral organ specification are therefore an ideal subject for comparative analyses of flower development, which will lead to a better understanding of plant evolution, plant development and the complexity of molecular mechanisms that control flower development and morphology.

Arabidopsis↗
PubMed2003

Variation and evolution of plant virus populations.

Over the last 15 years, interest in plant virus evolution has re-emerged, as shown by the increasing number of papers published on this subject. In recent times, research in plant virus evolution has been viewed from a molecular, rather than populational, standpoint, and there is a need for work aimed at understanding the processes involved in plant virus evolution. However, accumulated data from analyses of experimental and natural populations of plant viruses are beginning to delineate some trends that often run contrary to accepted opinion: (1) high mutation rates are not necessarily adaptive, as a large fraction of the mutations are deleterious or lethal; (2) in spite of high potential for genetic variation, populations of plant viruses are not highly variable, and genetic stability is the rule rather than the exception; (3) the degree of constriction of genetic variation in virus-encoded proteins is similar to that in their eukaryotic hosts and vectors; and (4) in spite of huge census sizes of plant virus populations, selection is not the sole factor that shapes their evolution, and genetic drift may be important. Here, we review recent advances in understanding plant virus evolution, and describe the experimental and analytical methods most suited to this purpose.

Biological Evolution↗
PubMed2004

Organelle nuclei in higher plants: structure, composition, function, and evolution.

Plant cells have two distinct types of energy-converting organelles: plastids and mitochondria. These organelles have their own DNAs and are regarded as descendants of endosymbiotic prokaryotes. The organelle DNAs associate with various proteins to form compact DNA-protein complexes, which are referred to as organelle nuclei or nucleoids. Various functions of organelle genomes, such as DNA replication and transcription, are performed within these compact structures. Fluorescence microscopy using the DNA-specific fluorochrome 4',6-diamidino-2-phenylindole has played a pivotal role in establishing the concept of "organelle nuclei." This fluorochrome has also facilitated the isolation of morphologically intact organelle nuclei, which is indispensable for understanding their structure and composition. Moreover, development of an in vitro transcription?DNA synthesis system using isolated organelle nuclei has provided us with a means of measuring and analyzing the function of organelle nuclei. In addition to these morphological and biochemical approaches, genomics has also had a great impact on our ability to investigate the components of organelle nuclei. These analyses have revealed that organelle nuclei are not a vestige of the bacterial counterpart, but rather are a complex system established through extensive interaction between organelle and cell nuclear genomes during evolution. Extensive diversion or exchange during evolution is predicted to have occurred for several important structural proteins, such as major DNA-compacting proteins, and functional proteins, such as RNA and DNA polymerases, resulting in complex mechanisms to control the function of organelle genomes. Thus, organelle nuclei represent the most dynamic front of interaction between the three genomes (cell nuclear, plastid, and mitochondrial) constituting eukaryotic plant cells.

Cell Nucleus↗
PubMed2005

MIKC-type MADS-domain proteins: structural modularity, protein interactions and network evolution in land plants.

MIKC-type proteins represent a class of MADS-domain transcription factors and are defined by a unique domain structure: in addition to the highly conserved DNA-binding MADS-domain, they have three other domains ('I', 'K' and 'C'), with the keratin-like K-domain being the most highly conserved and characteristic one. The number and functional diversity of MIKC-type proteins increased considerably during land plant evolution, culminating in higher flowering plants, where they dominate the control of reproductive development from early to late stages. We wonder how one special class of proteins became important in the control of essentially all stages of a morphogenetic process. All MADS-domain proteins appear to bind to DNA as homo- or heterodimers and may function as part of ternary transcription factor complexes involving non-MADS-domain proteins. Only MIKC-type proteins, however, generate complex intrafamily interaction networks. These are based on the special potential of MIKC-type proteins to form complexes involving more than two homologous proteins constituting transcriptional regulators. We speculate that the potential to form heteromultimers of homologous proteins was achieved by the acquisition of the K-domain during evolution. There is emerging evidence that organismal complexity arises from progressively more elaborate regulation of gene expression. We hypothesize that combinatorial multimer formation of MIKC-type MADS-domain proteins facilitated an unusually efficient and rapid functional diversification based on gene duplication, sequence divergence and fixation. This 'networking' may have enabled a more sophisticated transcriptional control of target genes which was recruited for controlling increasingly complex and diverse developmental pathways during the rapid origin and diversification of plant reproductive structures. Therefore, MIKC-type proteins may owe their evolutionary 'success' and present-day developmental importance in part to their modular domain structure. Investigating the evolution of MIKC-type genes may thus help to better understand origin and diversification of gene regulatory networks.

Amino Acid Sequence↗
PubMed1985

Evolution of green plants as deduced from 5S rRNA sequences.

We have constructed a phylogenic tree for green plants by comparing 5S rRNA sequences. The tree suggests that the emergence of most of the uni- and multicellular green algae such as Chlamydomonas, Spirogyra, Ulva, and Chlorella occurred in the early stage of green plant evolution. The branching point of Nitella is a little earlier than that of land plants and much later than that of the above green algae, supporting the view that Nitella-like green algae may be the direct precursor to land plants. The Bryophyta and the Pteridophyta separated from each other after emergence of the Spermatophyta. The result is consistent with the view that the Bryophyta evolved from ferns by degeneration. In the Pteridophyta, Psilotum (whisk fern) separated first, and a little later Lycopodium (club moss) separated from the ancestor common to Equisetum (horsetail) and Dryopteris (fern). This order is in accordance with the classical view. During the Spermatophyta evolution, the gymnosperms (Cycas, Ginkgo, and Metasequoia have been studied here) and the angiosperms (flowering plants) separated, and this was followed by the separation of Metasequoia and Cycas (cycad)/Ginkgo (maidenhair tree) on one branch and various flowering plants on the other.

Journal Article↗
PubMed2006

The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants.

The phylogenetic positions of bryophytes and charophytes, together with their genome features, are important for understanding early land plant evolution. Here we report the complete nucleotide sequence (105,340 bp) of the circular-mapping mitochondrial DNA of the moss Physcomitrella patens. Available evidence suggests that the multipartite structure of the mitochondrial genome in flowering plants does not occur in Physcomitrella. It contains genes for 3 rRNAs (rnl, rns, and rrn5), 24 tRNAs, and 42 conserved mitochondrial proteins (14 ribosomal proteins, 4 ccm proteins, 9 nicotinamide adenine dinucleotide dehydrogenase subunits, 5 ATPase subunits, 2 succinate dehydrogenase subunits, apocytochrome b, 3 cytochrome oxidase subunits, and 4 other proteins). We estimate that 5 tRNA genes are missing that might be encoded by the nuclear genome. The overall mitochondrial genome structure is similar in Physcomitrella, Chara vulgaris, Chaetosphaeridium globosum, and Marchantia polymorpha, with easily identifiable inversions and translocations. Significant synteny with angiosperm and chlorophyte mitochondrial genomes was not detected. Phylogenetic analysis of 18 conserved proteins suggests that the moss-liverwort clade is sister to angiosperms, which is consistent with a previous analysis of chloroplast genes but is not consistent with some analyses using mitochondrial sequences. In Physcomitrella, 27 introns are present within 16 genes. Nine of its intron positions are shared with angiosperms and 4 with Marchantia, which in turn shares only one intron position with angiosperms. The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes.

Base Sequence↗
PubMed2000

Maize as a model for the evolution of plant nuclear genomes.

The maize genome is replete with chromosomal duplications and repetitive DNA. The duplications resulted from an ancient polyploid event that occurred over 11 million years ago. Based on DNA sequence data, the polyploid event occurred after the divergence between sorghum and maize, and hence the polyploid event explains some of the difference in DNA content between these two species. Genomic rearrangement and diploidization followed the polyploid event. Most of the repetitive DNA in the maize genome is retrotransposable elements, and they comprise 50% of the genome. Retrotransposon multiplication has been relatively recent-within the last 5-6 million years-suggesting that the proliferation of retrotransposons has also contributed to differences in DNA content between sorghum and maize. There are still unanswered questions about repetitive DNA, including the distribution of repetitive DNA throughout the genome, the relative impacts of retrotransposons and chromosomal duplication in plant genome evolution, and the hypothesized correlation of duplication events with transposition. Population genetic processes also affect the evolution of genomes. We discuss how centromeric genes should, in theory, contain less genetic diversity than noncentromeric genes. In addition, studies of diversity in the wild relatives of maize indicate that different genes have different histories and also show that domestication and intensive breeding have had heterogeneous effects on genetic diversity across genes.

Biological Evolution↗
PubMed2005

Symbiosis versus competition in plant virus evolution.

Darwin's theory of evolution by natural selection has been supported by molecular evidence and by experimental evolution of viruses. However, it might not account for the evolution of all life, and an alternative model of evolution through symbiotic relationships also has gained support. In this review, the evolution of plant viruses has been reinterpreted in light of these two seemingly opposing theories by using evidence from the earliest days of plant virology to the present. Both models of evolution probably apply in different circumstances, but evolution by symbiotic association (symbiogenesis) is the most likely model for many evolutionary events that have resulted in rapid changes or the formation of new species. In viruses, symbiogenesis results in genomic reassortment or recombination events among disparate species. These are most noticeable by phylogenetic comparisons of extant viruses from different taxonomic groups.

Evolution, Molecular↗
PubMed1996

CP12: a small nuclear-encoded chloroplast protein provides novel insights into higher-plant GAPDH evolution.

Higher-plant chloroplast NAD(P)-glyceraldehyde 3-phosphate dehydrogenase (NAD(P)-GAPDH; EC 1.2.1.13) is composed of two different nuclear-encoded subunits, GAPA and GAPB, forming the highly active heterotetrameric A2B2 enzyme. The main difference between these two subunits is a C-terminal extension of about 30 amino acid residues of GAPB. We present cDNA clones for a nuclear-encoded chloroplast protein from pea, spinach and tobacco, which we have named CP12. The mature protein consists of only 74, 75 and 76 amino acid residues, respectively and contains two domains with significant homology to the C-terminal extension of GAPB. Affinity chromatography approaches reveal also a specific interaction between CP12 and chloroplast GAPDH. Northern blot analysis indicates that CP12 is, like plastid GAPDH, expressed in green and also in etiolated leaves. Further homology is observed between CP12 and ORF3, an open reading frame located in the hox gene cluster of Anabaena variabilis. This gene cluster encodes the subunits of the bidirectional NADP(+)-dependent [NiFeS] dehydrogenase. We propose therefore a common evolutionary origin of CP12 and higher-plant chloroplast GAPDH subunit GAPB from the cyanobacterial ORF3.

Amino Acid Sequence↗
PubMed2002

The genetics of plant morphological evolution.

Considerable progress has been made in identifying genes that are involved in the evolution of plant morphologies. Elements of the ABC model of flower development are conserved throughout angiosperms, and homologous MADS-box genes function in gymnosperm reproduction. Candidate gene and mapping analyses of floral symmetry, sex determination, inflorescence architecture, and compound leaves provide intriguing glimpses into the evolution of morphological adaptations.

ATP-Binding Cassette Transporters↗
PubMed2000

Insights into the structural and functional evolution of plant genomes afforded by the nucleotide sequences of chromosomes 2 and 4 of Arabidopsis thaliana.

The rapidly accumulating genome sequence data from the plant Arabidopsis thaliana allows more detailed analysis of genome content and organisation than ever before possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing significant homology to another protein of A. thaliana. Many duplicated genes occur in arrays of conserved order and indicate that A. thaliana is likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocations, duplication and loss of individual genes or small groups of genes.

Arabidopsis↗
PubMed2004

[The evolution of plant disease resistance gene].

The evolution of plant disease resistance genes has shaped in some kinds of common forms. The duplication of plant progenitor disease resistance gene creates disease resistance gene loci. The intragenic and extragenic recombination results in variation. Recombination also is involved in generation novel resistance specificities. In addition, the leucine-rich repeats (LRRs) involved in recognitional specificity are subject to adaptive selection. Insertion of transposable elements into several resistance gene loci result in further evolution of resistance genes. With the evolution of plant disease resistance genes, the R genes (resistance genes)-mediated response shows diversification which represents different stages in the oscillating evolution between plants and their pathogens.

Adaptation, Physiological↗
PubMed2003

Tertiary trisomics in the garden pea as a model of B chromosome evolution in plants.

It is hypothesized that, in plants, genetically empty B chromosomes may originate from the extra chromosome (E) of tertiary trisomics if (i) the region of basic chromosomes homologous to the E (H-region) harbors a sporophytic lethal covered by the wild-type allele in E, and (ii) crossing-over between E and the H-region is suppressed. Under these conditions, most loss-of-function mutations occurring in the H-region are deleterious for haploid gametophytes, whereas those occurring in E are neutral or advantageous for hyperploid (n+1) gametophytes. As a result, natural selection at the gametophyte level can lead to the degeneration of E, leaving the H-region intact. Using Hammarlund translocation T(3-6)a, we synthesized two trisomic lines of the garden pea (Pisum sativum L.), where E was composed of the short arms of chromosomes 3 and 6 and the H-region carried recessive markers. In the trisomic line TRIS, we found few crossovers between E and the H-region. In the trisomic line TRUST, obtained after a change of basic chromosome constitution, recombination in this region was completely suppressed. After induction in the H-region of TRUST of a recessive sporophytic mutation rmv, two 15-chromosome lines of stable trisomics were established. One of them passed 11 generations, having produced more than 6000 individuals, all of them trisomic, and E remained present as a single element with no pairing partners. No tetrasomics were detected in these lines. If such trisomics occurred in nature, their extra chromosomes are likely to become a B chromosome.

Chromosomes, Plant↗
PubMed2006

Mitosis, stature and evolution of plant mating systems: low-Phi and high-Phi plants.

There is a long-recognized association in plants between small stature and selfing, and large stature and outcrossing. Inbreeding depression is central to several hypotheses for this association, but differences in the evolutionary dynamics of inbreeding depression associated with differences in stature are rarely considered. Here, we propose and test the Phi model of plant mating system evolution, which assumes that the per-generation mutation rate of a plant is a function of the number of mitoses (Phi) that occur from zygote to gamete, and predicts fundamental differences between low-Phi (small-statured) and high-Phi (large-statured) plants in the outcomes of the joint evolution of outcrossing rate and inbreeding depression. Using a large dataset of published population genetic studies of angiosperms and conifers, we compute fitted values of inbreeding depression and deleterious mutation rates for small- and large-statured plants. Consistent with our Phi model, we find that populations of small-statured plants exhibit a range of mating systems, significantly lower mutation rates, and intermediate inbreeding depression, while large-statured plants exhibit very high mutation rates and the maximum inbreeding depression of unity. These results indicate that (i) inbred progeny typically observed in large-statured plant populations are completely lost prior to maturity in nearly all populations; (ii) evolutionary shifts from outcrossing to selfing are generally not possible in large-statured species, rather, large-statured species are more likely to evolve mating systems that avoid selfing such as self-incompatibility and dioecy; (iii) destabilization of the mating system-high selfing rate with high-inbreeding depression-might be a common occurrence in large-statured species; and (iv) large-statured species in fragmented populations might be at higher risk of extinction than previously thought. Our results help to unify and simplify a large and diverse field of research, and serve to emphasize the importance that developmental and genetic constraints play in the evolution of plant mating systems.

Evolution, Molecular↗
PubMed2003

Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family.

Homologues of barley Mlo encode the only family of seven-transmembrane (TM) proteins in plants. Their topology, subcellular localization, and sequence diversification are reminiscent of those of G-protein coupled receptors (GPCRs) from animals and fungi. We present a computational analysis of MLO family members based on 31 full-size and 3 partial sequences, which originate from several monocot species, the dicot Arabidopsis thaliana, and the moss Ceratodon purpureus. This enabled us to date the origin of the Mlo gene family back at least to the early stages of land plant evolution. The genomic organization of the corresponding genes supports a monophyletic origin of the Mlo gene family. Phylogenetic analysis revealed five clades, of which three contain both monocot and dicot members, while two indicate class-specific diversification. Analysis of the ratio of nonsynonymous-to-synonymous changes in coding sequences provided evidence for functional constraint on the evolution of the DNA sequences and purifying selection, which appears to be reduced in the first extracellular loop of 12 closely related orthologues. The 31 full-size sequences were examined for potential domain-specific intramolecular coevolution. This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function.

Amino Acid Sequence↗