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PubMed2003

Plant LTR-retrotransposons and MITEs: control of transposition and impact on the evolution of plant genes and genomes.

Transposons are genetic elements that can move, and sometimes spread, within genomes, and that constitute an important fraction of eukaryote genomes. Two types of transposons, long terminal repeat (LTR)-retrotransposons and miniature inverted-repeat transposable elements (MITEs), are highly represented in plant genomes, and can account for as much as 50-80% of the total DNA content. In the last few years it has been shown that, in spite of their mutagenic capacity, both LTR-retrotransposons and MITEs can be found associated to genes, suggesting that their activity has influenced the evolution of plant genes. In this review we will summarise recent data on the control of the activity and the impact of both LTR-retrotransposons and MITEs on the evolution of plant genes and genomes.

DNA Transposable Elements↗
PubMed2001

Directed molecular evolution in plant improvement.

Directed molecular evolution is a powerful tool to evolve genes with commercial applications. Its most common application is to evolve enzymes with improved kinetics, altered substrate or product specificities, or improved function in different cellular environments. The technique is beginning to be applied to goals relevant to agriculture. Recent examples include the generation of novel carotenoids, enhanced herbicide detoxification, and the improvement of insect resistance genes.

Bacillus thuringiensis↗
PubMed1998

Maize as a model system for investigating the molecular basis of morphological evolution in plants.

The genetic and molecular bases of morphological evolution in plants are largely unknown. To address questions surrounding this issue, my laboratory has been investigating the evolution of maize from its wild ancestor, teosinte. Our research suggests that a few gene changes of large effect were involved in the evolution of several different traits including plant and ear architecture and kernel color. In cases where gene function could be identified, the genes involved in maize evolution were regulatory in nature. Additional evidence suggests that changes in cis regulatory elements of the regulatory genes rather than changes in protein function underlie the evolution of the traits analyzed. Future work with other plant species, especially wild plants, will be required to test the generality of our observations with maize.

Biological Evolution↗
PubMed2001

Co-evolution and plant resistance to natural enemies.

Co-evolution between plants and their natural enemies is generally believed to have generated much of the Earth's biological diversity. A process analogous to co-evolution occurs in agricultural systems, in which natural enemies adapt to crop resistance introduced by breeding or genetic engineering. Because of this similarity, the investigation of resistance mechanisms in crops is helping to elucidate the workings of co-evolution in nature, while evolutionary principles, including those derived from investigation of co-evolution in nature, are being applied in the management of resistance in genetically engineered crops.

Animals↗
PubMed1989

Evolution of plant mitochondrial genomes via substoichiometric intermediates.

Comparison of the modern fertile maize mitochondrial genome (N) with an ancestral maize mitochondrial genome (RU) reveals a 12 kb duplication (containing the atpA gene) in the modern genome that is absent from the ancestor. Cloning, mapping, and sequencing of the relevant portions of the ancestral genome shows that this duplication probably arose via a three-stage recombination process involving substoichiometric intermediates. Comparison with analogous observations on yeast mitochondrial genomes suggests that this three-stage model of genome reorganization can be generally applied to plant mitochondrial genomes to explain both deletions and the creation of novel repeats, common features of plant mitochondrial genome evolution.

Base Sequence↗
PubMed2002

Structure and evolution of plant disease resistance genes.

This article reviews recent advances that shed light on plant disease resistance genes, beginning with a brief overview of their structure, followed by their genomic organization and evolution. Plant disease resistance genes have been exhaustively investigated in terms of their structural organization, sequence evolution and genome distribution. There are probably hundreds of NBS-LRR sequences and other types of R-gene-like sequences within a typical plant genome. Recent studies revealed positive selection and selective maintenance of variation in plant resistance and defence-related genes. Plant resistance genes are highly polymorphic and have diverse recognition specificities. R-genes occur as members of clustered gene families that have evolved through duplication and diversification. These genes appear to evolve more rapidly than other regions of the genome, and domains such as the leucine-rich repeat, are subject to adaptive selection

Evolution, Molecular↗
PubMed2005

Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution.

The traditional approach to plant molecular phylogenetics involves amplifying, sequencing and analyzing one or a few genes from many species and is conducive to broad taxon sampling. An independent approach involves chloroplast genome sequencing, providing much larger amounts of data per taxon but for a smaller number of species. In principle, the two strategies can inform each other but in practice their results sometimes conflict for reasons that are currently debated. An Opinion article published in the October 2004 issue of Trends in Plant Science cautioned against the pursuit of genome-based phylogenies. Here, we provide a different perspective on issues at the heart of the current debate and defend the use of chloroplast genome phylogenetics for crucial species because it provides an independent test of hypotheses generated by the traditional approach.

Chloroplasts↗
PubMed1987

The evolution of plant reproductive characters; sexual versus natural selection.

The rôle of sexual selection in the evolution of plant reproductive characters has become a widely discussed topic among plant population biologists. For many reproductive characters, it is difficult to distinguish whether sexual selection or natural selection has been the more important force. We propose a definition of sexual selection for cosexual species and critically review the topic of sexual selection in plants. The emphasis of the chapter is on the evolution of plant reproductive characters, rather than on the issue of whether certain phenomena should be classified as sexual or natural selection. We do, however, argue that the category of sexual selection should not include the phenomena of inbreeding depression, genetically based self-incompatibility systems controlled by one or a few loci, or the effects of wide crossing and specific combining ability. We then discuss the available information on pollen competition and progeny quality, fruit and seed abortion, and the rôle of pollinator attraction in male and female fertility.

Biological Evolution↗
PubMed1998

The evolution of plant development.

There has been much recent interest in the evolution of plant development and especially in trying to understand the developmental genetic basis of morphological evolution. Significant progress has been made in understanding the evolution of floral organization and the mechanisms that might underlie the evolution of compound leaves and inflorescence morphology. These advances are reinforcing the idea that phenotypic evolution can proceed via changes at few loci of large effect and that promoter evolution may be an important and frequent mechanism.

Evolution, Molecular↗
PubMed2002

Genetic variation for disease resistance and tolerance among Arabidopsis thaliana accessions.

Pathogens can be an important selective agent in plant evolution because they can severely reduce plant fitness and growth. However, the role of pathogen selection on plant evolution depends on the extent of genetic variation for resistance traits and their covariance with host fitness. Although it is usually assumed that resistance traits will covary with plant fitness, this assumption has not been tested rigorously in plant-pathogen interactions. Many plant species are tolerant to herbivores, decoupling the relationship between resistance and fitness. Tolerance to pathogens can reduce selection for resistance and alter the effect of pathogens on plant evolution. In this study, we measured three components of Arabidopsis thaliana resistance (pathogen growth, disease symptoms, and host fitness) to the bacteria Pseudomonas syringae and investigated their covariation to determine the relative importance of resistance and tolerance. We observed extensive quantitative variation in the severity of disease symptoms, the bacterial population size, and the effect of infection on host fitness among 19 accessions of A. thaliana infected with P. syringae. The severity of disease symptoms was strongly and positively correlated with bacterial population size. Although the average fitness of infected plants was smaller than noninfected plants, we found no correlation between the bacterial growth or symptoms expressed by different accessions of A. thaliana and their relative fitness after infection. These results indicate that the accessions studied vary in tolerance to P. syringae, reducing the strength of selection on resistance traits, and that symptoms and bacterial growth are not good predictors of host fitness.

Arabidopsis↗
PubMed2003

Azolla--a model organism for plant genomic studies.

The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N2-fixing cyanobacterium, Anabaena azollae, and its moderate-sized genome. The goals of this genome project are not only to understand the biology of the Azolla genome to promote its applications in biological research and agriculture practice but also to gain critical insights about evolution of plant genomes. Together with the strategic and technical improvement as well as cost reduction of DNA sequencing, the deciphering of their genetic code is imminent.

Cyanobacteria↗
PubMed2001

[Studies of the meiosis of 2n gamete apomictic wheat grass (Elymus rectisetus)].

The formation of polyploid was mainly through the combination of 2n gamete, and the apomixis played an important role in plant evolution and plant breeding. In general, the formation of male gamete and female gamete in apomictic plants are obviously different, i.e., the formation of embryo sac was through apomixis (form into 2n female gamete); however, the formation of male gamete was through normal meiosis (form into 1n male gamete). The 2n male gamete apomictic wheat grass was more important than 1n male gamete apomictic wheat grass, because the 2n male gamete can bring all genes including apomictic gene into other plant. The meiosis of 2n male gamete apomictic wheat grass (Elymus. rectisetus) was observed through Olympus AH3 microscope; the results showed that the meiosis of 2n gamete apomictic wheat grass was very abnomal. In the interphase, lots of mini-nucleus were found. Inverted cycle, multibivalent and lagging chromosome were also found in the prophase. In metaphase, chromosomes frequently show unequal division tendency; In anaphase I and telophase I, completely unequal division, modified meiosis, the tendency of nucleus fusion and other abnormal phenomena were found. These phenomena directly lead to the production of 2n gamete. In meiosis II, the abnormalities mainly lie in the proceeding of microspore, dyad (55.7%), triad (23.7%) and tetrad (21.6%) were found. The abnormal of those proceeding also lead to the production of 2n gamete.

Meiosis↗
PubMed1990

Gene expression and parental dominance in hybrid plants.

Genomic imprinting, where the genes from one parent have different expression properties to those of the other parent, occurs in plants. It has potentially significant consequences because of the importance of hybrids in plant evolution and plant breeding, and provides a mechanism that can hide genetic variation for many generations. The study of nuclear organization shows that chromosome and genome position relates to imprinting in F1 hybrids, with peripheral genomes tending to be expressed preferentially. In some inbred, polyploid hybrids, such as Triticale (a wheat x rye hybrid), treatment with the demethylation agent azacytidine releases hidden variation, which was perhaps lost because of imprinting phenomena.

Chromosomes↗
PubMedDate not supplied

Evolution of the class III HD-Zip gene family in land plants.

Arabidopsis class III homeodomain-leucine zipper (HD-Zip III) proteins play overlapping, distinct, and antagonistic roles in key aspects of development that have evolved during land plant evolution. To better understand this gene family's role in plant evolution and development as well as to address broader questions of how duplicated genes functionally diversify, we investigated the evolutionary history of this gene family. Phylogenetic analyses including homologs from diverse land plants indicate that a gene duplication event before the angiosperm--gymnosperm split gave rise to two gene lineages that diversified during angiosperm plant radiation. Heterologous expression of an HD-Zip III gene from the nonvascular plant moss within the Arabidopsis HD-zip III revoluta mutant modified but did not complement the phenotype. Comparison of the expression domains of flowering and nonflowering plant homologs indicate an ancestral role in vascular development and organ initiation but not in specifying organ polarity, a prominent role for angiosperm homologs.

Arabidopsis↗
PubMed2000

Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes.

The majority of plant disease resistance genes are members of very large multigene families. They encode structurally related proteins containing nucleotide binding site domains (NBS) and C-terminal leucine rich repeats (LRR). The N-terminal region of some resistance genes contain a short sequence called TIR with homology to the animal innate immunity factors, Toll and interleukin receptor-like genes. Only a few plant resistance genes have been functionally analyzed and the origin and evolution of plant resistance genes remain obscure. We have reconstructed gene phylogeny by exhaustive analysis of available genome and amplified NBS domain sequences. Our study shows that NBS domains faithfully predict whole gene structure and can be divided into two major groups. Group I NBS domains contain group-specific motifs that are always linked with the TIR sequence in the N terminus. Significantly, Group I NBS domains and their associated TIR domains are widely distributed in dicot species but were not detected in cereal databases. Furthermore, Group I specific NBS sequences were readily amplified from dicot genomic DNA but could not be amplified from cereal genomic DNA. In contrast, Group II NBS domains are always associated with putative coiled-coil domains in their N terminus and appear to be present throughout the angiosperms. These results suggest that the two main groups of resistance genes underwent divergent evolution in cereal and dicot genomes and imply that their cognate signaling pathways have diverged as well.

Amino Acid Sequence↗
PubMed2002

Plant genome evolution: lessons from comparative genomics at the DNA level.

Angiosperm genomes show tremendous variability in genome size and chromosome number. Nevertheless, comparative genetic mapping has revealed genome collinearity of closely related species. Sequence-based comparisons were used to assess the conservation of gene arrangements. Numerous small rearrangements, insertions/deletions, duplications, inversions and translocations have been detected. Importantly, comparative sequence analyses have unambiguously shown micro-collinearity of distantly related plant species. Duplications and subsequent gene loss have been identified as a particular important factor in the evolution of plant genomes.

Base Composition↗
PubMed2006

EdiPy: a resource to simulate the evolution of plant mitochondrial genes under the RNA editing.

EdiPy is an online resource appropriately designed to simulate the evolution of plant mitochondrial genes in a biologically realistic fashion. EdiPy takes into account the presence of sites subjected to RNA editing and provides multiple artificial alignments corresponding to both genomic and cDNA sequences. Each artificial data set can successively be submitted to main and widespread evolutionary and phylogenetic software packages such as PAUP, Phyml, PAML and Phylip. As an online bioinformatic resource, EdiPy is available at the following web page: http://biologia.unical.it/py_script/index.html.

Computational Biology↗
PubMedDate not supplied

[The evolution of plant life span: facts and hypotheses].

There are two different views on the evolution of life forms in Cormophyta: from woody plants to herbaceous ones or in opposite direction - from herbs to trees. In accordance with these views it is supposed that life span in plants changed in the course of evolution from many years (perennials) to few years (annuals, biennials), or went in reverse - from few years to many years. The author discusses the problems of senescence and longevity in Cormophyta in the context of various hypotheses of ageing (programmed death theory, mutation accumulation, antagonistic pleiotropy, disposable soma, genes of ageing, genes of longevity). Special attention is given to bio-morphological aspects of longevity and cases of non-ageing plants ("negative senescence", "potential immortality"). It is proposed to distinguish seven models of simple ontogenesis in Cormophyta that can exemplify the diversity of mechanisms of ageing and longevity. The evolution of life span in plants is considered as an indirect result of natural selection of other characteristics of organisms or as a consequence of fixation of modifications (episelectional evolution). It seems that short life span could emerge several times during evolution of one group of plants, thus favoring its adaptive radiation.

Biological Evolution↗