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PubMed1994

Chloroplast and nuclear gene sequences indicate late Pennsylvanian time for the last common ancestor of extant seed plants.

We have estimated the time for the last common ancestor of extant seed plants by using molecular clocks constructed from the sequences of the chloroplastic gene coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcL) and the nuclear gene coding for the small subunit of rRNA (Rrn18). Phylogenetic analyses of nucleotide sequences indicated that the earliest divergence of extant seed plants is likely represented by a split between conifer-cycad and angiosperm lineages. Relative-rate tests were used to assess homogeneity of substitution rates among lineages, and annual angiosperms were found to evolve at a faster rate than other taxa for rbcL and, thus, these sequences were excluded from construction of molecular clocks. Five distinct molecular clocks were calibrated using substitution rates for the two genes and four divergence times based on fossil and published molecular clock estimates. The five estimated times for the last common ancestor of extant seed plants were in agreement with one another, with an average of 285 million years and a range of 275-290 million years. This implies a substantially more recent ancestor of all extant seed plants than suggested by some theories of plant evolution.

Biological Evolution↗

PubMedDate not supplied

[Molecular biological research on the origin of the angiosperms].

Nucleotide sequence of 23S-5S chloroplast rDNA spacer region including 4.5S rRNA gene of several dozens of seed plants was determined. The data obtained were used to construct phylogenetic trees and to compare them with the analogous data from literature. Topologies of trees constructed for various types of macromolecules and by different methods demonstrate obvious similarities although they are not identical. Some clue stages of seed plants evolution still remain obscure. Critical analysis of all the available information allows to come to several more or less definite conclusions. All the data say that angiosperms are a monophyletic group which diversified far before their fossils are definitely registered, i.e., before lower Cretaceous. Ancestral angiosperms were not genealogicaly related to modern woody Magnoliales but were represented by "paleoherbs", i. e. herbaceous and semiherbaceous magnoliids and monocots. Monocots originated at the earliest stages of angiosperms evolution and are not, probably, monophyletic. Woody Magnoliales and eudicots with tricolpate pollen seem to appear later in evolution. The conclusion that Gnetales is a sister group to angiosperms does not find enough support in molecular studies. Summing up, it looks as if a long period of existence of angiophytes preceded the pre-Cretaceous angiosperms irradiation. This line of development originated simultaneously with phylogenetic lineages of modern gymnosperms.

Base Sequence↗

PubMed2006

Hybridization, polyploidy, and the evolution of sexual systems in Mercurialis (Euphorbiaceae).

Hybridization and polyploidy are widely believed to be important sources of evolutionary novelty in plant evolution. Both can lead to novel gene combinations and/or novel patterns of gene expression, which in turn provide the variation on which natural selection can act. Here, we use nuclear and plastid gene trees, in conjunction with morphological data and genome size measurements, to show that both processes have been important in shaping the evolution of the angiosperm genus Mercurialis, particularly a clade of annual lineages that shows exceptional variation in the sexual system. Our results indicate that hexaploid populations of M. annua, in which the rare sexual system androdioecy is common (the occurrence of males and hermaphrodites) is of allopolyploid origin involving hybridization between an autotetraploid lineage of M. annua and the related diploid species M. huetii. We discuss the possibility that androdioecy may have evolved as a result of hybridization between dioecious M. huetii and monoecious tetraploid M. annua, an event that brought together the genes for specialist males with those for hermaphrodites.

Biological Evolution↗

PubMed2025

Subgenomic divergence and functional innovation following whole-genome duplication in Maleae species of Rosaceae.

Whole-genome duplication (WGD) drives plant evolution by inducing karyotype rearrangements and gene loss through subgenome fractionation. In this study, we investigate post-WGD evolutionary dynamics in Rosaceae, focusing on Maleae species, which uniquely experienced an additional WGD. Using phylogenetic and synteny analyses, we reveal that chromosomal breakpoints act as hotspots for localized fractionation, contributing to blurred homoeologous origins and influencing gene retention patterns. Here, we reconstruct karyotype evolution across Rosaceae subfamilies, highlighting chromosome reductions and lineage-specific rearrangements in Dryadoideae, Rosoideae, and Amygdaloideae. We also identify a bias for retaining transcription factors and hormone-related genes from older WGDs in subsequent polyploidy events. Transcriptome analysis classifies WGD-derived genes in Maleae species, such as apple and loquat, into three expression groups, with hormone-enriched genes playing roles in lignification and fruit-related innovations. These findings demonstrate the interplay between chromosomal breakpoints, biased retention, and functional divergence, revealing their contributions to genomic and phenotypic evolution in Maleae and their adaptive success within Rosaceae.

Genome, Plant↗

PubMed1992

Evolution of the plastid ribosomal RNA operon in a nongreen parasitic plant: accelerated sequence evolution, altered promoter structure, and tRNA pseudogenes.

The nucleotide sequence of a 7.4 kb region containing the entire plastid ribosomal RNA operon of the nongreen parasitic plant Epifagus virginiana has been determined. Analysis of the sequence indicates that all four rRNA genes are intact and almost certainly functional. In contrast, the split genes for tRNA(Ile) and tRNA(Ala) present in the 16S-23S rRNA spacer region have become pseudogenes, and deletion upstream of the 16S rRNA gene has removed a tRNA(Val) gene and most of the promoter region for the rRNA operon. The rate of nucleotide substitution in 16S and 23S rRNAs is several times higher in Epifagus than in tobacco, a related photosynthetic plant. Possible reasons for this, including relaxed translational constraints, are discussed.

Base Sequence↗

PubMed2006

Allelic configuration and polysomic inheritance of highly variable microsatellites in tetraploid gynodioecious Thymus praecox agg.

Polyploidy plays a pivotal role in plant evolution. However, polyploids with polysomic inheritance have hitherto been severely underrepresented in plant population genetic studies, mainly due to a lack of appropriate molecular genetic markers. Here we report the establishment and experimental validation of six fully informative microsatellite markers in tetraploid gynodioecious Thymus praecox agg. Sequence data of 150 microsatellite alleles and their flanking regions revealed high variation, which may be characteristic for polyploids with a reticulate evolutionary history. Understanding the patterns of mutation (indels and substitutions) in microsatellite flanking-sequences was a prerequisite for the development of co-dominant markers for fragment analyses. Allelic segregation patterns among progeny arrays from ten test crosses revealed tetrasomic inheritance in T. praecox agg. No evidence of frequent double reduction was detected. Polymerase chain reaction (PCR) based dosage effects allowed for precise assignment of allelic configuration at all six microsatellite loci. The quantification of allele copy numbers in PCR was verified by comparisons of observed and expected gametic allele frequencies and heterozygosities in test crosses. Our study illustrates how PCR based markers can provide reliable estimates of heterozygosity and, thus, powerful tools for breeding system and population genetic analyses in polyploid organisms.

Alleles↗

PubMed1998

The gain of three mitochondrial introns identifies liverworts as the earliest land plants.

The first evidence for the emergence of land plants (embryophytes) consists of mid-Ordovician spore tetrads (approximately 476 Myr old). The identity of the early plants that produced these spores is unclear; they are sometimes claimed to be liverworts, but there are no associated megafossils, and similar spores can be produced by a diversity of plants. Indeed, the earliest unequivocal megafossils of land plants consist of early vascular plants and various plants of uncertain affinity. Different phylogenetic analyses have identified liverworts, hornworts and bryophytes as each being the first lineage of land plants; the consensus of these conflicting topologies yields an unresolved polychotomy at the base of land plants. Here we survey 352 diverse land plants and find that three mitochondrial group II introns are present, with occasional losses, in mosses, hornworts and all major lineages of vascular plants, but are entirely absent from liverworts, green algae and all other eukaryotes. These results indicate that liverworts are the earliest land plants, with the three introns having been acquired in a common ancestor of all other land plants, and have important implications concerning the early stages of plant evolution.

Base Sequence↗

PubMed1989

Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data.

The divergence between monocots and dicots represents a major event in higher plant evolution, yet the date of its occurrence remains unknown because of the scarcity of relevant fossils. We have estimated this date by reconstructing phylogenetic trees from chloroplast DNA sequences, using two independent approaches: the rate of synonymous nucleotide substitution was calibrated from the divergence of maize, wheat, and rice, whereas the rate of nonsynonymous substitution was calibrated from the divergence of angiosperms and bryophytes. Both methods lead to an estimate of the monocot-dicot divergence at 200 million years (Myr) ago (with an uncertainty of about 40 Myr). This estimate is also supported by analyses of the nuclear genes encoding large and small subunit ribosomal RNAs. These results imply that the angiosperm lineage emerged in Jurassic-Triassic time, which considerably predates its appearance in the fossil record (approximately 120 Myr ago). We estimate the divergence between cycads and angiosperms to be approximately 340 Myr, which can be taken as an upper bound for the age of angiosperms.

Animals↗

PubMed2000

Intersectional gene flow between insular endemics of Ilex (Aquifoliaceae) on the Bonin Islands and the Ryukyu Islands.

Hybridization and introgression play important roles in plant evolution, and their occurrence on the oceanic islands provides good examples of plant speciation and diversification. Restriction fragment length polymorphisms (RFLPs) and trnL (UAA) 3'exon-trnF (GAA) intergenic spacer (IGS) sequences of chloroplast DNA (cpDNA), and the sequences of internal transcribed spacer (ITS) of nuclear ribosomal DNA were examined to investigate the occurrence of gene transfer in Ilex species on the Bonin Islands and the Ryukyu Islands in Japan. A gene phylogeny for the plastid genome is in agreement with the morphologically based taxonomy, whereas the nuclear genome phylogeny clusters putatively unrelated endemics both on the Bonin and the Ryukyu Islands. Intersectional hybridization and nuclear gene flow were independently observed in insular endemics of Ilex on both sets of islands without evidence of plastid introgression. Gene flow observed in these island systems can be explained by ecological features of insular endemics, i.e., limits of distribution range or sympatric distribution in a small land area.

Journal Article↗

PubMed1999

Phylogeny of early land plants: insights from genes and genomes.

A large body of evidence from molecular systematic studies has confirmed the charophytic origin of land plants, and clarified monophyly of many lineages in charophytes and land plants. These studies have also identified liverworts as the earliest land plants, and the lycopods as the extant sister group to all other vascular plants. Two traditionally defined groups-bryophytes and pteridophytes-are now recognized as early grades of land plant evolution. However, several problems that complicate the use of sequence data in reconstructing plant phylogeny have become apparent; reconstruction of an accurate land plant phylogeny will require analysis of sequences of multiple genes and genomic structural characters of all three genomes.

Journal Article↗

PubMed2002

Mode of amplification and reorganization of resistance genes during recent Arabidopsis thaliana evolution.

The NBS-LRR (nucleotide-binding site plus leucine-rich repeat) genes represent the major class of disease resistance genes in flowering plants and comprise 166 genes in the ecotype Col-0 of Arabidopsis thaliana. NBS-LRR genes are organized in single-gene loci, clusters, and superclusters. Phylogenetic analysis reveals nine monophyletic clades and a few phylogenetic orphans. Most clusters contain only genes from the same phylogenetic lineage, reflecting their origin from the exchange of sequence blocks as a result of intralocus recombination. Multiple duplications increased the number of NBS-LRR genes in the progenitors of Arabidopsis, suggesting that the present complexity in Col-0 may derive from as few as 17 progenitors. The combination of physical and phylogenetic analyses of the NBS-LRR genes makes it possible to detect relatively recent gene rearrangements, which increased the number of NBS-LRR genes by about 50, but which are almost never associated with large segmental duplications. The identification of 10 heterogeneous clusters containing members from different clades demonstrates that sequence sampling between different resistance gene loci and clades has occurred. Such events may have taken place early during flowering plant evolution, but they generated modules that have been duplicated and remobilized also more recently.

Arabidopsis↗

PubMed2004

Heterogeneous evolution of the Myc-like Anthocyanin regulatory gene and its phylogenetic utility in Cornus L. (Cornaceae).

Anthocyanin is a major pigment in vegetative and floral organs of most plants and plays an important role in plant evolution. The anthocyanin regulatory genes are responsible for regulating transcription of genes in the anthocyanin synthetic pathway. To assess evolutionary significance of sequence variation and evaluate the phylogenetic utility of an anthocyanin regulatory gene, we compared nucleotide sequences of the myc-like anthocyanin regulatory gene in the genus of dogwoods (Cornus: Cornaceae). Phylogenetic analyses demonstrate that the myc-like anthocyanin regulatory gene has potential as an informative phylogenetic marker at different taxonomic levels, depending on the data set considered (DNA or protein sequences) and regions applied (exons or introns). Pairwise nonsynonymous and synonymous substitution rate tests and codon-based substitution models were applied to characterize variation and to identify sites under diversifying selection. Mosaic evolution and heterogeneous rates among different domains and sites were detected.

Anthocyanins↗

PubMed2002

Plant sex determination and sex chromosomes.

Sex determination systems in plants have evolved many times from hermaphroditic ancestors (including monoecious plants with separate male and female flowers on the same individual), and sex chromosome systems have arisen several times in flowering plant evolution. Consistent with theoretical models for the evolutionary transition from hermaphroditism to monoecy, multiple sex determining genes are involved, including male-sterility and female-sterility factors. The requirement that recombination should be rare between these different loci is probably the chief reason for the genetic degeneration of Y chromosomes. Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant sex chromosomes.

Evolution, Molecular↗

PubMed2001

How do mitochondrial genes get into the nucleus?

It is well known that genes from chloroplasts and mitochondria were transferred to the nucleus many times during plant evolution. But in what form do the transferred genes physically make that intracellular journey--as RNA, as cDNA, as pieces of organelle DNA, or as whole organelle chromosomes? Current views focus upon cDNA as the vehicle, based upon some examples from plants. But other mechanisms, involving direct transfer of DNA from organelle chromosomes, could also account for the available data. Direct DNA transfer, rather than cDNA-mediated transfer, does occur today, and it probably prevailed during the early phases of organelle evolution.

Cell Nucleus↗

PubMed1992

Retroelements in higher plants.

Representatives of several classes of retroelements have been characterized in a broad range of plant species, where they appear at variable and sometimes very high copy numbers. So far, only a very small number of plant elements have been shown to be active, and this activity seems to be restricted to specific situations of 'genomic shock'. Although it is not yet known whether the presence of retroelements is linked to the high level of variability found in plant genomes, it is now clear that retrotransposons are ancient and ubiquitous components of plant genomes, and could play an important role in plant evolution.

Biological Evolution↗

PubMed2004

Biophysical constraints on the origin of leaves inferred from the fossil record.

The molecular tool kit for producing flat-bladed photosynthetic structures evolved in marine and terrestrial plants during the middle Paleozoic, but it took a further 20 million years before leaves suddenly spread throughout land floras. This delay has long been difficult to explain, given the apparent advantage of leaves for photosynthetic primary production. Theory and experiments predict that exceptionally high atmospheric CO2 levels in the middle Paleozoic delayed the origin of leaves by restricting stomatal development. This would have limited evaporative cooling, leading to lethal overheating of leaves absorbing large quantities of solar energy. Here we test the central prediction of this argument with a morphometric analysis of 300 plant fossils from major European collections. We show a 25-fold enlargement of leaf blades in two phylogenetically independent clades as atmospheric CO2 levels fell during the late Paleozoic. Furthermore, preliminary data suggest that the first abrupt increase in leaf size was accompanied by an 8-fold rise in stomatal density. These evolutionary patterns support the relaxation of biophysical constraints on leaf area predicted by theory and point to a significant role for CO2 in plant evolution.

Atmosphere↗

PubMed1995

[Tannins, a new family of bio-active natural organic compounds (questions and answers)].

Twelve questions concerning tannin selected from questions raised by other workers on the author's research were picked up. The answers of each question are as follows. 1. What is tannin?--the differences between the old concept and the new definition of tannin. 2. Is tannic acid the same as tannin? 3. How could each tannin be analyzed as a pure compound? 4. Which tannin found in recent years is implicated with the change of the concept of tannin in medicinal plants? 5. Is it possible that one to several chemical structures represent tannins contained in each plant species? 6. Which tannin-containing plants met in the human life are rich in tannins? 7. Is tannin produced by all species of plants?--a correlation between the occurrence of hydrolyzable tannins and the plant evolution system. 8. When and where are the hydrolyzable tannin oligomers produced, in the plant or after extraction? 9. Are tannins bound to other substances in the plants? 10. Is it appropriate to call tannins "plant polyphenols"? 11. Is it true that tannins are inhibitors of enzymes? 12. What kind of biological activities have been found for tannins.

Animals↗

PubMed2005

A conserved transcription factor mediates nuclear control of organelle biogenesis in anciently diverged land plants.

Land plant chloroplasts evolved from those found in the green algae. During land plant evolution, nuclear regulatory mechanisms have been modified to produce morphologically and functionally diverse chloroplasts in distinct developmental contexts. At least some of these mechanisms evolved independently in different plant lineages. In angiosperms, GOLDEN2-LIKE (GLK) transcription factors regulate the development of at least three chloroplast types. To determine whether GLK-mediated regulation of chloroplast development evolved within angiosperms or is a plesiomorphy within land plants, gene function was examined in the moss Physcomitrella patens. Gene expression patterns and loss-of-function mutant phenotypes suggested that GLK gene function is conserved between P. patens and Arabidopsis thaliana, species that diverged >400 million years ago. In support of this suggestion, moss genes partially complement Arabidopsis loss-of-function mutants. Therefore, GLK-mediated regulation of chloroplast development defines one of the most ancient conserved regulatory mechanisms identified in the plant kingdom.

Arabidopsis↗