Plant Molecular Systematics Research Articles

Molecular Characterization of Maturase K Gene and Protein Prediction of Vanda spathulata (L.) - An Ayurinformatics Approaches

Vanda spathulata (L.) Spreng. is an important plant of the orchid family of botanical and horticultural importance in the Ayurvedic medicinal system. The Maturase K (matK) gene of plant chloroplast is a strong marker in studying plant molecular systematics, evolution, and genetic polymorphism and is considered as the standard DNA barcode for plants. The gene has an important role in the phylogenetic reconstruction of terrestrial plants. The present study investigated the phylogenetic characterization of matK gene obtained from the plant species V. spathulata (L.) through extraction, purification, PCR amplification, and gel elution. The nucleotide BLAST search revealed similarity with 103 sequences in various closely and distantly related orchid taxa. Mega software and a real-time divergence tree discovered Apostasia odorata has the primitive species for all the sequences, including the V. spathulata which diverged about 114 million years ago. Limited gene flow was observed among the vanda and related taxa and the Tajima neutrality test was negative, indicating the purifying selection in the matK gene sequence, that evolutionary selection had played a major role rather than the neutral evolution. The species and related other species exhibited higher polymorphism at the nucleotide level. Secondary structure was predicted for the single-stranded matK gene of V. spathulata and the ancestor plant species A. odorata using the Zucker MFold web server and translated through a comparison of ORF with NCBI and BLASTN. The protein was modeled in SWISS MODELLER and compared between the two species. The sequence had high similarity with its ancestor gene sequence and the protein modeled showed a complex structure than the ancestor protein due to significant evolutionary changes.

DNA barcoding and molecular systematics in genus Coelogyne Lindl. (Orchidaceae)

ISHS IX International Scientific and Practical Conference on Biotechnology as an Instrument for Plant Biodiversity Conservation (physiological, biochemical, embryological, genetic and legal aspects) DNA barcoding and molecular systematics in genus Coelogyne Lindl. (Orchidaceae)

Do latex and resin canals spur plant diversification? Re‐examining a classic example of escape and radiate coevolution

AbstractThe association between increased lineage diversification rates and the evolution of latex and resin canals is widely cited as a paradigmatic example of Ehrlich and Raven’s ‘escape‐and‐radiate’ hypothesis of co‐evolution. However, it has been over a quarter‐century since the original study, and updates to phylogenetic comparative methods, plant molecular systematics, and phenotypic data warrant a reassessment of this classic finding.We gathered data on latex and resin canals across 345 families and 986 genera of vascular plants and conducted a multi‐scale test of the association between these traits and lineage diversification rates. At a broad scale (across clades), we used sister‐clade comparisons to test whether 28 canal‐bearing clades had higher net diversification rates than their canal‐lacking sister clades. At a finer scale (within clades), we used ancestral state reconstructions and phylogenetic models of lineage diversification rates to examine the relationship between trait evolution and the timing of diversification rate shifts in two better‐characterized clades – Araceae and Papaveraceae.At both scales of our analyses we found poor support for the predicted relationship between diversification and the evolution of latex and resin canals. Follow‐up analyses clarified that the qualitative change between our results and those of the Farrell et al.’s classic study is not the result of different phylogenetic comparative methods. Instead, the differences are attributable to updates to plant systematic hypotheses and new data on laticifers and resin canal presence/absence.Synthesis.Our updated study reveals that there is no longer strong evidence for latex or resin canals as general, consistently replicable drivers of species diversity across plants. However, we cannot rule out a relationship in all groups. We therefore argue that theoretical and empirical work aimed at understanding ecological factors that condition ‘escape‐and‐radiate’ dynamics will allow for more nuanced tests of the hypothesis in the future.

Plastome sequences and exploration of tree-space help to resolve the phylogeny of riceflowers (Thymelaeaceae: Pimelea)

Data sets comprising small numbers of genetic markers are not always able to resolve phylogenetic relationships. This has frequently been the case in molecular systematic studies of plants, with many analyses being based on sequence data from only two or three chloroplast genes. An example of this comes from the riceflowers Pimelea Banks & Sol. ex Gaertn. (Thymelaeaceae), a large genus of flowering plants predominantly distributed in Australia. Despite the considerable morphological variation in the genus, low sequence divergence in chloroplast markers has led to the phylogeny of Pimelea remaining largely uncertain. In this study, we resolve the backbone of the phylogeny of Pimelea in comprehensive Bayesian and maximum-likelihood analyses of plastome sequences from 41 taxa. However, some relationships received only moderate to poor support, and the Pimelea clade contained extremely short internal branches. By using topology-clustering analyses, we demonstrate that conflicting phylogenetic signals can be found across the trees estimated from individual chloroplast protein-coding genes. A relaxed-clock dating analysis reveals that Pimelea arose in the mid-Miocene, with most divergences within the genus occurring during a subsequent rapid diversification. Our new phylogenetic estimate offers better resolution and is more strongly supported than previous estimates, providing a platform for future taxonomic revisions of both Pimelea and the broader subfamily. Our study has demonstrated the substantial improvements in phylogenetic resolution that can be achieved using plastome-scale data sets in plant molecular systematics.

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.

Comparison of DNA barcoders in identifying medicinal materials

The DNA barcoding of traditional Chinese medicine was summarized in this article. Based on analyzing a number of research findings, the authors discussed the possibility of nuclear DNA sequence and chloroplast genes in identifying medicinal materials. ITS was considered to evolve faster, which was used for plant molecular systematics analysis and species identification,while ITS2 was more suitable to identify medicinal materials. So, it is important that we should select suitable DNA sequences as barcodes based on the objective of a study. With the cost reduction of sequencing, identifying medicinal materials by cp-genome barcoding would be applied broadly and effectively in the future.

Highly Variable Chloroplast Markers for Evaluating Plant Phylogeny at Low Taxonomic Levels and for DNA Barcoding

BackgroundAt present, plant molecular systematics and DNA barcoding techniques rely heavily on the use of chloroplast gene sequences. Because of the relatively low evolutionary rates of chloroplast genes, there are very few choices suitable for molecular studies on angiosperms at low taxonomic levels, and for DNA barcoding of species.Methodology/Principal FindingsWe scanned the entire chloroplast genomes of 12 genera to search for highly variable regions. The sequence data of 9 genera were from GenBank and 3 genera were of our own. We identified nearly 5% of the most variable loci from all variable loci in the chloroplast genomes of each genus, and then selected 23 loci that were present in at least three genera. The 23 loci included 4 coding regions, 2 introns, and 17 intergenic spacers. Of the 23 loci, the most variable (in order from highest variability to lowest) were intergenic regions ycf1-a, trnK, rpl32-trnL, and trnH-psbA, followed by trnSUGA-trnGUCC, petA-psbJ, rps16-trnQ, ndhC-trnV, ycf1-b, ndhF, rpoB-trnC, psbE-petL, and rbcL-accD. Three loci, trnSUGA-trnGUCC, trnT-psbD, and trnW-psaJ, showed very high nucleotide diversity per site (π values) across three genera. Other loci may have strong potential for resolving phylogenetic and species identification problems at the species level. The loci accD-psaI, rbcL-accD, rpl32-trnL, rps16-trnQ, and ycf1 are absent from some genera. To amplify and sequence the highly variable loci identified in this study, we designed primers from their conserved flanking regions. We tested the applicability of the primers to amplify target sequences in eight species representing basal angiosperms, monocots, eudicots, rosids, and asterids, and confirmed that the primers amplified the desired sequences of these species.Significance/ConclusionsChloroplast genome sequences contain regions that are highly variable. Such regions are the first consideration when screening the suitable loci to resolve closely related species or genera in phylogenetic analyses, and for DNA barcoding.

Plant molecular systematics: prospects for identifying species and for analysing bioactive compound evolution

Plant molecular systematics: prospects for identifying species and for analysing bioactive compound evolution

Plant molecular systematics in Latin America: status, realities, and perspectives

Molecular biology techniques have had a great impact in modern studies of biodiversity across the globe, and they have contributed significantly to our understanding of evolutionary relationships across all kingdoms. Protein and DNA sequence data have provided a seemingly endless amount of characters to be used in phylogenetic studies, and they have allowed comparisons across divergent groups for which it is very difficult to establish morphological homologies. Researchers in Latin America have not escaped this revolution, and in several institutions efforts have been made to begin utilizing them. Economical, social and political factors have both slowed and stimulated the development of molecular systematics and phylogenetics in Latin America. Even though the continent is not homogeneous, and these factors may differ from country to country, some general patterns do exist across the region. In the present document, we will attempt to summarize the status of molecular systematic studies throughout Latin America, analyze which factors have stimulated or slowed down its development, and we will conclude with some suggestions on how to improve the current state of affairs.

The rise and fall of plant species: a population biologist's perspective

The rise and fall of plant species: a population biologist's perspective

Contributions of plant molecular systematics to studies of molecular evolution.

Dobzhansky stated that nothing in biology makes sense except in the light of evolution. A close corollary, and the central theme of this paper, is that everything makes a lot more sense in the light of phylogeny. Systematics is in the midst of a renaissance, heralded by the widespread application of new analytical approaches and the introduction of molecular techniques. Molecular phylogenetic analyses are now commonplace, and they have provided unparalleled insights into relationships at all levels of plant phylogeny. At deep levels, molecular studies have revealed that charophyte green algae are the closest relatives of the land plants and suggested that liverworts are sister to all other extant land plants. Other studies have suggested that lycopods are sister to all other vascular plants and clarified relationships among the ferns. The impact of molecular phylogenetics on the angiosperms has been particularly dramatic--some of the largest phylogenetic analyses yet conducted have involved the angiosperms. Inferences from three genes (rbcL, atpB, 18S rDNA) agree in the major features of angiosperm phylogeny and have resulted in a reclassification of the angiosperms. This ordinal-level reclassification is perhaps the most dramatic and important change in higher-level angiosperm taxonomy in the past 200 years. At lower taxonomic levels, phylogenetic analyses have revealed the closest relatives of many crops and 'model organisms' for studies of molecular genetics, concomitantly pointing to possible relatives for use in comparative studies and plant breeding. Furthermore, phylogenetic information has contributed to new perspectives on the evolution of polyploid genomes. The phylogenetic trees now available at all levels of the taxonomic hierarchy for angiosperms and other green plants should play a pivotal role in comparative studies in diverse fields from ecology to molecular evolution and comparative genetics.

Reappraising adaptive radiation

Reappraising adaptive radiation

Molecular Ecology and Evolution: Approaches and Applications.

I: DNA fingerprinting and behavioral ecology.- Arbitrary primer mediated fingerprinting in plants: Case studies in plant breeding, taxonomy and phylogeny.- DNA amplification fingerprinting: A general tool with applications in breeding, identification and phylogenetic analysis of plants.- The analysis of simple repeat loci as applied in evolutionary and behavioral sciences.- Multilocus DNA fingerprinting and genetic relatedness in plants: A case study with banana and tomato.- Measuring reproductive success in insects.- Unravelling the components that underlie insect reproductive traits using a simple molecular approach.- Molecular analysis of kinship in birds: Interesting questions and useful techniques.- II: Population biology.- Molecular techniques in population genetics: A brief history.- Organization of genetic variation at the molecular level: Lessons from Drosophila.- The use of microsatellite analysis in population biology: Background, methods and potential applications.- The use of microsatellites for genetic analysis of natural populations.- PCR assays of variable nucleotide sites for identification of conservation units.- Concerted evolution and RAPping in mitochondrial VNTRs and the molecular geography of cricket populations.- Molecular markers and evolutionary processes in hermaphrodite freshwater snails.- Extinction and the formation of phylogenetic lineages: Diagnosing units of conservation management in the tiger beetle Cicindela dorsalis.- Perspective on conservation genetics.- III: Molecular systematics.- Advances in the theory and practice of DNA-hybridization as a systematic method.- Allozymes in mammalian population genetics and systematics: Indicative function of a marker system reconsidered.- Analysis of DNA from natural history museum collections.- Sources of ambiguity in nucleic acid sequence alignment.- Computational problems in molecular systematics.- The comparison of morphological and molecular data in phylogenetic systematics.- Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level.- Developing model systems for molecular biogeography: Vicariance and interchange in marine invertebrates.- Bridging phylogenetics and population genetics with gene tree models.- IV: Speciation, development and genome organization.- The role of molecular genetics in speciation studies.- The origin and evolution of species differences in Escherichia coli and Salmonella typhimurium.- The evolutionary ecology of Daphnia.- Diversity within diversity: Molecular approaches to studying microbial interactions with insects.- Evolutionary analysis of genes involved in early embryonic pattern formation in Drosophila.- Developmental genes and the origin and evolution of Metazoa.- To what extent does genetic information determine structural characteristics and document homologies?.- Evolution and multi-functionality of the chitin system.- Genome evolution: Between the nucleosome and the chromosome.- Individual genes underlying quantitative traits: Molecular and analytical methods.- Perspectives on future applications of experimental biology to evolution.

Chloroplast DNA systematics: a review of methods and data analysis

The field of plant molecular systematics is expanding rapidly, and with it new and refined methods are coming into use. This paper reviews recent advances in experimental methods and data analysis, as applied to the chloroplast genome. Restriction site mapping of the chloroplast genome has been used widely, but is limited in the range of taxonomic levels to which it can be applied. The upper limits (i.e., greatest divergence) of its application are being explored by mapping of the chloroplast inverted repeat region, where rates of nucleotide substitution are low. The lower limits of divergence amenable to restriction site study are being examined using restriction enzymes with 4‐base recognition sites to analyze polymerase chain reaction (PCR)‐amplified portions of the chloroplast genome that evolve rapidly. The comparison of DNA sequences is the area of molecular systematics in which the greatest advances are being made. PCR and methods for direct sequencing of PCR products have resulted in a mushrooming of sequence data. In theory, any degree of divergence is amenable to comparative sequencing studies. In practice, plant systematists have focused on two slowly evolving sequences (rbcL and rRNA genes). More rapidly evolving DNA sequences, including rapidly changing chloroplast genes, chloroplast introns, and intergenic spacers, and the noncoding portions of the nuclear ribosomal RNA repeat, also are being investigated for comparative purposes. The relative advantages and disadvantages of comparative restriction site mapping and DNA sequencing are reviewed. For both methods, the analysis of resulting data requires sufficient taxon and character sampling to achieve the best possible estimate of phylogenetic relationships. Parsimony analysis is particularly sensitive to the issue of taxon sampling due to the problem of long branches attracting on a tree. However, data sets with many taxa present serious computational difficulties that may result in the inability to achieve maximum parsimony or to find all shortest trees.

Rates and patterns of chloroplast DNA evolution.

The chloroplast genome (cpDNA) of plants has been a focus of research in plant molecular evolution and systematics. Several features of this genome have facilitated molecular evolutionary analyses. First, the genome is small and constitutes an abundant component of cellular DNA. Second, the chloroplast genome has been extensively characterized at the molecular level providing the basic information to support comparative evolutionary research. And third, rates of nucleotide substitution are relatively slow and therefore provide the appropriate window of resolution to study plant phylogeny at deep levels of evolution. Despite a conservative rate of evolution and a relatively stable gene content, comparative molecular analyses reveal complex patterns of mutational changes. Non-coding regions of cpDNA diverge through insertion/deletion changes that are sometimes site dependent. Coding genes exhibit different patterns of codon bias that appear to violate the equilibrium assumptions of some evolutionary models. Rates of molecular change often vary among plant families and orders in a manner that violates the assumption of a simple molecular clock. Finally, protein-coding genes exhibit patterns of amino acid change that appear to depend on protein structure, and these patterns may reveal subtle aspects of structure/function relationships. Only comparative studies of molecular sequences have the resolution to reveal this underlying complexity. A complete description of the complexity of molecular change is essential to a full understanding of the mechanisms of evolutionary change and in the formulation of realistic models of mutational processes.

Non-coding chloroplast DNA for plant molecular systematics at the infrageneric level.

With primers constructed against highly conserved regions of tRNA genes (trnTUGU, trnLUAA and trnFGAA) in chloroplast DNA, we have amplified two different non-coding spacers and one intron from four species within the genus Echium L. (Boraginaceae) and from two confamilial outgroups. The trnTUGU-trnLUAA intergenic spacer contains a greater number of polymorphic sites than the trnLUAA intron or the trnLUAA-trnFGAA intergenic spacer. We analyzed a total of 11 kb of sequence data from this non-coding DNA. Total nucleotide divergence between Echium species is on the order of 1% for these regions, all of which possess infrageneric length polymorphisms. The latter two regions contain indels which occur only in the 14 Macaronesian Island endemic species of Echium studied and suggest that these may form a monophyletic group.

The progress of DNA analyzing techniques and its impact on plant molecular systematics

Recent advances in manipulating nucleic acids have opened a new research field called plant molecular systematics. This short review provides an overview of molecular techniques which have been used in the analysis of DNA molecules for the study of plant systematics, with a special emphasis on PCR. The early application of DNA analysis, DNA/DNA hybridization, has not become popular with plant systematists, because of several disadvantages inherent in the method. The survey of restriction fragment length polymorphisms (RFLPs), on the contrary, has become one of the preferred methods used by plant molecular systematists, since the method is relatively easy to perform. Although unambiguous data can be obtained by both long-range restriction mapping and nucleotide sequencing, these approaches may have limited use in plant molecular systematics because of their laborious experimental procedures relying on conventional molecular cloning techniques. To date, PCR based analyses of the DNA molecule seem to be the most suitable experimental approach for plant molecular systematics. Several advantages of the method have changed both the quality and quantity of the DNA data. Further application of PCR to plant molecular systematics will open up a new era in the field.