Plant carnivory in the Caryophyllales: phylogenetic relationships, morphological adaptations, and molecular evolution of digestive enzymes among carnivorous genera

Phylogenetic relationships among carnivorous plants of the angiosperm order Caryophyllales are explored using Bayesian statistics and maximum-likelihood based searches of phylogeny. Nuclear ribosomal (ITS) and chloroplast intergenic spacer (PY-IGS) regions, along with previously- sequenced DNA are utilized for phylogenetic reconstructions. Taxonomic relationships across genera are refined and three strongly supported clades are identified: monophyletic Droseraceae, Nepenthaceae, and a third clade containing Ancistrocladaceae, Dioncophyllaceae, and Drosophyllaceae. In combination with phylogenetic reconstruction, stochastic character mapping is utilized to assess evolutionary changes in the morphology of glands found on the lamina and involved in the digestion of prey. Adaptive changes resulting in the evolution of the carnivorous gland are discussed, which may have occurred either by emargination of the leaf blade or homologous transformation of pinnae.A variety of enzymes are excreted from the carnivorous gland that aid in prey digestion. Within the carnivorous plants of the Caryophyllales, two subclasses of class I chitinases have been identified to play a role in the digestion of prey. Proteins produced by the large and diverse chitinase gene family are involved in the hydrolyzation of glycosidic bonds in chitin, a polymer of N-acetylglucosamines. Members of these subclasses, depending on the presence or absence of a C-terminal extension, can be secreted from specialized digestive glands found within morphologically diverse traps that develop from plant leaves. Homology among carnivorous plant class I chitinases and the method by which these enzymes have been adapted for the carnivorous habit are investigated. Novel class I chitinase homologs are recovered from Ancistrocladus, Dionaea, Drosera, Nepenthes, and Triphyophyllum, in addition to class I chitinases available from sequenced angiosperm genomes. Substitutions specific to carnivorous plant class I chitinases are revealed by detecting sites under positive selection, which may confer functional differences as indicated by protein structure homology-modeling.To study gene function in non-model organisms, a virus induced gene silencing (VIGS) method was developed. VIGS has been shown to be effective for transient knockdown of gene expression in plants to analyze the effects of specific genes in development and stress related responses. It is demonstrated that the barley stripe mosaic virus (BSMV) is able to infect two species within the Zingiberaceae, and that BSMV-VIGS can be applied to specifically downregulate phytoene desaturase in the culinary ginger Zingiber officinale. BSMV-VIGS is likely to be effective in other angiosperms susceptible to BSMV infection. This should enable targeted studies for identifying gene function to be carried out in ecologically and evolutionarily important groups

Comparative genomic analysis of the Hsp70s from five diverse photosynthetic eukaryotes

We have identified 24 members of the DnaK subfamily of heat shock 70 proteins (Hsp70s) in the complete genomes of 5 diverse photosynthetic eukaryotes. The Hsp70s are a ubiquitous protein family that is highly conserved across all domains of life. Eukaryotic Hsp70s are found in a number of subcellular compartments in the cell: cytoplasm, mitochondrion (MT), chloroplast (CP), and endoplasmic reticulum (ER). Although the Hsp70s have been the subject of intense study in model organisms, very little is known of the Hsp70s from early diverging photosynthetic lineages. The sequencing of the complete genomes of Thalassiosira pseudonana (a diatom), Cyanidioschyzon merolae (a red alga), and 3 green algae (Chlamydomonas reinhardtii, Ostreococcus lucimarinus, Ostreococcus tauri) allow us to conduct comparative genomics of the Hsp70s present in these diverse photosynthetic eukaryotes. We have found that the distinct lineages of Hsp70s (MT, CP, ER, and cytoplasmic) each have different evolutionary histories. In general, evolutionary patterns of the mitochondrial and endoplasmic reticulum Hsp70s are relatively stable even among very distantly related organisms. This is not true of the chloroplast Hsp70s and we discuss the distinct evolutionary patterns between “green” and “red” plastids. Finally, we find that, in contrast to the angiosperms Arabidopsis thaliana and Oryza sativa that have numerous cytoplasmic Hsp70, the 5 algal species have only 1 cytoplasmic Hsp70 each. The evolutionary and functional implications of these differences are discussed

Independent Co-Option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas

UA Open Access Publishing FundCompetition between microbes is widespread in nature, especially among those that are closely related. To combat competitors, bacteria have evolved numerous protein-based systems (bacteriocins) that kill strains closely related to the producer. In characterizing the bacteriocin complement and killing spectra for the model strain Pseudomonas syringae B728a, we discovered that its activity was not linked to any predicted bacteriocin but is derived from a prophage. Instead of encoding an active prophage, this region encodes a bacteriophage-derived bacteriocin, termed an R-type syringacin. This R-type syringacin is striking in its convergence with the well-studied R-type pyocin of P. aeruginosa in both genomic location and molecular function. Genomic alignment, amino acid percent sequence identity, and phylogenetic inference all support a scenario where the R-type syringacin has been co-opted independently of the R-type pyocin. Moreover, the presence of this region is conserved among several other Pseudomonas species and thus is likely important for intermicrobial interactions throughout this important genus.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Independent Co-Option of a Tailed Bacteriophage into a Killing Complex in Pseudomonas

UA Open Access Publishing FundCompetition between microbes is widespread in nature, especially among those that are closely related. To combat competitors, bacteria have evolved numerous protein-based systems (bacteriocins) that kill strains closely related to the producer. In characterizing the bacteriocin complement and killing spectra for the model strain Pseudomonas syringae B728a, we discovered that its activity was not linked to any predicted bacteriocin but is derived from a prophage. Instead of encoding an active prophage, this region encodes a bacteriophage-derived bacteriocin, termed an R-type syringacin. This R-type syringacin is striking in its convergence with the well-studied R-type pyocin of P. aeruginosa in both genomic location and molecular function. Genomic alignment, amino acid percent sequence identity, and phylogenetic inference all support a scenario where the R-type syringacin has been co-opted independently of the R-type pyocin. Moreover, the presence of this region is conserved among several other Pseudomonas species and thus is likely important for intermicrobial interactions throughout this important genus.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

The value of avian genomics to the conservation of wildlife

Background: Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution. Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care). In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes. Results: Genotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology. Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2(m) and 3(a) are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2(m) existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2(m) form, originally thought to be the derived condition, might actually be the ancestral one. Conclusion: Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease. In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology