Primer development for the plastid region ycf1 in Annonaceae and other magnoliids

? Premise of the study: Primers were developed for a portion of the ycf1 plastid gene in magnoliid taxa to investigate the utility of ycf1 in phylogenetic analyses. ? Methods and Results: Twenty-six species across six families within the magnoliid group (Canellales, Piperales, Laurales, and Magnoliales) were sampled to examine the ability to amplify ycf1. Additionally, 29 accessions of Asimina and Deeringothamnus (Annonaceae) were sequenced to assess levels of variation in ycf1 compared to matK and trnL-F. ? Conclusions: Results indicate that ycf1 is easily amplified and sequenced. In Annonaceae, ycf1 provides more informative phylogenetic characters than commonly used markers such as matK and trnL-F.     

Phylogenetic analysis of chloroplast matK gene from Zingiberaceae for plant DNA barcoding

MaturaseK gene (MatK) of chloroplast is highly conserved in plant systematics which is involved in Group II intron splicing. The size of the gene is 1500 bp in length, located with in the intron of trnK. In the present study, matK gene from Zingiberaceae was taken for the analysis of variants, parsimony site, patterns, transition/tranversion rates and phylogeny. The family of Zingiberaceae comprises 47 genera with medicinal values. The matK gene sequence have been obtained from genbank and used for the analysis. The sequence alignments were performed by Clustal X, transition/transversion rates were predicted by MEGA and phylogenetic analyses were carried out by PHYLIP package. The result indicates that the Zingiberaceae genus Afromonum, Alpinia, Globba, Curcuma and Zingiber shows polyphylogeny. The overall variants between the species are 24% and transition/transversion rate is 1.54. Phylogenetic tree was designed to identify the ideal regions that could be used for defining the inter and intera-generic relationships. From this study it could be concluded that the matK gene is a good candidate for DNA barcoding of plant family Zingiberaceae.     

Molecular characterization of endangered endemic plant Aloe pseudorubroviolacea using chloroplast matK and plastid rbcL gene

An endangered and rare species Aloe pseudorubroviolacea from the plant family Asphodelaceae which is presently recorded as endangered in Saudi Arabia collected from Al-Baha region of Saudi Arabia its GPS Latitude and Longitude coordinates 19.8345, 41.5481. The chloroplast matK and rbcL gene was considered in this study based on molecular identification the size is about 571 and 664 bp respectively. From the sequence analysis the gene matK and rbcL confirm that this species is very much closely related with A. rubroviolacea and also inter related with the species Astroloba rubriflora, Chrysopogon gryllus, Chortolirion angolense shows about 98.7% sequence homology. The partial matK and rbcL gene sequence discriminate Aloe pseudorubroviolacea from the closely related plant species, A. rubroviolacea. The gene sequence of rbcL discriminates the species from Chrysopogon gryllus and Chortolirion angolense, demonstrates the nucleotide variations in 3 different sites (623C/T; 653C/T; 700C/A). This study showed that matK and rbcL sequence region of chloroplast gene used to authenticate the samples of A. pseudorubroviolacea and which provide to help in correct identification and conservation process of this medicinally valuable endangered plant species.     

Molecular systematics of Malpighiaceae: evidence from plastid rbcL and matK sequences

Phylogenetic analyses of DNA nucleotide sequences from the plastid genes rbcL and matK were employed to investigate intergeneric relationships within Malpighiaceae. Cladistic relationships generated from the independent data matrices for the family are generally in agreement with those from the combined matrix. At the base of Malpighiaceae are several clades mostly representing genera from a paraphyletic subfamily Byrsonimoideae. Intergeneric relationships among these byrsonimoid malpighs are well supported by the bootstrap, and the tribe Galphimeae is monophyletic. There is also a well-supported clade of genera corresponding to tribes Banisterieae plus Gaudichaudieae present in all trees, and many of the relationships among these banisterioid malpighs are well supported by the bootstrap. However, tribes Hiraeae and Tricomarieae (the hiraeoid malpighs) are paraphyletic and largely unresolved. Species of Mascagnia are distributed throughout these hiraeoid clades, confirming the suspected polyphyly of this large genus. Optimization of selected morphological characters on these trees demonstrates clear phylogenetic trends such as the evolution of globally symmetrical from radially symmetrical pollen, increased modification and sterilization of stamens, and switch from base chromosome number n = 6 to n = 10.     

Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants

In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The resulting plastid DNA phylogeny was congruent with that recently obtained from analyses of rps2 and provided much better resolution. This phylogeny was then used to examine the relative degrees of evolutionary constraint of both the matK gene and the non-protein-coding regions that flank it inside the trnK intron. The method of subtree contrasts was introduced to compare levels of constraint. matK has evolved with a low but significant level of constraint on its amino acid sequence in both photosynthetic and nonphotosynthetic plants. Constraint is greater in photosynthetic than in nonphotosynthetic plants of this group. Domain X, thought to contain the active site of the protein, is not significantly more constrained than the rest of the protein. The portions of the flanking regions that are thought to form paired stem structures also show constraint, but in this case, there is no significant difference in degree of constraint between photosynthetic and nonphotosynthetic plants.     

Thy-1: more than a mouse pan-T cell marker

Thy-1 (CD90) is a small GPI-anchored protein that is particularly abundant on the surface of mouse thymocytes and peripheral T cells. T cell proliferation and cytokine synthesis in response to Thy-1 cross-linking by specific mAb suggests a role for Thy-1 in mouse T lymphocyte activation. However, a physiological ligand or counterreceptor for murine Thy-1 in the lymphoid compartment has not yet been identified. Thy-1 cross-linking, in the context of strong costimulatory signaling through CD28, results in an activating signal that can at least partially substitute for TCR signaling during mouse T cell activation. Remarkably, Thy-1 cross-linking also results in the potent costimulation of T cells activated through the TCR. This novel dual signaling capacity suggests a possible role for Thy-1 in the maintenance of T cell homeostasis in the absence of TCR triggering, as well as potentiating Ag-induced T cell responses.     

Relationships and evolution of matK in a group of leafless orchids (Corallorhiza and Corallorhizinae; Orchidaceae: Epidendroideae)

Corallorhizinae are a small group of Old and New World temperate orchids of which a core monophyletic group comprises Govenia, Cremastra, Aplectrum, Oreorchis and the leafless Corallorhiza, and which according to phylogenetic analysis of nuclear ITS and plastid matK sequences, are related in this way: (Govenia (Cremastra (Aplectrum (Oreorchis (Corallorhiza))))). This hypothesis is consistent with the progressive deletion of the trnK intron and matK ORF. Frameshift-resulting indels yield a predicted loss of translation for the critical "domain X" region of matK and are evidence that matK is a probable pseudogene in Aplectrum, Oreorchis, and Corallorhiza. Within Corallorhiza, a previous hypothesis based on plastid DNA restriction site analysis is confirmed, with the thickened-labellum C. striata group being sister to the thin-labellum remainder of the genus, within which the circumboreal C. trifida is sister to the remainder, which then comprise two further sister groups: C. maculata + C. bulbosa + C. mertensiana and C. odontorhiza + C. wisteriana. A close relationship between C. striata and the recently described Appalachian C. bentleyi is shown; in particular, C. bentleyi is more closely allied to a southern Mexican population of C. striata than it is to northern North American C. striata populations, suggesting that two lineages, each with Mexican and northern North American populations, exist within the C. striata group.     

Phylogenetic utility of the nuclear gene arginine decarboxylase: an example from Brassicaceae

Arginine decarboxylase (ADC) is an important enzyme in the production of putrescine and polyamines in plants. It is encoded by a single or low-copy nuclear gene that lacks introns in sequences studied to date. The rate of Adc amino acid sequence evolution is similar to that of ndhF for the angiosperm family studied. Highly conserved regions provide several target sites for PCR priming and sequencing and aid in nucleotide and amino acid sequence alignment across a range of taxonomic levels, while a variable region provides an increased number of potentially informative characters relative to ndhF for the taxa surveyed. The utility of the Adc gene in plant molecular systematic studies is demonstrated by analysis of its partial nucleotide sequences obtained from 13 representatives of Brassicaceae and 3 outgroup taxa, 2 from the mustard oil clade (order Capparales) and 1 from the related order Malvales. Two copies of the Adc gene, Adc1 and Adc2, are found in all members of the Brassicaceae studied to data except the basal genus Aethionema. The resulting Adc gene tree provides robust phylogenetic data regarding relationships within the complex mustard family, as well as independent support for proposed tribal realignments based on other molecular data sets such as those from chloroplast DNA.      

Phylogenetic relationships of Empetraceae inferred from sequences of chloroplast gene matK and nuclear ribosomal DNA ITS region

We used sequences of nrDNA ITS and chloroplast gene matK to evaluate the monophyly of Empetrum and Corema and to examine phylogenetic relationships of the Empetraceae. Sequences of these two DNA markers were obtained for 11 plant samples, representing species of Empetrum from both the Southern and Northern Hemispheres, species and subspecies of Corema, and the monotypic Ceratiola. Sequences of four species of Rhododendron were used for rooting purposes. Our results show that species of Empetrum form a clade sister to the clade containing both Corema and Ceratiola. These two clades are strongly supported in both the matK and ITS trees, suggesting that Ceratiola is more closely related to Corema than to Empetrum, and is not of a hybrid origin between the ancestors of the latter two genera. In the matK tree, Corema conradii is more closely related to Ceratiola than to Corema album and C. album subsp. azoricum, whereas in the ITS tree, Ceratiola is allied with Corema album and C. album subsp. azoricum. This suggests that C. conradii might be a hybrid between ancestral populations of Ceratiola and C. album. The monophyly of Empetrum rejects the hypothesis of its independent origin in the two Hemispheres. Our trees also suggest the fact that the modern amphitropical distribution of Empetrum is the result of long distance dispersal, not of the vicarious events.     

Phylogenetic signal in matK vs. trnK: a case study in early diverging eudicots (angiosperms)

The matK gene has been among the most useful loci for resolving plant phylogenetic relationships at different evolutionary time-scales, but much less is known about the phylogenetic utility of the flanking trnK intron, especially for deep level phylogenetics. We compared the relative performance of matK and trnK intron regions for resolving the relationships of the early diverging eudicots (angiosperms). The two regions display similar nucleotide compositions and distributions of rate variation among sites. The trnK intron sequences also provide similar levels of phylogenetic information per-site as matK. Combining the trnK intron sequences with matK increases overall bootstrap support for the early diverging eudicots compared to analyses of matK alone. MP, ML and Bayesian analyses provide strong support for eudicots, the sister group relationship of Ranunculales to remaining eudicots, and a Buxales+Trochodendraceae+core eudicots clade. matK and the trnK intron support conflicting positions for Buxales and Trochodendrales in relation to the core eudicots.     

Phylogenetic utility and evolution of indels: a study in neognathous birds

Indels are increasingly used in phylogenetics and play a major role in genome size evolution, and yet both the phylogenetic information content of indels and their evolutionary significance remain to be better assessed. Using three presumably independently evolving nuclear gene fragments (28S rDNA, β-fibrinogen, ornithine decarboxylase) from 29 families of neognathous birds, we have obtained a topology that is in general agreement with the current molecular consensus tree, supports the monophyly of Metaves, and provides evidence for the unresolved relationships within the Charadriiformes. Based on the retrieved topology, we assess the relative impact of indels and nucleotide substitutions and demonstrate that the superposition of the two kinds of data yields a topology that could not be obtained from either data set alone. Although only two out of three gene fragments reveal the deletion bias, the combined nucleotide insertion-to-deletion ratio is 0.22, indicating a rapid decrease of intron length. The average indel fixation rate in the neognaths is 2.5 times faster than that in therian (placental) mammals of similar geologic age. As in mammals, there is a considerable variation of indel fixation rate that is 1.5 times higher in Galloanseres compared to Neoaves, and 2.4 times higher in the Rallidae compared to the average for Neoaves (8.2 times higher compared to the related Gruidae). Our results add to the evidence that indel fixation rates correlate with lineage-specific evolutionary rates.     

Lipolysis: more than just a lipase

Successful adaptation to starvation in mammals depends heavily on the regulated mobilization of fatty acids from triacylglycerols stored in adipose tissue. Although it has long been recognized that cyclic AMP represents the critical second messenger and hormone-sensitive lipase (HSL)**Abbreviations used in this paper: ADRP, adipocyte differentiation-related protein; HSL, hormone-sensitive lipase; PKA, protein kinase A; TAG, triacylglycerol. the rate-determining enzyme for lipolysis, simple activation of the enzyme has failed to account for the robust augmentation of fatty release in response to physiological agonists. In this issue, Sztalryd et al. (2003) provide convincing support to the notion that the subcellular compartmentalization of lipase also regulates lipolysis, and, more importantly, that proteins other than HSL are localized to the lipid droplet and are indispensable for its optimal hydrolysis.     

Mitochondria: more than just a powerhouse

Pioneering biochemical studies have long forged the concept that the mitochondria are the 'energy powerhouse of the cell'. These studies, combined with the unique evolutionary origin of the mitochondria, led the way to decades of research focusing on the organelle as an essential, yet independent, functional component of the cell. Recently, however, our conceptual view of this isolated organelle has been profoundly altered with the discovery that mitochondria function within an integrated reticulum that is continually remodeled by both fusion and fission events. The identification of a number of proteins that regulate these activities is beginning to provide mechanistic details of mitochondrial membrane remodeling. However, the broader question remains regarding the underlying purpose of mitochondrial dynamics and the translation of these morphological transitions into altered functional output. One hypothesis has been that mitochondrial respiration and metabolism may be spatially and temporally regulated by the architecture and positioning of the organelle. Recent evidence supports and expands this idea by demonstrating that mitochondria are an integral part of multiple cell signaling cascades. Interestingly, proteins such as GTPases, kinases and phosphatases are involved in bi-directional communication between the mitochondrial reticulum and the rest of the cell. These proteins link mitochondrial function and dynamics to the regulation of metabolism, cell-cycle control, development, antiviral responses and cell death. In this review we will highlight the emerging evidence that provides molecular definition to mitochondria as a central platform in the execution of diverse cellular events.