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A recircumscription of Begonia based on nuclear ribosomal sequences
Plant Systematics and Evolution, 2003
With c. 1400 known species, Begonia is one of the largest plant genera. In order to address the evolution of Begonia we have produced maximum parsimony and maximum likelihood cladograms for 26S and ITS sequence data. Sequences were obtained from a total of 35 species of Begonia, one species of Symbegonia and two species of Datisca. The resulting phylogenetic hypotheses suggest that the most basal members of Begonia are from Africa, with American and Asian clades nested within the paraphyletic African Begonia. Despite marked morphological heterogeneity the endemic Begonia of Madagascar and the south Indian ocean islands form a monophyletic group. As currently circumscribed, Begonia is paraphyletic with the New Guinean endemic Symbegonia nested deeply within it and most closely related to species from the Asian section Petermannia. Analysis of a smaller ITS dataset, including three accessions of Symbegonia and nine accessions of Begonia section Petermannia, further suggests that Symbegonia is nested within section Petermannia, resolving within a monophyletic clade of New Guinean species. Morphological synapomorphies of Symbegonia are reviewed and this taxon is sunk into the genus Begonia, where it is given sectional status.
Identification and validation of stable reference genes in camellia species
2020
We aimed at finding and validating a stable reference gene in Camellia sinensis and Camellia assamica from a set of four putative housekeeping genes in various samples exposed to different experimental conditions mainly biotic and abiotic stresses. Variation in gene expression across Camellia sinensis leaf tissues exposed to nine different kind of experimental sets was studied. The suitability of 18S rRNA, 26s rRNA, rubisco bis phosphatase (RuBP) and camellia actin (Act) as reference genes were validated by geNorm and BestKeeper programs and revealed 18S rRNA and RuBP to be the most stably expressing housekeeping gene. We therefore recommend use of RuBP as a stable reference gene for normalisation of transcripts abundance experiments in tea leaf samples.
ProQuest Dissertations & Theses,, 1993
Liquid and solid bacterial growth media 2 .1 .7 Antibiotics 2 .2 G row th and illum ination of plants 65 2 .2 .1 Growth and harvesting of plant material 2 .2 .2 Illumination of plants 2.2.3 Light measurement 2 .2 .3 .1 Fluence rate measurement 2 .2 .3 .2 Spectral photon distribution measurement 2 .3 G eneral p rep arato ry procedures 2 .3 .1 pH measurement 2 .3 .2 Autoclaving 2 .3 .3 Filter sterilisation 2 .3 .4 Glassware 2 .3 .5 Solutions and equipment for RNA work 2 .4 P rep aratio n of total RNA from prim ary leaves 2 .4 .1 Preparation of phenol reagent 2 .4 .2 Preparation of Kirby reagent (Parish and Kirby, 1966) 2 .4 .3 Isolation of total plant RNA (modified from Parish and Kirby, 1966) 2 .4 .4 DNAase treatment of RNA preparations 2 .5 The am plification and purification of plasm id DNA 70 2 .5 .1 Preparation of competent cells (essentially as described in Sambrook et al., 1989) 2 .5 .2 Transformation of competent cells 2 .5 .3 Large scale plasmid DNA preparation 2 .6 Q uantification of DNA and RNA 72 2 .7 A garose gel electrophoreseis 73 2 .7 .1 Electrophoresis of DNA 2 .7 .2 Non-denaturing electrophoresis of RNA • 3 .1 .1 .1 .2 3 .1 .3 3 .1 .4 Reaction mixture 87 Extraction and purification of labelled RNA from nuclei 87 Hybridisation of RNA from run-on transcription reactions 88 Reverse tran scrip tase-polym erase chain reaction 89 (RT-PCR) m easurem ent of rbcS tra n sc rip t levels First strand cDNA synthesis 89 Gel purification of the labelled 5' oligonucleotide 90 Polymerase chain reaction 93 Acrylamide / urea gel electrophoresis of DNA 94 The m easurem ent of oxygen evolution from 95 Phaseolus vulgaris leaf discs M easurem ent of the stom atal resistance of 95 Phaseolus vulgaris p rim ary leaves R e su lts 101 Validity of the m ethods used to m easure rbcS 101 tra n sc rip t levels in this study Experiments to demonstrate the quality of the 101 total RNA used in this study Formaldehyde gel electrophoresis and northern blotting 102 of P. vulgaris total RNA Experiments to estimate the sizes of the transcripts 103 hybridised to the P. vulgaris pPvSS191 rbcS cDNA probe and a Chlamydomonas reinhardtii a tubulin cDNA probe Determination of the washing conditions used for the rbcS 104
Genomic Resources for Evolutionary Studies in the Large, Diverse, Tropical Genus, Begonia
Tropical Plant Biology, 2012
Begonia is one of the ten largest angiosperm genera with over 1,500 species found throughout the tropics. To use this group as a model for the evolution of diversity in tropical herbaceous plants, we have produced three species transcriptomes, physical genome size measures, and two backcross genetic maps. We chose to focus on two Central American species, B. conchifolia and B. plebeja, and one SE Asian species, B. venusta, allowing us to pose questions at widely different evolutionary scales within the genus. We used next generation sequencing of cDNA libraries to produce annotated transcriptome databases for each of the three species. Though Begonia is functionally diploid, transcriptome analysis suggested a genome duplication occurred at or near the base of the Begonia clade. The genetic maps were built from first generation backcrosses in both directions between B. plebeja and B.conchifolia using 105 SNP markers in genes known to regulate development that were identified from the transcriptomes and the map bulked out with 226 AFLP loci. The genetic maps had 14 distinct linkage groups each and mean marker densities of between 3.6 and 5.8 cM providing between 96 and 99 % genomic coverage within 10 cM. We measured genome size 1C value of 0.60 and 0.63 pg for B. conchifolia and B. plebeja corresponding to recombination rates of between 441 and 451 Kb per cM in the genetic maps. Altogether, these new data represent a powerful new set of molecular genetic tools for evolutionary study in the genus Begonia.
Current Genetics, 1981
of double-stranded circular DNA molecules, 101 Megadalton (160 kbp) in circumference. In neutral CsC1 equilibrium gradients, this DNA displays a density of 1.697 g • cm -3 which is equivalent to an average base composition of 37.7 mole-% G+C. 2) A restriction endonuclease fragment map of the tobacco plastid chromosome is presented for the enzymes Bgl I, Sal I, Xho I and Pvu II which together dissect the DNA molecule into about 60 fragments. The map was derived by sequential digestion employing the previously described Seaplaque technique. The tobacco plastid chromosome has an anatomy similar to that of many other higher plants; the circular DNA is segmentally organized into two unique sequence segments of approximately 24 and 95 kbp separated on each side by a large inverted duplication of at least 20.4 kbp. 3) Saturation and blot hybridization showed that the genes for the 16S and 23S pt-rRNAs are duplicated. Each copy of the inverted repeat contains one set of rRNA genes; about 26 kbp (short distance) separate the sets from each other. 4) Cloned fragments of spinach ptDNA nick translated to high specific activity in vitro were used to probe the location of the large subunit gene of ribulose Offprint requests to: P. Seyer, Laboratoire Physiologic Cellulaire V6g6tale, Universit6 de Grenoble BP 53X, 38041 Grenoble Cedex, France Abbreviations: kbp -kilobase pairs; ptDNA -plastid DNA, chloroplast DNA; nucDNA -nuclear DNA; mtDNA -mitochondrial DNA; cDNA -Copy DNA; RuBPcase/oase -ribulose 1,5-biophosphate carboxylase/oxygenase; LSU -large subunit; EDTA -ethylene diamine tetraacetic acid (disodium salt); SDS sodium dodecylsuffate
Molecular and General Genetics MGG, 1987
We have cloned and sequenced all five members of the gene family for the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase/oxygenase from tomato, Lycopersicon esculentum cv. VFNT LA 1221 cherry line. Two of the five genes, designated Rbcs-1 and Rbcs-2, are present as single genes at individual loci. Three genes, designated Rbcs-3A, Rbcs-3B and Rbcs-3C, are organized in a tandem array within 10 kb at a third independent locus. The Rbcs-2 gene contains three introns; all the other members of the tomato gene family contain two introns. The coding sequence of Rbcs-1 differs by 14.0% from that of Rbcs-2 and by 13.3% from that of Rbes-3 genes. Rbcs-2 shows 10.4% divergence from Rbcs-3. The exon and intron sequences of Rbcs-3A are identical to those of Rbcs-3C, and differ by 1.9% from those of Rbcs-3B. Nucleotide sequence analysis suggests that the five rbcS genes encode four different precursors, and three different mature polypeptides. $1 nuclease mapping of the 5' end of rbcS mRNAs revealed that the mRNA leader sequences vary in length from 8 to 75 nucleotides. Northern analysis using gene-specific oligonucleotide probes from the 3' non-coding region of each gene reveals a four to five-fold difference among the five genes in maximal steady-state mRNA levels in leaves.
AFRICAN JOURNAL OF BIOTECHNOLOGY, 2011
BURP domain-containing proteins are a new class of plant-specific proteins that play important roles in the growth, development and stress response of plants. In this paper, a novel BURP domain-containing gene from Camellia sinensis (CsBDP, GenBank accession No. EU715397) was isolated and cloned using reverse transcription-polymerase chain reaction (RT-PCR) followed by 5′ and 3′ rapid amplification of cDNA ends (RACE) reactions. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot were then applied to detect the expression of CsBDP gene in Escherichia coli. Sequence comparison showed that the deduced protein sequence of CsBDP gene shared high sequence similarity to other BURP domain-containing proteins and contained four typical modules: an N-terminal hydrophobic region, a short conserved segment, a variable region containing two repeats of about 19 amino acids, which is unique for the RD22-like proteins of BURP family and a C-terminal BURP domain. Furthermore, phylogenetic tree revealed that the BURP protein family can be classified into eight subfamilies, and CsBDP was distinctly clustered into subfamily III with all RD22-like proteins. Therefore, CsBDP gene might be a stress-inducible gene and important for the stress tolerance of tea plant.
Phylogenetic relationships within the cosmopolitan family Rhamnaceae using ATPb gene promoter
Pakistan Journal of Botany, 2019
Eighteen species of Rhamnaceae were collected from different geographical regions of Pakistan to resolve its controversial phylogenetic position using morphological and molecular analysis. The phylogenetic tree based on 71 different micro and macro-morphological characters using Paleontological and statistical software (PAST) with Dice's coefficient showed an overall genetic diversity of 32%. Further, in each species the atpβ gene promoter was amplified, purified, sequenced and the dendrogram was constructed using Molecular evolutionary genetic analysis (MEGA7) tool which divided the sequences into two main clades showing a narrow genetic diversity of 0.05% with well supported bootstrap's values (95-100%). Pairwise's distance ranged from 0.12 to 0.73 with a mean value of 0.396. The phylogenetic study confirmed the work done by earlier phylogeneticist with additional reports of some new species, Berchemia pakistanica, Berchemia edgworthii, Berchemia floribunda, Helinus lanceolatus and Rhamnella gilgitica which are indigenous to Pakistan. The analysis of Cis-regulatory elements and its mapping via Plant cis-acting regulatory DNA element (PLACE) and Domain graph (DOG) revealed numerous elements including 50 common and 28 unique, showing variation in copy numbers and locations. It was observed that Berchemia pakistanica and Berchemia edgworthii have the unique features possessing diverse cis-regulatory elements with diverse functions.
Begonia yenyeniae is a new species of horticultural value known only from the Endau Rompin National Park, Peninsular Malaysia. It is similar to Begonia rajah with which it had previously been confused in the number of tepals and leaf characters. The new species is compared with three similar species, B. foxworthyi, B. rajah and B. reginula and photographs of all four species and descriptions of B. yenyeniae and B. rajah are provided. Molecular analysis using the ndhF-rpl132 chloroplast marker confirms the four species as distinct. Amongst native species, the three variegated species, B. yenyeniae, B. rajah and B. reginula, are some of the most popular Malaysian begonias in cultivation. Based on its restricted distribution, Begonia yenyeniae, under the IUCN Red List Categories and Criteria, is assessed as Critically Endangered.
Plant Molecular Biology, 1990
The gene family encoding the small subunit (SSU) of ribulose-l,5-bisphosphate carboxylase/oxygenase in the monocot Lemna gibba contains approximately twelve members. We have isolated six of these genes from a genomic library, and sequenced five of the coding regions. The transit peptide nucleotide sequences are conserved, but less highly than the mature polypeptide coding sequence. The mature polypeptide amino acid sequences are identical to each other and to the sequence deduced from a cDNA clone derived from a seventh gene. Each of the five fully characterized genomic sequences contains a single intron in precisely the same position as the second intron of several dicots. The intron sequences differ in length and are less conserved than the coding sequences.