Non-coding Chloroplast DNA Research Articles

Molecular analysis of interspecific and intergeneric relationships of Banksia using RAPDs and non-coding chloroplast DNA sequences

Random amplified polymorphic DNA (RAPD) and chloroplast DNA (cpDNA) markers were used to study interspecific and intergeneric relationships of Banksia (Proteaceae) to aid breeding of the genus for cut flower production. The accepted morphological phylogeny of Banksia, with two subgenera, two sections and 13 series, is unclear regarding the relationships of the commercial cut flower species B. coccinea. Fifteen RAPD primers and a non-coding cpDNA sequence between the trnL (UAA) and trnF (GAA) gene were applied to species of Banksia, the related genus Dryandra, and to Musgravea heterophylla as the outgroup, with cluster analysis applied to the results. The two methods were in broad agreement with each other, and with the accepted taxonomy, with closely related species pairs and groups clustering together, but RAPDs were not informative between distantly related species or species pairs. Banksia coccinea clustered with Dryandra and formed a polytomy with 2 Dryandra species and the two sections of subgenus Banksia. Subgenus Isostylis formed a polytomy with D. formosa, basal to subgenus Banksia, but with B. cuneata and B. illicifolia (both in subgenus Isostylis) polyphyletic. Dryandra did not separate as a clade and fell within Banksia, raising questions about the currently accepted view of the two as sister genera with parallel morphological development. The results indicate that interspecific and intergeneric hybridisation with genus Dryandra and subgenus Banksia may be possible routes for improvement of the commercial species B. coccinea.

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.

Noncoding chloroplast DNA variation in Mexican pines

Universal primers were used for PCR amplification of three noncoding regions of chloroplast DNA in order to study restriction site variation in 12 Mexican pine species. Two length mutations were identified that are of diagnostic value for two subgenera or sections of the genus. Phylogenetic analysis of the restriction site and length variation showed patterns of variation largely consistent with previous arrangements of these pines, except for the position of Pinus nelsonii, indicating that Pinus section Parraya Mayr, as circumscribed by Little and Critchfield (1969) and later authors, is not a monophyletic group.

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.

New or Little Known North American Trees. IV

Previous articleNext article FreeNew or Little Known North American Trees. IVCharles S. SargentCharles S. Sargent Search for more articles by this author PDFPDF PLUS Add to favoritesDownload CitationTrack CitationsPermissionsReprints Share onFacebookTwitterLinkedInRedditEmail SectionsMoreDetailsFiguresReferencesCited by Volume 33, Number 2Feb., 1902 Article DOIhttps://doi.org/10.1086/328201 Views: 21Total views on this site Citations: 1Citations are reported from Crossref Journal History This article was published in the Botanical Gazette (1876-1991), which is continued by International Journal of Plant Sciences (1992-present). PDF download Crossref reports the following articles citing this article:Joey Shaw, Randall L. Small Addressing the “hardest puzzle in American pomology:” Phylogeny of Prunus sect. Prunocerasus (Rosaceae) based on seven noncoding chloroplast DNA regions, American Journal of Botany 91, no.66 (Jun 2004): 985–996.https://doi.org/10.3732/ajb.91.6.985