Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

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Universal primers for amplification of three non-coding regions of chloroplast DNA.

Pierre Taberlet, Ludovic Gielly, Guy Pautou … (1991)

Six primers for the amplification of three non-coding regions of chloroplast DNA via the polymerase chain reaction (PCR) have been designed. In order to find out whether these primers were universal, we used them in an attempt to amplify DNA from various plant species. The primers worked for most species tested including algae, bryophytes, pteridophytes, gymnosperms and angiosperms. The fact that they amplify chloroplast DNA non-coding regions over a wide taxonomic range means that these primers may be used to study the population biology (in supplying markers) and evolution (inter- and probably intraspecific phylogenies) of plants.

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Use of DNA barcodes to identify flowering plants.

W. John Kress, Kenneth J Wurdack, Elizabeth Zimmer … (2005)

Methods for identifying species by using short orthologous DNA sequences, known as "DNA barcodes," have been proposed and initiated to facilitate biodiversity studies, identify juveniles, associate sexes, and enhance forensic analyses. The cytochrome c oxidase 1 sequence, which has been found to be widely applicable in animal barcoding, is not appropriate for most species of plants because of a much slower rate of cytochrome c oxidase 1 gene evolution in higher plants than in animals. We therefore propose the nuclear internal transcribed spacer region and the plastid trnH-psbA intergenic spacer as potentially usable DNA regions for applying barcoding to flowering plants. The internal transcribed spacer is the most commonly sequenced locus used in plant phylogenetic investigations at the species level and shows high levels of interspecific divergence. The trnH-psbA spacer, although short ( approximately 450-bp), is the most variable plastid region in angiosperms and is easily amplified across a broad range of land plants. Comparison of the total plastid genomes of tobacco and deadly nightshade enhanced with trials on widely divergent angiosperm taxa, including closely related species in seven plant families and a group of species sampled from a local flora encompassing 50 plant families (for a total of 99 species, 80 genera, and 53 families), suggest that the sequences in this pair of loci have the potential to discriminate among the largest number of plant species for barcoding purposes.

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Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms.

Michael Moore, Charles D Bell, Pamela Soltis … (2007)

Although great progress has been made in clarifying deep-level angiosperm relationships, several early nodes in the angiosperm branch of the Tree of Life have proved difficult to resolve. Perhaps the last great question remaining in basal angiosperm phylogeny involves the branching order among the five major clades of mesangiosperms (Ceratophyllum, Chloranthaceae, eudicots, magnoliids, and monocots). Previous analyses have found no consistent support for relationships among these clades. In an effort to resolve these relationships, we performed phylogenetic analyses of 61 plastid genes ( approximately 42,000 bp) for 45 taxa, including members of all major basal angiosperm lineages. We also report the complete plastid genome sequence of Ceratophyllum demersum. Parsimony analyses of combined and partitioned data sets varied in the placement of several taxa, particularly Ceratophyllum, whereas maximum-likelihood (ML) trees were more topologically stable. Total evidence ML analyses recovered a clade of Chloranthaceae + magnoliids as sister to a well supported clade of monocots + (Ceratophyllum + eudicots). ML bootstrap and Bayesian support values for these relationships were generally high, although approximately unbiased topology tests could not reject several alternative topologies. The extremely short branches separating these five lineages imply a rapid diversification estimated to have occurred between 143.8 +/- 4.8 and 140.3 +/- 4.8 Mya.

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Journal

Title: Plant Systematics and Evolution

Abbreviated Title: Plant Syst Evol

Publisher: Springer Nature

ISSN (Print): 0378-2697

ISSN (Electronic): 1615-6110

Publication date Created: October 2009

Publication date (Print): September 2009

Volume: 282

Issue: 3-4

Pages: 169-199

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DOI: 10.1007/s00606-009-0210-8

SO-VID: c550f114-5b9b-4e06-b2aa-391c6c8faf66

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Mutational dynamics and phylogenetic utility of noncoding chloroplast DNA

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Most cited references 159

Universal primers for amplification of three non-coding regions of chloroplast DNA.

Use of DNA barcodes to identify flowering plants.

Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms.

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