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Annette W Coleman

Publications and source records attributed to Annette W Coleman.

5 recordsLinked to original sources
PubMed2005

Portrait of a species: Chlamydomonas reinhardtii.

Chlamydomonas reinhardtii, the first alga subject to a genome project, has been the object of numerous morphological, physiological, and genetic studies. The organism has two genetically determined mating types (plus and minus) and all stages of the simple life cycle can be evoked in culture. In the nearly 60 years since the first standard laboratory strains were isolated, numerous crosses and exchanges among laboratories have led to some confusion concerning strain genealogy. Here we use analyses of the nuclear internal transcribed spacer regions and other genetic traits to resolve these issues, correctly identify strains currently available, and analyze phylogenetic relationships with all other available similar chlamydomonad types. The presence of a 10-bp indel in ITS2 in some but not all copies of the nuclear ribosomal cistrons of an individual organism, and the changing ratios of these in crosses, provide a tool to investigate mechanisms of concerted evolution. The standard C. reinhardtii strains, plus C. smithii +, plus the new eastern North American C. reinhardtii isolates, comprise one morphological species, one biological species of high sexual intercompatibility, and essentially identical ITS sequences (except the tip of helix I of ITS2). However, variant RFLP patterns characterize strains from each geographic site.

Animals↗
PubMed2004

The advantages of the ITS2 region of the nuclear rDNA cistron for analysis of phylogenetic relationships of insects: a Drosophila example.

We examined the utility for phylogenetic reconstruction of the second internal transcribed spacer (ITS2), lying between the nuclear 5.8S gene and the gene for large subunit ribosomal RNA, using sequences of Ceratitis, Bactrocera, Musca, and Drosophila. We aligned and analyzed 13 sequences from GenBank and 11 new sequences from diverse species of Drosophila. Derivation of the secondary structure of the ITS2, the RNA transcript folding pattern required for transcript processing into functional RNA units, revealed the facets of sequence conservation common to all the sequences, that then allowed alignment of all the genera. The resultant tree, though including only a sparse representation of the enormous Drosophila diversity, conforms generally with the consensus of all prior phylogenetic reconstructions, using eight other nuclear and mitochondrial gene regions; where species representation is greater, as in the melanogaster subgroup of the Sophophora subgenus representatives, it conforms exactly. The paradigm ITS2 secondary structure presented can now be used to assess the genus more thoroughly, since its base pairing pattern makes alignment of sequences obvious. In addition, it shows that these insects share the ITS2 secondary structure characteristics of the other major animal groups as well as the green line of eukaryote evolution. The relatively short (<400 bp) ITS2 region seems ideal for reconstructing evolutionary relationships at the levels of species, genera, and perhaps even higher.

Animals↗
PubMed2002

Exploring the phylogenetic utility of ITS sequences for animals: a test case for abalone (Haliotis).

To evaluate the general utility of sequences of the nuclear rDNA internal transcribed spacer (ITS) regions for phylogenetic analyses of animal species groups and their broader relationships, sequences were obtained for 19 species of the genus Haliotis plus a keyhole limpet and a more distantly related gastropod, the Chilean abalone. Three subclades of Haliotis species appear consistently, each encompassing little variation. They are (A) the North Pacific species, (B) the European species, and (C) the Australia species. The one Caribbean species examined clearly groups with the North Pacific clade, not the European clade. H. midae (South Africa) and H. diversicolor supertexta (Taiwan) both diverge basal to the European and Australian species groups in the phylogenetic trees. Sequence comparisons showed that one species of Haliotis, H. iris from New Zealand, is quite distant from the remaining Haliotis species, almost as much as the more obvious outgroup, the keyhole limpet, an observation common to other DNA sequence analyses of these taxa. Using the rate of nucleotide change calculated from the sister Caribbean-Pacific pair, the length of the H. iris long branch is compatible with the suggestion that its ancestry became isolated on New Zealand at Gondwandan breakup. Use of ITS permits a totally independent estimate of the phylogenetic relationships, yet branching order was very similar to that established using other DNA regions studied previously, including those under strong positive selection. Knowledge of the RNA transcript secondary structure is particularly useful in the optimal alignment of more distantly related taxa. The RNA transcript secondary structure of Haliotis ITS2 shows conservation of features found also in ITS2 of angiosperms and algal taxa. Since ITS, particularly ITS2, is not saturated with nucleotide changes even at the family level, it should be useful for phylogenetic reconstruction of animal groups, not just at the species and genus levels but perhaps also for families and above.

Animals↗