Molecular phylogeny and taxonomic revision of chaetophoralean ...
Molecular phylogeny and taxonomic revision of chaetophoralean ... Molecular phylogeny and taxonomic revision of chaetophoralean ...
Introduction 7 Many phylogenetic markers, such as the SSU and LSU (18S rRNA and 5.8S +28S rRNA), including the internal transcribed spacers (ITS) region, of the nuclear-encoded ribosomal operon; the SSU and LSU (16S rRNA and 23S rRNA) plastid-encoded ribosomal operon; and several chloroplast (rbcL, atpB), mitochondrial (coxI) or nuclear, protein-coding genes (e.g. actin), have been employed for studies at various taxonomic levels (e.g. Watanabe et al. 1998, Coleman 2009, Del Campo et al. 2010, Marin and Melkonian 2010, O’Kelly et al. 2010). However, the small subunit nuclear ribosomal operon (SSU rRNA) remains probably to be one of the most frequently-used molecular markers of all (Ouvrard et al. 2000, Meyer et al. 2010) In fact, there are various good reasons for this practice: the existence of (1) a large database, (2) universal primers (3) an appropriate number of nucleotide positions for alignment and over which to perform analyses, and (4), as yet, no evidence for lateral gene transfer within this region in eukaryotes. Various studies indicate that the nuclear-encoded ribosomal operon (Fig. 5), which shows a mosaic of conserved and divergent regions, has become a popular tool in green algal phylogeny (e.g. Buchheim et al. 2001, Gontcharov et al. 2004, Buchheim et al. 2005). Fig 5. Nuclear-encoded ribosomal operon consisting of three rRNA genes (18S, 5.8S, 28S) and two internal transcribed spacers (ITS1 and ITS2). The small subunit ribosomal DNA (SSU rDNA) and the large subunit ribosomal DNA (LSU rDNA) are indicated by pink and blue color, respectively. (modified after Coleman 2003) Generally, it is assumed that the slowly-evolving SSU rRNA (18S rRNA) is a marker suitable for evolutionary studies at higher taxonomical levels (e.g. family, order, class). However, the suitability of SSU rRNA to taxonomic classification is highly dependent on the evolutionary rate of sequences investigated. Many studies also evaluate the utility of the LSU rRNA (28S rRNA) as a potential marker for identification at the various taxonomic levels (e.g. Medina et al. 2001, Sonnenberg et al. 2007). The conservative segments of LSU rRNA are alignable across kingdoms and have probably a comparable potential of resolution as the SSU rRNA gene (Kuzoff et al. 1998). In contrast, the variable segments (e.g. the C domain) evolved more rapidly and thus might be more informative at the lower taxonomic levels, especially at the species level (e.g. Ellegaard et al. 2008, Howard et al. 2009). In addition, the internal transcribed spacer (ITS), especially ITS2, is a favourite marker in taxonomy. The ITS2 is a fast-evolving part of the nuclear rRNA operon localized between the 5.8S and 28S rRNA genes. Although the primary sequence of ITS2 is highly variable, the typical secondary structure, which comprises four helices (Fig. 6), is
Introduction 8 displayed among many eukaryotic organisms (Coleman and Mai 1997, Joseph et al. 1999, Coleman 2007). Of these four helices, Helix 1 and Helix 4 show a degree of variability both in sequence and in length. In contrast Helix 2 and Helix 3 contain motifs that are essential during the excision process of ITS2 (e.g. Thomson and Tollervey 2010) and therefore these two helices are more conserved (Coleman 2007). Because of the combination of (1) the rapid evolution of the ITS2 region and (2) the presence of conserved regions within it (Helix 2 with at least one pyrimidine-pyrimidine mismatch and Helix 3 with its YGGY motif), it was assumed that the ITS2 might be a highly appropriate marker for taxonomy (Hershkovitz and Lewis 1996, Hershkovitz and Zimmer 1996, Schultz et al. 2005, Coleman 2007, Coleman 2009), and especially useful to differentiate among closely related organisms i.e. to delimit ‘biological species’ (e.g. Coleman 2000). Fig. 6.: Typical secondary structure of ITS2 consisting of four helices (Helix 1 – 4). The important regions for species delimitation (pink colour in Helix 2 and 3) and the conservative motifs (pyrimidin-pyrimidin mismatch in Helix 2 and YGGY in Helix 3) are highlighted. (modified after Mai and Coleman 1997)
- Page 1 and 2: University of South Bohemia in Čes
- Page 3: Declaration I declare that this dis
- Page 7 and 8: Thesis content 1. Introduction ....
- Page 9 and 10: Introduction 2 Zeltner 1994, Friedl
- Page 11 and 12: Introduction 4 unbranched taxa into
- Page 13: Introduction 6 depending on the tax
- Page 17 and 18: Introduction 10 The CBC species con
- Page 19 and 20: 3. Objectives of the thesis This st
- Page 21 and 22: 5. Paper 1 Paper 1 14 POLYPHYLY OF
- Page 23 and 24: Paper 1 16 lalokovitý tvar koloni
- Page 25 and 26: Abstract Paper 2 18 Background The
- Page 27 and 28: 7. Conclusions of the thesis In the
- Page 29 and 30: References of the thesis 22 Coleman
- Page 31 and 32: References of the thesis 24 Luo, W.
- Page 33 and 34: References of the thesis 26 Present
- Page 35 and 36: Curriculum vitae Name: Lenka Caisov
- Page 37: Curriculum vitae 30 2009 - 2012 The
Introduction 8<br />
displayed among many eukaryotic organisms (Coleman <strong>and</strong> Mai 1997, Joseph et al.<br />
1999, Coleman 2007). Of these four helices, Helix 1 <strong>and</strong> Helix 4 show a degree <strong>of</strong><br />
variability both in sequence <strong>and</strong> in length. In contrast Helix 2 <strong>and</strong> Helix 3 contain<br />
motifs that are essential during the excision process <strong>of</strong> ITS2 (e.g. Thomson <strong>and</strong><br />
Tollervey 2010) <strong>and</strong> therefore these two helices are more conserved (Coleman 2007).<br />
Because <strong>of</strong> the combination <strong>of</strong> (1) the rapid evolution <strong>of</strong> the ITS2 region <strong>and</strong> (2) the<br />
presence <strong>of</strong> conserved regions within it (Helix 2 with at least one pyrimidine-pyrimidine<br />
mismatch <strong>and</strong> Helix 3 with its YGGY motif), it was assumed that the ITS2 might be a<br />
highly appropriate marker for taxonomy (Hershkovitz <strong>and</strong> Lewis 1996, Hershkovitz <strong>and</strong><br />
Zimmer 1996, Schultz et al. 2005, Coleman 2007, Coleman 2009), <strong>and</strong> especially useful<br />
to differentiate among closely related organisms i.e. to delimit ‘biological species’ (e.g.<br />
Coleman 2000).<br />
Fig. 6.: Typical secondary structure <strong>of</strong> ITS2 consisting <strong>of</strong> four helices (Helix 1 – 4). The important<br />
regions for species delimitation (pink colour in Helix 2 <strong>and</strong> 3) <strong>and</strong> the conservative motifs<br />
(pyrimidin-pyrimidin mismatch in Helix 2 <strong>and</strong> YGGY in Helix 3) are highlighted. (modified<br />
after Mai <strong>and</strong> Coleman 1997)
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