Ribosomal ITS sequences and plant phylogenetic inference

Álvarez, Inés; Wendel, Jonathan F.

doi:10.1016/s1055-7903(03)00208-2

Cited by 1,632 publications

(1,214 citation statements)

References 156 publications

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“…Therefore, it remains elusive whether ITS-based trees reflect the actual phylogeny or rather the reticulate pattern of ITS evolution (Álvarez and Wendel 2003). C. irregularis and the Conringia species do not possess segmented (heteroarthrocarpous) fruits and/or conduplicate cotyledons characteristic for the Brassiceae (Appel and Al-Shehbaz 2003).…”

Section: Chromosome Triplication In Brassiceaementioning

confidence: 99%

Chromosome triplication found across the tribe Brassiceae

Lysak¹,

Koch²,

Pečinka³

et al. 2005

Genome Res.

616

519

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We have used an ∼8.7-Mb BAC contig of Arabidopsis thaliana Chromosome 4 to trace homeologous chromosome regions in 21 species of the family Brassicaceae. Homeologs of this segment could be identified in all tested species. Painting of pachytene chromosomes of Calepina, Conringia, and Sisymbrium species (2n = 14, 16), traditionally placed in tribe Brassiceae, showed one homeologous copy of the Arabidopsis contig, while the remaining taxa of the tribe (2n = 14-30) revealed three, and three Brassica species (2n = 34, 36, and 38) and Erucastrum gallicum (2n = 30) had six copies corresponding to the 8.7-Mb segment. The multiple homeologous copies corresponded structurally to the Arabidopsis segment or were rearranged by inversions and translocations within the diploidized genomes. These chromosome rearrangements accompanied by chromosome fusions/fissions led to the present-day chromosome number variation within the Brassiceae. Phylogenetic relationships based on the chloroplast 5Ј-trnL (UAA)-trnF(GAA) region and estimated divergence times based on sequence data of the chalcone synthase gene are congruent with comparative painting data and place Calepina, Conringia, and Sisymbrium outside the clade of Brassiceae species with triplicated genomes. Most likely, species containing three or six copy pairs descended from a common hexaploid ancestor with basic genomes similar to that of Arabidopsis. The presumed hexaploidization event occurred after the Arabidopsis-Brassiceae split, between 7.9 and 14.6 Mya.[The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper:The Brassiceae is one of the most morphologically distinct tribes within the Brassicaceae family (Cruciferae). The Brassiceae tribe is a monophyletic group (e.g., Warwick and Black 1997a,b; Anderson and Warwick 1999) comprising ∼240 species in 49-54 genera (Gómez-Campo 1999;Warwick et al. 2000), and includes economically important Brassica crops. Although the basic genome structure of six Brassica crop species was unraveled early (e.g., U 1935), there is a long-lasting debate on the origin and evolution of karyotypes in the genus Brassica and the tribe Brassiceae. The variation in basic chromosome numbers (x = 6-18) (Warwick et al. 2000) makes it difficult to decide whether species with higher basic chromosome numbers are genuine diploids or polyploids. In many Brassiceae genera, species with the lowest chromosome number are considered as diploid. Several hypotheses on ancestral basic numbers (x = 3-7) and karyotype evolution in the Brassiceae have been put forward (for review, see Prakash and Hinata 1980;Truco et al. 1996;Anderson and Warwick 1999;Prakash et al. 1999). However, without knowing phylogenetic relationships and the history of polyploidy of the Brassiceae, unambiguous conclusions cannot be drawn.Already early studies suggested that diploid Brassica species represent "balanced secondary polyploids" exhibiting internal chromosome homeology and genome duplications (e.g., Catcheside 1934;Röbbelen 196...

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Section: Chromosome Triplication In Brassiceaementioning

confidence: 99%

Chromosome triplication found across the tribe Brassiceae

Lysak¹,

Koch²,

Pečinka³

et al. 2005

Genome Res.

616

519

View full text Add to dashboard Cite

show abstract

“…Recently, it was suggested, that the internal transcribed spacer 2 region (ITS2) of the nuclear rDNA cistron might be a marker suitable for taxonomic classification over a wide range of levels (Coleman 2003). As the sequence of the ITS2 region evolves comparably fast, it already found a wide application for phylogenetic reconstructions on the species and genus level (Alvarez and Wendel 2003). The suggestion of a more general use is mainly based on reports that find a conservation of its structure in organisms as divergent as vertebrates and yeast (Joseph et al 1999) or green algae and higher plants .…”

Section: Introductionmentioning

confidence: 99%

A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota

Schultz

Maisel²,

Gerlach³

et al. 2005

RNA

350

296

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The ongoing characterization of novel species creates the need for a molecular marker which can be used for species-and, simultaneously, for mega-systematics. Recently, the use of the internal transcribed spacer 2 (ITS2) sequence was suggested, as it shows a high divergence in sequence with an assumed conservation in structure. This hypothesis was mainly based on small-scale analyses, comparing a limited number of sequences. Here, we report a large-scale analysis of more than 54,000 currently known ITS2 sequences with the goal to evaluate the hypothesis of a conserved structural core and to assess its use for automated large-scale phylogenetics. Structure prediction revealed that the previously described core structure can be found for more than 5000 sequences in a wide variety of taxa within the eukaryotes, indicating that the core secondary structure is indeed conserved. This conserved structure allowed an automated alignment of extremely divergent sequences as exemplified for the ITS2 sequences of a ctenophorean eumetazoon and a volvocalean green alga. All classified sequences, together with their structures can be accessed at http://www.biozentrum.uni-wuerzburg.de/bioinformatik/projects/ITS2.html. Furthermore, we found that, although sample sequences are known for most major taxa, there exists a profound divergence in coverage, which might become a hindrance for general usage. In summary, our analysis strengthens the potential of ITS2 as a general phylogenetic marker and provides a data source for further ITS2-based analyses.

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“…Intragenomic polymorphisms of the ITS region have also been reported in other eukaryotes, including plants (Baldwin et al 1995; Alvarez and Wendel 2003), beetles (Vogler and DeSalle 1994), nematodes (Zijlstra et al 1995), sponges (Wörheide et al 2004) and filamentous fungi (O’Donnell and Cigelnik 1997; Wang and Yao 2005). The divergent ITS types in the same individual genomes of these organisms are usually described as nonorthologous and attributed to the origin of ancient interspecific hybridisation (xenologous origin) or gene duplication (paralogous origin), but direct evidences have not been presented.…”

Section: Discussionmentioning

confidence: 92%

Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast speciesPichia membranifaciens

Wang

Liu

et al. 2016

Mycology

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A concerted evolution model has been proposed to explain the observed lack of sequence variation among the multiple ribosomal RNA (rRNA) gene copies in many different eukaryotic species. Recent studies on the level of intragenomic variations in the rRNA gene repeats of fungi resulted in controversial conclusions. In this study, we clearly showed that significant polymorphisms of the internal transcribed spacers (ITS1 and ITS2) of ribosomal DNA (rDNA) exist within the genome of a strain of the yeast species Pichia membranifaciens. More interestingly, we showed that the intragenomic ITS sequence polymorphisms were formed by intergenomic rDNA recombination among different P. membranifaciens strains with significantly different ITS sequences. Intergenomic rDNA recombination was also responsible for the diversification of rDNA sequences in different strains of the species. After the events bring together different rDNA types in individual genomes of the P. membranifaciens strains compared, rDNA sequence heterogeneity has remained in the genome of one but eliminated by homogenisation in the genomes of other strains. Our findings show new clue for further investigation on the mechanism of concerted evolution of rRNA genes in eukaryotes.

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Ribosomal ITS sequences and plant phylogenetic inference

Cited by 1,632 publications

References 156 publications

Chromosome triplication found across the tribe Brassiceae

Chromosome triplication found across the tribe Brassiceae

A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota

Intragenomic polymorphism and intergenomic recombination in the ribosomal RNA genes of strains belonging to a yeast speciesPichia membranifaciens

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