Fine-scale Geographical Structure, Intra-individual Polymorphism and Recombination in Nuclear Ribosomal Internal Transcribed Spacers in Armeria (Plumbaginaceae)

Feliner, Gonzalo Nieto; Larena, Belén Gutiérrez; Aguilar, Javier Fuertes

doi:10.1093/aob/mch027

Cited by 104 publications

(88 citation statements)

References 49 publications

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“…Rare chimeric clones (usually o5%) probably represent PCR artifacts (Cronn et al, 2002) rather than true genomic recombinants. In contrast, recombinant ITS types have been observed in allopolyploid systems with regular meiosis (Buckler et al, 1997;Franzke and Mummenhoff, 1999;Nieto Feliner et al, 2004;Kovarik et al, 2005). The situation here may resemble that of paeonia hybrids, which frequently undergo vegetative reproduction and whose ITSs have retained much of the parental features (Sang et al, 1995).…”

Section: Discussionmentioning

confidence: 77%

Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae)

et al. 2009

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The polyploid species in Rosa section Caninae (2n ¼ 21, 28 or 35) are characterized by an unusual reproductive system known as odd (or asymmetric) meiosis. Only two chromosome sets form bivalents in meiosis, whereas the remaining chromosomes are transmitted as univalents through the female germline. Evolution of ribosomal rRNA genes (rDNA) does not seem to be significantly affected by interlocus homogenization in dogroses. As a consequence, most species contain several rDNA families falling into two main clades (b and g) thought to be differentially distributed between bivalent and univalent chromosomes, respectively. Here, we have investigated expression of rRNA gene families in five pentaploid species (R. canina, R. rubiginosa, R. dumalis, R. sherardii and R. caesia, 2n ¼ 35) and in one tetraploid (R. mollis, 2n ¼ 28). Using extensive sequencing of ITS clones and cleaved amplified polymorphism sequence (CAPS) analysis, we found that the b-family was constitutively expressed in all species. However, there was large variation in the expression patterns of families constituting the g-clade. In addition, a single family can be active in one species, whereas silenced in another. The data show that the families on bivalent-forming chromosomes dominate rDNA expression in all dogrose species. We hypothesize that genes on bivalent genomes are stably expressed, whereas those on univalent genomes undergo variable levels of epigenetic silencing. Nonetheless, mosaic expression of univalent genomes could contribute to phenotypic variation between the species.

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Section: Discussionmentioning

confidence: 77%

Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae)

et al. 2009

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“…3), which do not all group with other accessions from the same area. Indeed, our sampling is not sufficiently detailed to rule out alternative explanations such as convergent evolution or lineage sorting and, in addition, the occurrence of long distance dispersal of caryopses would clutter a clear geographical structure to the cpDNA data (Feliner et al, 2004). Bearing this in mind we are, at this stage, forced to conclude that aspects of this phylogeny remain enigmatic and that its resolution would require denser sampling, at the population level, and of the nuclear genome in addition.…”

Section: Fit With Ecology and Distributionmentioning

confidence: 97%

“…3A). The existence of a geographical structure to the cpDNA data, such that samples show affinity according to geographical area of origin rather than to morphology and thus traditional systematic arrangement, could confuse patterns at morphological and ecological levels (Fuertes Aguilar et al, 1999a;Feliner et al, 2004). Geographical patterning in cpDNA markers has been reported for the Tasmanian eucalypts (McKinnon et al, 2001(McKinnon et al, , 2004, for Iberian species of Phlomis (Albaladejo et al, 2005) and for white oaks in Europe (Dumolin-Lapé-gue et al, 1997;Petit et al, 2002).…”

Section: Fit With Ecology and Distributionmentioning

confidence: 99%

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Humphreys¹,

Pirie²,

Linder³

2010

Molecular Phylogenetics and Evolution

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Rytidosperma s.l., wallaby grasses and allies, is in dire need of a single, unanimously accepted generic taxonomy. Motivated by the desire to establish a generic classification that complies with phylogeny, we investigated how much phylogenetic signal is contained within a plastid (cpDNA) tree, given that the nrDNA tree (ITS) was uninformative and that a phylogenetic hypothesis based on a single genome may not be reliable. We find that the plastid tree is significantly different from a morphological cladogram and show that this is the result of homoplasy in the morphological dataset. Treated individually, several morphological characters fit the plastid tree very well. Similarly, we find a good fit of the plastid tree with ecological and distribution characters and with biogeographical patterns in the Southern Hemisphere. We conclude that a significant level of the species phylogeny is resolved by the plastid tree and are confident it can form a sound basis for a reconsideration of generic limits. None of the currently recognised seven genera in the Rytidosperma clade is monophyletic. Therefore, we propose combining the segregate genera in Australasia within a broadly construed Rytidosperma, including all the species from Australia, New Guinea, New Zealand and South America.

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“…ITS1 and ITS2) and the conserved 5.8S gene between ITS1 and ITS2 (Baldwin et al, 1995). Although reliance on the use of ITS sequence of nrDNA as the sole source of phylogenetic evidence has come under serious criticism (Alvarez and Wendel, 2003); even then, it is one of the most common molecular markers used for generating species-specific phylogenetic inferences in most groups of plants, fungi and animals (Poczai and Hyvönen, 2010;Ali et al, 2014) and DNA barcoding Yao et al, 2010;Ali et al, 2014Ali et al, , 2015c owing to the patterns of polymorphism and ITS types which are specific to particular taxon and population (Baldwin et al, 1995;Feliner et al, 2004;Szabo et al, 2005). The ITS sequence of nrDNA has gained much attention as smartest gene available for the genotyping of taxon and the epitome of species identification has thus now been changed due to application of genotyping in systematics .…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic implication of molecular genotyping of <i>Euryops jaberiana</i> Abedin & Chaudhary (Asteraceae)

Ali

Lee

Rahman

et al. 2016

Bangladesh J. Plant Taxon

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The taxonomic status of Euryops jaberiana Abedin & Chaudhary (tribe Senecioneae, family Asteraceae), endemic to northern Saudi Arabia was evaluated based on molecular phylogenetic analyses of internal transcribed spacer sequence (ITS) of nuclear ribosomal DNA (nrDNA) in order to ascertain its position within the genus. The phylogenetic tree constructed by the Neighbour Joining, Maximum Parsimony and Maximum Likelihood analyses showed a clear resolution of taxon included in the analyses at the level of sections, and E. jaberiana nested within the clade of the section Angustifoliae. E. jaberiana showed proximity with the allied species E. arabicus; however, a total number of eight nucleotide differences were evident between E. jaberiana and E. arabicus, indicating E. jaberiana as distinct from its allied species.

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Fine-scale Geographical Structure, Intra-individual Polymorphism and Recombination in Nuclear Ribosomal Internal Transcribed Spacers in Armeria (Plumbaginaceae)

Cited by 104 publications

References 49 publications

Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae)

Frequent silencing of rDNA loci on the univalent-forming genomes contrasts with their stable expression on the bivalent-forming genomes in polyploid dogroses (Rosa sect. Caninae)

A plastid tree can bring order to the chaotic generic taxonomy of Rytidosperma Steud. s.l. (Poaceae)

Phylogenetic implication of molecular genotyping of <i>Euryops jaberiana</i> Abedin & Chaudhary (Asteraceae)

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