Sònia Garcia

Genome size in Echinops L. and related genera (Asteraceae, Cardueae): karyological, ecological and phylogenetic implications.

Abstract Genome size was assessed by flow cytometry in 33 species belonging to seven genera of the tribe Cardueae (Asteraceae), which can be grouped in three taxonomic complexes. 2C nuclear DNA content ranged from 1.49 to 16.98 pg, which is more than elevenfold variation. Genome size correlated well with some karyological traits. Nuclear DNA amount variations also have systematic and evolutionary implications and/or are linked to adaptations to ecological conditions.

Extensive ribosomal DNA (18S-5.8S-26S and 5S) colocalization in the North American endemic sagebrushes (subgenus Tridentatae, Artemisia, Asteraceae) revealed by FISH

Chromomycin A3 banding and fluorescent in situ hybridization (FISH) have been performed for six Artemisia species with special emphasis on subgenus Tridentatae. Morphometrical data on karyotype characters were calculated and idiograms with the position of GC-rich regions and 18S-5.8S-26S and 5S sites of ribosomal DNA were constructed. These sites were all colocalized. To our knowledge, this is the first time in the large family Asteraceae, indeed in angiosperms in general, that colocalization of the two rDNA regions studied is found at every single marked locus. In addition, transcriptionally active nucleolar organizer regions were detected after silver nitrate staining. Tridentatae is a cytogenetically homogeneous subgenus, which suggests that evolution of these species has not been coupled with important karyotypic reorganization. However, a few species are taxonomically difficult and show substantial differences. A loss of rDNA loci has been detected in a tetraploid taxon with respect to the diploids studied. These data provide clarifying insight into interspecific relationships between the studied taxa and overall evolutionary and systematic relationships of the Tridentatae.

Value of p16INK4a as a marker of progression/regression in cervical intraepithelial neoplasia grade 1

OBJECTIVE The objective of this study was to evaluate the usefulness of p16(INK4a) staining to classify cervical intraepithelial neoplasia grade 1 according to its progression/regression risk. STUDY DESIGN Patients with a histologic diagnosis of cervical intraepithelial neoplasia grade 1 were prospectively recruited (n = 138). Simultaneous detection of high-risk human papillomaviruses and p16(INK4a) evaluation were performed. Follow-up was conducted every 6 months by cytology and colposcopy and annually by high-risk human papillomavirus testing, for at least 12 months (mean, 29.0). Progression was defined as a histologic diagnosis of cervical intraepithelial neoplasia grades 2-3, regression as a negative cytology and high-risk human papillomaviruses, and persistence as a cytologic result of low-grade squamous intraepithelial lesions and/or a positive test for high-risk human papillomaviruses. RESULTS Progression was observed in 14 women (10.1%), 66 (47.6%) regressed, and 58 (42.0%) had a persistent disease. p16(INK4a) was positive in 77 (55.8%) initial biopsy specimens. Progression to cervical intraepithelial neoplasia grades 2-3 was identified in 14 of 77 (18.2%) women with positive and none of 61 (0.00%) women with negative p16(INK4a) immunostaining (P < .001). CONCLUSION p16(INK4a) negative cervical intraepithelial neoplasia grade 1 lesions rarely progress and may benefit from a less intensive follow-up.

p16INK4a Immunostaining Identifies Occult CIN Lesions in HPV-positive Women

To evaluate whether p16INK4a staining could help to recognize underestimated cervical intraepithelial neoplasia (CIN) in women positive for high-risk human papillomavirus (HR-HPV) with negative biopsy. Out of 1,259 women undergoing a histologic study and a simultaneous HR-HPV detection using the Hybrid Capture 2 test, we selected all patients testing positive for HR-HPV and having a negative biopsy (n=139), as well as all women testing negative for HR-HPV with a biopsy of either CIN 1 (26 cases) or CIN 2 to 3 (11 cases). Of the remaining 1,083 women, we randomly selected for the purpose of controls, 50 cases negative for HR-HPV with negative biopsy and 100 cases positive for HR-HPV and with biopsy of CIN (50 CIN 1, 50 CIN 2–3). In all cases, immunohistochemical staining for p16INK4a and a second evaluation of the initial biopsy was carried out. Thirty-four out of 139 biopsies (24.5%) testing positive for HR-HPV but having a negative biopsy were positive for p16INK4a. Thirty of these cases (21.6%) were classified as harboring a CIN (11 CIN 1, 19 CIN 2/3) after reevaluation. Both the number of cases reclassified as CIN of any grade, or as CIN 2/3, were significantly higher for cases with HR-HPV load above 100 relative light unit (P<0.005). Particular attention should be paid to biopsies from patients having positive Hybrid Capture 2. The risk of harboring undetected CIN of any type or CIN 2/3 is significantly higher for patients with high HR-HPV load. Immunostaining with p16INK4a should be considered as a highly desirable addition to the histologic evaluation of cervical biopsy specimens in HR-HPV–positive women.

Plant rDNA database: ribosomal DNA loci information goes online

Number, position and structure of the 5S and 18S-5.8S-26S ribosomal DNA (rDNA) loci are important species characteristics. In recent decades, we have witnessed accumulation of rDNA data, and there is a need to compile, store and analyse this information, and to make it accessible to a broader scientific community. An online resource, accessible at www.plantrdnadatabase.com, has been developed to accomplish these goals. Current knowledge regarding chromosomal rDNA sites is provided for more than 1,000 plant species (including more than 1,400 different accessions). The data comes from fluorescent in situ hybridisation experiments (FISH) from more than 300 publications. Additional information is also displayed, such as ploidy level, mutual arrangement of rRNA genes, genome size and life cycle. The webpage is intuitive and user-friendly, including different search options, and currently holds information published (or in press) up until January 2011; frequent updates are planned. We expect this database to be used for data-mining, analysing rDNAs from different angles, unit organisation, distribution, evolution and linkage of rDNA patterns with phylogenetic relationships.

Recent updates and developments to plant genome size databases

Two plant genome size databases have been recently updated and/or extended: the Plant DNA C-values database (http://data.kew.org/cvalues), and GSAD, the Genome Size in Asteraceae database (http://www.asteraceaegenomesize.com). While the first provides information on nuclear DNA contents across land plants and some algal groups, the second is focused on one of the largest and most economically important angiosperm families, Asteraceae. Genome size data have numerous applications: they can be used in comparative studies on genome evolution, or as a tool to appraise the cost of whole-genome sequencing programs. The growing interest in genome size and increasing rate of data accumulation has necessitated the continued update of these databases. Currently, the Plant DNA C-values database (Release 6.0, Dec. 2012) contains data for 8510 species, while GSAD has 1219 species (Release 2.0, June 2013), representing increases of 17 and 51%, respectively, in the number of species with genome size data, compared with previous releases. Here we provide overviews of the most recent releases of each database, and outline new features of GSAD. The latter include (i) a tool to visually compare genome size data between species, (ii) the option to export data and (iii) a webpage containing information about flow cytometry protocols.

Dancing together and separate again: gymnosperms exhibit frequent changes of fundamental 5S and 35S rRNA gene (rDNA) organisation

In higher eukaryotes, the 5S rRNA genes occur in tandem units and are arranged either separately (S-type arrangement) or linked to other repeated genes, in most cases to rDNA locus encoding 18S–5.8S–26S genes (L-type arrangement). Here we used Southern blot hybridisation, PCR and sequencing approaches to analyse genomic organisation of rRNA genes in all large gymnosperm groups, including Coniferales, Ginkgoales, Gnetales and Cycadales. The data are provided for 27 species (21 genera). The 5S units linked to the 35S rDNA units occur in some but not all Gnetales, Coniferales and in Ginkgo (∼30% of the species analysed), while the remaining exhibit separate organisation. The linked 5S rRNA genes may occur as single-copy insertions or as short tandems embedded in the 26S–18S rDNA intergenic spacer (IGS). The 5S transcript may be encoded by the same (Ginkgo, Ephedra) or opposite (Podocarpus) DNA strand as the 18S–5.8S–26S genes. In addition, pseudogenised 5S copies were also found in some IGS types. Both L- and S-type units have been largely homogenised across the genomes. Phylogenetic relationships based on the comparison of 5S coding sequences suggest that the 5S genes independently inserted IGS at least three times in the course of gymnosperm evolution. Frequent transpositions and rearrangements of basic units indicate relatively relaxed selection pressures imposed on genomic organisation of 5S genes in plants.

A molecular phylogenetic approach to western North America endemic Artemisia and allies (Asteraceae): Untangling the sagebrushes

PREMISE OF THE STUDY Artemisia subgenus Tridentatae plants characterize the North American Intermountain West. These are landscape-dominant constituents of important ecological communities and habitats for endemic wildlife. Together with allied species and genera (Picrothamnus and Sphaeromeria), they make up an intricate series of taxa whose limits are uncertain, likely the result of reticulate evolution. The objectives of this study were to resolve relations among Tridentatae species and their near relatives by delimiting the phylogenetic positions of subgenus Tridentatae species with particular reference to its New World geographic placement and to provide explanations for the relations of allied species and genera with the subgenus with an assessment of their current taxonomic placement. METHODS Bayesian inference and maximum parsimony analysis were based on 168 newly generated sequences (including the nuclear ITS and ETS and the plastid trnS(UGA)-trnfM(CAU) and trnS(GCU)-trnC(GCA)) and 338 previously published sequences (ITS and ETS). Genome size by flow cytometry of species from Sphaeromeria was also determined. KEY RESULTS The results support an expanded concept and reconfiguration of Tridentatae to accommodate additional endemic North American Artemisia species. The monotypic Picrothamnus and all Sphaeromeria species appear nested within subgenus Tridentatae clade. CONCLUSIONS A redefinition of subgenus Tridentatae to include other western North American endemics is supported. We propose a new circumscription of the subgenus and divide it into three sections: Tridentatae, Filifoliae, and Nebulosae. The position of the circumboreal and other North American species suggests that subgenus Artemisia is the ancestral stock for the New World endemics, including those native to South America.

Biology, Genome Evolution, Biotechnological Issues and Research Including Applied Perspectives in Artemisia (Asteraceae)

Abstract Artemisia is one of the largest genera of the family Asteraceae or Compositae, itself the biggest flowering plant family. It comprises around 600 taxa at specific and subspecific levels, present in all continents but Antarctica, mostly distributed in the Northern Hemisphere, with no more than 25 taxa in the Southern Hemisphere. The genus displays a huge ecological plasticity, with species occurring from sea level to high mountains and from arid zones to wetlands. Some species are cosmopolitan, including landscape-dominating plants over large areas, and others are endemics with a quite restricted distribution area. Many species of the genus have economic uses at both folk and industrial levels, and some of them are widely cultivated and submitted to breeding programmes as crops. In this review, we will set out the state of art of Artemisia systematics and phylogeny, as well as all the biological aspects of the genus, with particular attention paid to those of genome organization, and of applied questions related to its useful taxa. In the first part of this chapter, we will review all the systematic points in the genus and in some closely related genera that constitute, with the core genus Artemisia, a pool with controversial structuring. Besides, the infrageneric classification will be addressed. All these questions will be treated in the light of recent molecular phylogenetic studies, which have had an important impact on its systematics and taxonomy. A second part will be devoted to genome organization and evolution in Artemisia, with special attention to cytogenetic data, including genome size, and genetic variability. These points are relevant for understanding the evolutionary pathways in the genus and for applied purposes. The third and fourth parts of the chapter will review, respectively, the uses of Artemisia species in different domains and the biotechnological issues linked to their productivity. Finally, the perspectives of the knowledge and applied aspects of the genus will be addressed.

Ethnobotany of Food Plants in the High River Ter Valley (Pyrenees, Catalonia, Iberian Peninsula): Non-Crop Food Vascular Plants and Crop Food Plants with Medicinal Properties

The present study reports a part of the findings of an ethnobotanical research project conducted in the Catalan region of the high river Ter valley (Iberian Peninsula), concerning the use of wild vascular plants as food and the medicinal uses of both wild and cultivated food plants. We have detected 100 species which are or have been consumed in this region, 83 of which are treated here (the remaining are the cultivated food plants without additional medicinal uses). Some of them, such as Achillea ptarmica subsp. pyrenaica, Convolvulus arvensis, Leontodon hispidus, Molopospermum peloponnesiacum and Taraxacum dissectum, have not been previously reported, or have only very rarely been cited or indicated as plant foods in very restricted geographical areas. Several of these edible wild plants have a therapeutic use attributed to them by local people, making them a kind of functional food. They are usually eaten raw, dressed in salads or cooked; the elaboration of products from these species such as liquors or marmalades is a common practice in the region. The consumption of these resources is still fairly alive in popular practice, as is the existence of homegardens, where many of these plants are cultivated for private consumption.