Sònia Garcia

Sònia Garcia
Spanish National Research Council | CSIC · Institut Botànic de Barcelona

PhD

About

248
Publications
27,073
Reads
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2,216
Citations
Introduction
Ribosomal DNA evolution, Repetitive DNA, telomeres, Asteraceae, Invasive Alien Plant Species
Additional affiliations
December 2015 - present
Spanish National Research Council
Position
  • Researcher
February 2011 - December 2015
University of Barcelona
Position
  • PostDoc Position
February 2008 - July 2011
Institut Botànic de Barcelona
Position
  • PostDoc Position

Publications

Publications (248)
Preprint
This paper is not authored by me (Sònia Garcia), I just served as an editor, but I can't find how to correct this in ResearchGate.
Article
Full-text available
Plastid genomes are in general highly conserved given their slow evolutionary rate, and thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridization, b...
Article
BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they...
Preprint
Plastid genomes are in general highly conserved given their slow evolutionary rate, thus large changes in their structure are unusual. However, when specific rearrangements are present, they are often phylogenetically informative. Asteraceae is a highly diverse family whose evolution is long driven by polyploidy (up to 48x) and hybridisation, both...
Article
Full-text available
We report on a major update to the animal rDNA loci database, which now contains cytogenetic information for 45S and 5S rDNA loci in more than 2600 and 1000 species, respectively. The data analyses show the following: (i) A high variability in 5S and 45S loci numbers, with both showing 50-fold or higher variability. However, karyotypes with an extr...
Article
This article comments on: Lucas Costa, André Marques, Chris Buddenhagen, William Wayt Thomas, Bruno Huettel, Veit Schubert, Steven Dodsworth, Andreas Houben, Gustavo Souza and Andrea Pedrosa-Harand, Aiming off the target: recycling target capture sequencing reads for investigating repetitive DNA, Annals of Botany, Volume 128, Issue 7, 2 December 20...
Preprint
Full-text available
BACKGROUND: Long terminal repeat (LTR) retrotransposons are widespread in plant genomes and play a large role in the generation of genomic variation. Despite this, their identification and characterization remains challenging, especially for non-model genomes. Hence, LTR retrotransposons remain undercharacterized in Vaccinium genomes, although they...
Article
Full-text available
El tamaño del genoma de 18 especies del género Carduncellus, dos especies de los géneros relacionados, Phonus y el género monotípico Femeniasia (F. balearica) ha sido medido por primera vez mediante citometría de flujo. Los niveles de ploidía se asignaron utilizando datos de tamaño del genoma junto con los recuentos de cromosomas previamente report...
Article
Full-text available
Telomerase RNA (TR) carries the template for synthesis of telomere DNA and provides a scaffold for telomerase assembly. Fungal TRs are long and have been compared to higher eukaryotes, where they show considerable diversity within phylogenetically close groups. TRs of several Saccharomycetaceae were recently identified, however, many of these remai...
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Full-text available
Pandemics are as old as humanity and since ancient times we have turned to plants to find solutions to health-related problems. Traditional medicines based mostly on plants are still the only therapeutic possibility in many developing countries, but even in the richest ones, herbal formulation currently receives increased attention. Plants are natu...
Article
A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment such as the loss of stomatal genes, while other functions like an algal-like cell wall composition were acquired. Beyond these, the genome structure and organiza...
Article
Colobanthus quitensis (Kunth) Bartl. and Deschampsia antarctica Desv., the only two native flowering plants in the Antarctica, are interesting study cases from the ecological, biogeographic, and evolutionary points of view. Here, we present the first genome size analysis focused in several populations from the Antarctic Peninsula and the surroundin...
Article
Full-text available
Sex determination and sex chromosomes have been extensively studied due to their importance in evolutionary biology. Species of dioecious plants, which may have sex chromosomes, offer us unique insights into the history of this phenomenon across the Tree of Life. Here, we present Sex‐chrom: a database on plant sex chromosomes (www.sexchrom.csic.es)...
Preprint
A previous study describing the genome of Zostera marina, the most widespread seagrass in the Northern hemisphere, revealed some genomic signatures of adaptation to the aquatic environment. Important features related to the "back-to-the-sea" reverse evolutionary pathway were found, such as the loss of stomatal genes, while other functions like an a...
Article
Full-text available
Telomeres are basic structures of eukaryote genomes. They distinguish natural chromosome ends from double-stranded breaks in DNA and protect chromosome ends from degradation or end-to-end fusion with other chromosomes. Telomere sequences are usually tandemly arranged minisatellites, typically following the formula (TxAyGz)n. Although they are well...
Article
Full-text available
IntroductionRibosomal DNA (rDNA) loci have been widely used for identification of allopolyploids and hybrids, although few of these studies employed high-throughput sequencing data. Here we use graph clustering implemented in the RepeatExplorer (RE) pipeline to analyze homoeologous 5S rDNA arrays at the genomic level searching for hybridogenic orig...
Article
A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, thi...
Article
Background and aims: Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to find out...
Article
Introgression is a poorly understood evolutionary outcome of hybridization because it may remain largely undetected whenever it involves the transfer of small parts of the genome from one species to another. A putative case of introgression from the southernmost border of Armeria pungens range from its congener A. macrophylla is revisited following...
Preprint
A recent phylogenetic method based on genome-wide abundance of different repeat types proved to be useful in reconstructing the evolutionary history of several plant and animal groups. Here, we demonstrate that an alternative information source from the repeatome can also be employed to infer phylogenetic relationships among taxa. Specifically, thi...
Article
Full-text available
The Genome Size in Asteraceae Database (GSAD, http://www.asteraceaegenomesize.com) has been recently updated, with data from papers published or in press until July 2018. This constitutes the third release of GSAD, currently containing 4350 data entries for 1496 species, which represent a growth of 22.52% in the number of species with available gen...
Article
This article contributes first genome size assessments by flow cytometry for 16 species, 12 genera, and 3 tribes from family Asteraceae, mostly belonging to the Heliantheae alliance, an assembly of 13 tribes from subfamily Asteroideae with a large majority of its species in the New World. Most genome sizes are accompanied by their own chromosome co...
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Full-text available
The study of genome size variation can contribute valuable information on species relationships as well as correlate to several morphological or ecological features, among others. Here we provide an extensive report on genome sizes on genus Tripleurospermum and its closely related genus Matricaria, which are two typically Mediterranean genera parti...
Data
DNA sequence matrix of ITS+ETS rDNA regions for the studied species. (FAS)
Data
Data used for the statistical analyses together with source references. (DOCX)
Article
Full-text available
Introduction: Gnetophytes, comprising the genera Ephedra, Gnetum and Welwitschia, are an understudied, enigmatic lineage of gymnosperms with a controversial phylogenetic relationship to other seed plants. Here we examined the organization of ribosomal DNA (rDNA) across representative species. Methods: We applied high-throughput sequencing approa...
Article
Full-text available
Ribosomal DNA (rDNA) loci encoding 5S and 45S (18S-5.8S-28S) rRNAs are important components of eukaryotic chromosomes. Here, we set up the animal rDNA database containing cytogenetic information about these loci in 1343 animal species (264 families) collected from 542 publications. The data are based on in situ hybridisation studies (both radioacti...
Article
Full-text available
Unfortunately in page 116, second paragraph, the sentence that starts with “Other exceptions include…” was incorrectly published. The complete correct sentence is given below. Other exceptions include the recently discovered Cestrum-type (TTTTTTAGGG) (Peška et al. 2015) and Allium-type telomeres (CTCGGTTATGGG) (Fajkus et al. 2016).
Article
Full-text available
Here we present the third release of the plant rDNA database (March 2017), an open access online resource with information on numbers, locations and structure of 5S and 18S-5.8S-26S (35S) ribosomal DNA (rDNA) (www.plantrdnadatabase.com). Data are now available for 2148 species (3783 entries), extracted from 785 papers published until the end of 201...
Article
We present here B-chrom (www.bchrom.csic.es), an online database with comprehensive information on B chromosomes (Bs) for plants, animals and fungi. Data have been extracted from 3041 sources published between 1907 and July 2016. There are 5760 entries corresponding to 2828 species. Besides presence, number or range of B chromosomes, the database p...
Article
Full-text available
Background Pikes represent an important genus (Esox) harbouring a pre-duplication karyotype (2n = 2x = 50) of economically important salmonid pseudopolyploids. Here, we have characterized the 5S ribosomal RNA genes (rDNA) in Esox lucius and its closely related E. cisalpinus using cytogenetic, molecular and genomic approaches. Intragenomic homogenei...
Article
The online resource www.plantrdnadatabase.com stores information on number, chromosomal locations and structure of the 5S and 18S-5.8S-26S (35S) ribosomal DNAs (rDNA) in plants. This resource was exploited to study relationships between rDNA locus number, distribution, the occurrence of linked (L-type) and separated (S-type) 5S and 35S rDNA units,...
Article
Full-text available
Artemisia herba-alba is a largely-distributed and often landscape-dominating taxon in arid areas of the Mediterranean and Irano-Turanian regions. In Algeria, in 2010 its communities covered 10% of the steppe territory, but its populations have been subjected to overgrazing. A karyological study based on 22 populations together with a cytogenetic ch...
Article
Full-text available
In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing...
Article
Full-text available
Molecular cytogenetics and the study of genome size have been used to understand evolutionary and systematic relationships in many species. However, this approach has seldom been applied to alpine plants. A group of dysploid–polyploid high mountain Artemisia species, distributed from the European Sierra Nevada to Central Asian mountains, through th...
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Full-text available
Genome size was assessed by flow cytometry in 55 populations of 53 taxa with different kinds of relationship with freshwater environments (25 populations of aquatic plants, 24 of wetland plants and six occurring both in aquatic and wetland habitats). Nuclear DNA content is provided for the first time for one family, five genera, 28 species, four su...
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Full-text available
Although karyologically well studied, the genus Tanacetum (Asteraceae) is poorly known from the perspective of molecular cytogenetics. The prevalence of polyploidy, including odd ploidy warranted an extensive cytogenetic study. We studied several species native to Iran, one of the most important centres of diversity of the genus. We aimed to charac...
Article
Full-text available
The Asteraceae family has been broadly studied, but the values of genome size of only 3.5% of their species are known. To expand these data, we carried out a flow cytometric study of nuclear DNA content in a wide range of taxa of this family, filling gaps in some less studied groups. In addition, some chromosome counts have been performed (46 taxa,...
Article
Full-text available
Most Calligonum species are desert plants, characteristic of the Saharan bioclimatic region. All species karyologically analyzed until present have the basic chromosome number x = 9 and comprise diploids, triploids and tetraploids. The Tunisian flora comprises diploid Calligonum arich and C. azel, of restricted distribution, and the tetraploid C. c...