A genome size and phylogenetic survey of Mediterranean Tripleurospermum and Matricaria (Anthemideae, Asteraceae)

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 particularly widespread and diverse in Turkey, the origin of most of the populations here studied. We analyse and discuss genome size variation in the first relatively complete molecular phylogenetic framework of Tripleurospermum (based on ITS and ETS ribosomal DNA-rDNA-regions). We find cases of intraspecific genome size variation, which could be taxonomically significant. Genome downsizing is also detected as the typical response to polyploidisation in Tripleurospermum taxa, being most conspicuous at the tetraploid level. Several positive correlations with genome size, including those with pollen and stomatal size or cypsela length, among others, are also found. Remarkably, taxa presenting rhizomes tend to present higher genome sizes, confirming a trend to accumulate nuclear DNA in such species, which could be explained by the nutrient reserves availability in their storage organs, allowing genome expansion, or by the lower rates of sexual reproduction in rhizomatous taxa

Contribution to the knowledge of genome size evolution in edible blueberries (genus Vaccinium)

BACKGROUND: Vaccinium is one of the largest genera (ca. 500 species) of Ericaceae, well known for its edible and ornamental uses. Although there is certain karyological knowledge, information about genome size (GS) is scarce in the genus. OBJECTIVE: The main goal is providing GS data for several Vaccinium species with prevalence in Europe and Western Asia and analysing global GS variation in the genus, considering available data and phylogenetic context. METHODS: New GS assessments were obtained by flow cytometry and chromosome counts were verified. Phylogenetic analyses (using nuclear ITS, and chloroplastic matK and ndhF) were performed by Bayesian inference and reconstruction of ancestral GS by maximum parsimony. RESULTS: We obtained GS data for five Vaccinium species (13 populations). Three species are reported for the first time. Values (2C) ranged between 1.16-1.47 pg at the diploid (2n = 24) and between 3.13-3.16 pg at the tetraploid (2n = 48) levels. The five species here investigated have been placed and analysed in a reconstructed phylogenetic background (including 68 taxa). CONCLUSIONS: GS values of Vaccinium can be considered "very small". The preliminary reconstruction of ancestral GS would point to a reduction in Vaccinium, although more data is needed to establish global GS evolutionary trend in the genus

Sex-chrom, a database on plant sex chromosomes

This work has been supported by the Dirección General de Investigación Científica y Técnica (Spanish Government: CGL2016-75694-P AEI/FEDER, UE; CGL2017-84297-R), by the Generalitat de Catalunya (‘Ajuts a grups de recerca consolidats’ 2017SGR01116’), by the Czech Science Foundation (grants 16-08698S, 18-06147S and 19-03442S) and by CIJA PRESERVATION, SL. SG benefitted from a Ramón y Cajal contract (RYC-2014-16608) from the government of Spain, and SB and NS received Erasmus + grants from the European Union.Introduction Types of plant sex chromosomes, sex determination systems and their diversity Model systems in sex chromosome research Materials and Methods Information sources Data mining Database web environment and construction Results and Discussion Future directions Acknowledgements Author contribution

Plastome Diversity and Phylogenomic Relationships in Asteraceae

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, both processes usually complicating systematic inferences. In this study, we generated one of the most comprehensive plastome-based phylogenies of family Asteraceae, providing information about the structure, genetic diversity and repeat composition of these sequences. By comparing the whole-plastome sequences obtained, we confirmed the double inversion located in the long single-copy region, for most of the species analyzed (with the exception of basal tribes), a well-known feature for Asteraceae plastomes. We also showed that genome size, gene order and gene content are highly conserved along the family. However, species representative of the basal subfamily Barnadesioideae¿as well as in the sister family Calyceraceae¿lack the pseudogene rps19 located in one inverted repeat. The phylogenomic analysis conducted here, based on 63 protein-coding genes, 30 transfer RNA genes and 21 ribosomal RNA genes from 36 species of Asteraceae, were overall consistent with the general consensus for the family¿s phylogeny while resolving the position of tribe Senecioneae and revealing some incongruences at tribe level between reconstructions based on nuclear and plastid DNA data.This research was supported by grants CGL2016-75694-P and PID2020-119163GB-I00 and S.G. benefited from a Ramón y Cajal contract RYC-2014-16608, all funded by MCIN/AEI/10.13039/501100011033. We are also grateful to the “Ajuts a grups de recerca consolidats” 2017SGR01116 from the Generalitat de Catalunya.1. Introduction 2. Results 2.1. Plastome Reconstruction in Asteraceae 2.2. Phylogenetic Analysis 2.3. Structural Comparison of Plastomes 2.4. Characterization of Sequence Divergence, Repeats and SSRs 3. Discussion 3.1. Structural and Nucleotide Diversity of Asteraceae Plastomes 3.2. Asteraceae Plyogenomics Based on Plastid DNA 4. Materials and Methods 4.1. Taxon Sampling 4.2. DNA Preparation and Sequencing 4.3. Genome Assembly and Annotation 4.4. Plastome Phylogenetic Analyses 4.5. Plastome Diversity Analyses 5. Conclusions Author Contributions Funding Data Availability Statement Acknowledgments Conflicts of Interest Reference

Analysis of 5S rDNA Genomic Organization Through the RepeatExplorer2 Pipeline: A Simplified Protocol

he ribosomal RNA genes (rDNA) are universal genome components with a housekeeping function, given the crucial role of ribosomal RNA in the synthesis of ribosomes and thus for life-on-Earth. Therefore, their genomic organization is of considerable interest for biologists, in general. Ribosomal RNA genes have also been largely used to establish phylogenetic relationships, and to identify allopolyploid or homoploid hybridization. Here, we demonstrate how high-throughput sequencing data, through graph clustering implemented in RepeatExplorer2 pipeline (https://repeatexplorer-elixir.cerit-sc.cz/galaxy/), can be helpful to decipher the genomic organization of 5S rRNA genes. We show that the linear shapes of cluster graphs are reminiscent to the linked organization of 5S and 35S rDNA (L-type arrangement) while the circular graphs correspond to their separate arrangement (S-type). We further present a simplified protocol based on the paper by (Garcia et al., Front Plant Sci 11:41, 2020) about the use of graph clustering of 5S rDNA homoeologs (S-type) to identify hybridization events in the species history. We found that the graph complexity (i.e., graph circularity in this case) is related to ploidy and genome complexity, with diploids typically showing circular-shaped graphs while allopolyploids and other interspecific hybrids display more complex graphs, with usually two or more interconnected loops representing intergenic spacers. When a three-genomic comparative clustering analysis from a given hybrid (homoploid/allopolyploid) and its putative progenitor species (diploids) is performed, it is possible to identify the corresponding homoeologous 5S rRNA gene families, and to elucidate the contribution of each putative parental genome to the 5S rDNA pool of the hybrid. Thus, the analysis of 5S rDNA cluster graphs by RepeatExplorer, together with information coming from other sources (e.g., morphology, cytogenetics) is a complementary approach for the determination of allopolyploid or homoploid hybridization and even ancient introgression events

Sex-chrom v. 2.0: a database of green plant species with sex chromosomes

The work was supported by a grant from the Spanish Ministerio de Ciencia e Innovación, PID2020-119163 GB-I00, and SG benefited from a Ramón y Cajal contract (RYC-2014–16608), both funded by MCIN/AEI/10.13039/501100011033.Introduction Materials and methods Results and discussion Data availability References Acknowledgements Funding Author information Ethics declarations Additional information Rights and permissions About this articl

Repeat contribution to genome size ups and downs in family Asteraceae

Trabajo presentado en el XIX Jornades de Biologia Evolutiva, celebrada en Barcelona (España), el 28 de junio de 2019Peer reviewe

A genome size and phylogenetic survey of Mediterranean Tripleurospermum and Matricaria (Anthemideae, Asteraceae)

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 particularly widespread and diverse in Turkey, the origin of most of the populations here studied. We analyse and discuss genome size variation in the first relatively complete molecular phylogenetic framework of Tripleurospermum (based on ITS and ETS ribosomal DNA–rDNA–regions). We find cases of intraspecific genome size variation, which could be taxonomically significant. Genome downsizing is also detected as the typical response to polyploidisation in Tripleurospermum taxa, being most conspicuous at the tetraploid level. Several positive correlations with genome size, including those with pollen and stomatal size or cypsela length, among others, are also found. Remarkably, taxa presenting rhizomes tend to present higher genome sizes, confirming a trend to accumulate nuclear DNA in such species, which could be explained by the nutrient reserves availability in their storage organs, allowing genome expansion, or by the lower rates of sexual reproduction in rhizomatous taxa.This work was supported by the Dirección General de Investigación Científica y Técnica, Government of Spain (CGL2016-75694-P), the Generalitat de Catalunya, Government of Catalonia ("Ajuts a grups de recerca consolidats" 2017SGR1116) and the Scientific and Technological Research Council of Turkey (TUBITAK, project no. 106T162). SG benefited from a Ramón y Cajal contract from the Government of Spain (RYC-2014-16608). SYNTHESYS provided to HI the funding for the visit to the Royal Botanic Garden, Edinburgh (GB-TAF-1175).Peer reviewe

Online Resources Useful for Plant Cytogenetics and Cytogenomics Research

Authoritative and practical, Plant Cytogenetics and Cytogenomics: Methods and Protocols serves as an ideal resource for plant scientists interested in molecular and evolutionary biology, breeding, systematics, and plant -omics in general.The advancements in research in the field of plant cytogenetics and genomics in recent decades have led to a significant increase in publications. To simplify access to the widely dispersed data, there has been a rise in the number of online databases, repositories, and analytical tools. This chapter presents a comprehensive overview of these resources, which can be beneficial to researchers in these areas. It includes, among others, databases on chromosome numbers, special chromosomes (such as B chromosomes or sex chromosomes), some of which are taxon-specific; genome sizes, cytogenetics; and online applications and tools for genomic analysis and visualization.This work has been supported by the State Research Agency (PID2020-119163GB-I00). Maria Luisa Gutiérrez holds a Personal Técnico de Apoyo contract (PTA2018-015819-I), Roi Rodríguez-González and Inés Fuentes hold Garantía Juvenil contracts (MIN19/CAT/IBB001 and C19/CAT/IBB001, respectively), Joan Pere Pascual-Díaz holds a predoctoral fellowship (PRE2021-097873) and Sònia Garcia a Ramón y Cajal contract (RYC-2014-16608), all from the Government of Spai

Remote Sensing Vegetation Indices to study migratory insect seasonal movements and population outbreaks.

Póster presentado en el EGU23 General Assembly celebrado del 23 al 28 abril 202