Daniel Vitales

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.

Genome size variation and evolution in the family Asteraceae

The nuclear DNA content data available in “A genome size database in the Asteraceae” (GSAD: www.asteraceaegenomesize.com) have been analyzed, together with other parameters (i.e. ecological, karyological, cytogenetic), in order to establish hypotheses on the systematic, phylogenetic and evolutionary aspects of genome size in one of the largest angiosperm families. The novelty of this work is a comprehensive analysis of the whole family with the following aims: (1) to update the knowledge of genome size values in the Asteraceae; (2) to infer evolutionary trends of genome size, compared with other plant groups; and (3) to detect gaps in this field in the family and outline further research priorities. The analysis of this dataset shows that most Asteraceae genomes (57.23%) range from very small (1C ⩽ 1.4 pg) to small (1C ⩽ 3.5 pg). Gains and losses of DNA occur throughout the phylogeny of the family but although ancestral values for the basal nodes remain mostly equivocal, often small and very small ancestral genome sizes are reconstructed. Most genome size data (96.74%) are concentrated in five tribes, which broadly reflect their species richness. The relationships between genome size and other cytogenetic and ecological features have been analyzed and discussed, highlighting several general patterns. Further studies are needed to fill the gaps in genome size knowledge in the Asteraceae and more detailed research in some groups could provide information about mechanisms regulating genome expansions and contractions.

GSAD: a genome size in the Asteraceae database.

THE Asteraceae are one of the largest families of angiosperms, comprising 24,000 to 30,000 species in over 1,600 to 2,000 genera (1 and references therein). It has a worldwide distribution, with the exception of Antarctica and includes many economically important species which are used, for example, as foods, medicines, and ornamentals. Asteraceae species are the target of many evolutionary studies and more recently they have also become the focus of new genome sequencing programs. New model species for evolutionary-developmental (evo-devo) research have been selected within the Asteraceae such as Gerbera, Helianthus, and Senecio, whereas Tragopogon is the focus of intensive studies on polyploidization mechanisms (2). The first evo-devo studies in the Asteraceae have been very promising despite complications arising from the genetic and epigenetic changes associated with polyploidy which is very frequent in the family. The term ‘‘C-value’’ was coined by Swift (3) to define the gametic nuclear DNA content (genome size) expressed in picograms. Nowadays, genome size research covers a large and diverse range of biological fields and extends across all plant groups. For example, studies have been carried out on genome size nomenclature (4), to improve methodological aspects (5) and to find possible explanations of how and why genome size changes occur in plants (6). Data on nuclear DNA amounts are interesting not only per se but are also of practical use. For instance, the success of techniques such as AFLPs and nuclear microsatellites are influenced by genome size, while the choice of a species for possible genome sequencing or evo-devo project is also determined, in part, by genome size. Interest in genome size has increased over the years and this has led to the development of several related databases (e.g., for plants 7–9). Following on from our own research studies on genome size in the Asteraceae family and given that the family is one of the most intensely studied from many aspects, we have developed a genome size database focused specifically on the Asteraceae (which we have named the ‘‘Genome size in the Asteraceae database’’, GSAD). It is hoped that this will become a significant tool for comparative research and for future genome size studies.

The explosive radiation of Cheirolophus(Asteraceae, Cardueae) in Macaronesia

BackgroundConsidered a biodiversity hotspot, the Canary Islands have been the key subjects of numerous evolutionary studies concerning a large variety of organisms. The genus Cheirolophus (Asteraceae) represents one of the largest plant radiations in the Canarian archipelago. In contrast, only a few species occur in the Mediterranean region, the putative ancestral area of the genus. Here, our main aim was to reconstruct the phylogenetic and biogeographic history of Cheirolophus with special focus on explaining the origin of the large Canarian radiation.ResultsWe found significant incongruence in phylogenetic relationships between nuclear and plastid markers. Each dataset provided resolution at different levels in Cheirolophus: the nuclear markers resolved the backbone of the phylogeny while the plastid data provided better resolution within the Canarian clade. The origin of Cheirolophus was dated in the Mid-Late Miocene, followed by rapid diversification into the three main Mediterranean lineages and the Macaronesian clade. A decrease in diversification rates was inferred at the end of the Miocene, with a new increase in the Late Pliocene concurrent with the onset of the Mediterranean climate. Diversification within the Macaronesian clade started in the Early-Mid Pleistocene, with unusually high speciation rates giving rise to the extant insular diversity.ConclusionsClimate-driven diversification likely explains the early evolutionary history of Cheirolophus in the Mediterranean region. It appears that the exceptionally high diversification rate in the Canarian clade was mainly driven by allopatric speciation (including intra- and interisland diversification). Several intrinsic (e.g. breeding system, polyploid origin, seed dispersal syndrome) and extrinsic (e.g. fragmented landscape, isolated habitats, climatic and geological changes) factors probably contributed to the progressive differentiation of populations resulting in numerous microendemisms. Finally, hybridization events and emerging ecological adaptation may have also reinforced the diversification process.

Swarm of terminal 35S in Cheirolophus (Asteraceae, Centaureinae)

Island radiation constitutes a playground for species diversification, which has long fascinated researchers and still does today. Because only a small subset of taxa within the pool of island colonizers is concerned by this process, the question is raised on whether some factors could make a taxon prone to radiate. Cheirolophus is the only genus of Centaureinae subtribe to have experienced a radiation in the Canary Islands. Cytogenetic characterization through FISH of 5S and 35S ribosomal RNA genes in eight Cheirolophus species from continent and Canary Islands revealed an unusually high number of 35S predominantly at terminal position, together with a single interstitial 5S rDNA locus in all the studied taxa. Such an abundance of 35S rDNA signals is unique among Centaureinae and predates Cheirolophus arrival in Canary Islands. The possible link of the rDNA profile with radiation process is discussed through a comparison with two other case studies, the closely related Rhaponticum group and the genus Centaurea.

Tracing the introduction history of the brown seaweed Dictyota cyanoloma (Phaeophyceae, Dictyotales) in Europe

ABSTRACT Dictyota cyanoloma has recently been described from the Mediterranean Sea and Macaronesia but doubt had arisen as to whether this species was truly native in Europe. The species is mainly found on non-natural substrata (harbour walls, marinas, boat hulls, etc.), strongly suggesting that it is an introduction. Molecular sequence information from historical herbarium samples proves the presence of D. cyanoloma in the Adriatic Sea as early as 1935. Since approximately the year 2000, however, the number of records as well as the geographic range of the species has expanded significantly. The present-day distribution of D. cyanoloma occupies most of the Mediterranean Sea, Macaronesia, NW Africa and southern Portugal, but recent records from Galicia and SW England (Falmouth, Cornwall) indicate that the species is rapidly expanding northward. Collections from Australia demonstrated that the species is also present from Perth in Western Australia, over much of the southern Australian coastline up to Minnie Water in New South Wales. Phylogenetic analyses resolve D. cyanoloma in a sister clade to a previously unreported Australian Dictyota species. Analysis of genetic diversity of the mitochondrial markers (nad6–nad11 and atp9–orf11) reveals that even though Australian populations contain a much higher haplotype richness, European populations are also fairly diverse. Furthermore, only two out of 25 haplotypes are shared between both regions. These somewhat counterintuitive results could be indicative of a more complicated introduction history.

Third release of the plant rDNA database with updated content and information on telomere composition and sequenced plant genomes

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 2016. This means an expansion of 33.5% in terms of new species and 13% in new publications consulted. We appreciate an increased interest on rDNA loci research in recent years, since 10.78% of all data available were published only in 2016. The database has been expanded to include information on telomere composition and on species whose genome has been fully sequenced up to date. Telomere sequence is only known with certainty for 9.60% of species in the database and for 36.79% at the genus level, indicating, potentially, that the consensus plant telomere (Arabidopsis-type) might not be as extended as previously thought. We have also introduced the taxonomic category order as an additional option for data browsing. Similarly, we have included a new category to indicate the hybrid status of taxa. In addition, we upgraded and/or proofread tabs and links and slightly modified the website for a more dynamic appearance. This manuscript provides a synopsis of these changes and developments.

Phylogeny and biogeography of Artemisia subgenus Seriphidium (Asteraceae: Anthemideae)

19 p., tablas, figuras -- Contiene material suplementario -- Postprint del articulo publicado en Taxon. Version revisada y corregida

Cytogenetic insights into an oceanic island radiation: The dramatic evolution of pre-existing traits in Cheirolophus (Asteraceae: Cardueae: Centaureinae)

146–157 p., tablas, graficos -- El suplemento electronico (Fig. S1) esta disponible en la seccion Supplementary Data de la version online del articulo: http://www.ingentaconnect.com/content/iapt/tax/2017/00000066/00000001/art00009/supp-data

Phylogeographic insights of the lowland species Cheirolophus sempervirens in the southwestern Iberian Peninsula

The southwestern Iberian Peninsula is an important biogeographic region, showing high biodiversity levels and hosting several putative glacial refugia for European flora. Here, we study the genetic diversity and structure of the Mediterranean, thermophilous plant Cheirolophus sempervirens (Asteraceae) across its whole distribution range in SW Iberia, as a tool to disentangle some of the general biogeographic patterns shaping this southern refugia hotspot. Null genetic diversity was observed in the cpDNA sequencing screening. Nonetheless, AFLP data revealed high levels of among‐population genetic differentiation correlated to their geographic location. Our results suggest longer species persistence in southern Iberian refugia during glacial periods and subsequent founder effects northwards due to colonizations in warmer stages (i.e., the southern richness to northern purity pattern). Additionally, our phylogeographic analyses indicate the presence of two separate genetic lineages within Ch. sempervirens, supporting the hypothesis of multiple minor refugia for SW Iberia in agreement with the refugia within refugia model.