SSR-seq: Genotyping of microsatellites using next-generation sequencing reveals higher level of polymorphism as compared to traditional fragment size scoring

Microsatellites (or simple sequence repeats, SSR) are widely used markers in population genetics. Traditionally, genotyping was and still is carried out through recording fragment length. Now, next-generation sequencing (NGS) makes it easy to obtain also sequence information for the loci of interest. This avoids misinterpretations that otherwise could arise due to size homoplasy. Here, an NGS strategy is described that allows to genotype hundreds of individuals at many custom-designed SSR loci simultaneously, combining multiplex PCR, barcoding, and Illumina sequencing. We created three different datasets for which alleles were coded according to (a) length of the repetitive region, (b) total fragment length, and (c) sequence identity, in order to evaluate the eventual benefits from having sequence data at hand, not only fragment length data. For each dataset, genetic diversity statistics, as well as F ST and R ST values, were calculated. The number of alleles per locus, as well as observed and expected heterozygosity, was highest in the sequence identity dataset, because of single-nucleotide polymorphisms and insertions/deletions in the flanking regions of the SSR motif. Size homoplasy was found to be very common, amounting to 44.7%-63.5% (mean over all loci) in the three study species. Thus, the information obtained by next-generation sequencing offers a better resolution than the traditional way of SSR genotyping and allows for more accurate evolutionary interpretations.

New insights into the variability of reproduction modes in European populations of Rubus subgen. Rubus: how sexual are polyploid brambles?

Rubus subgen. Rubus includes common European species with highly complicated taxonomy, ongoing hybridisation and facultative apomixis. Out of approximately 750 species recognised in Europe, only 3 diploid sexual species are known, along with numerous apomictic brambles that are highly connected to polyploidy. One exception of a tetraploid taxon is R. ser. Glandulosi, which is known for prevalent sexuality. This taxon highly hybridises with tetraploid members of R. ser. Discolores and leads to the origin of many hybridogenous populations and individuals. In this study, we verify reproduction modes in different diploid, triploid and tetraploid species of subgen. Rubus, with focus on taxa putatively involved in such hybridisation by applying flow cytometric seed screen analysis. We found 100 % sexuality of diploid species, whereas triploid species had obligate unreduced embryo sac development. In contrast, tetraploid plants had varying degrees of sexuality. Additionally, we discovered that R. bifrons has the ability to undergo a reproduction mode switch as a reaction to environmental conditions. These results provide insight into reproductive modes of European brambles and shed light on their reticulate evolution and speciation.

Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers

BACKGROUND AND AIMS

Rubus subgenus Rubus is a group of mostly apomictic and polyploid species with a complicated taxonomy and history of ongoing hybridization. The only polyploid series with prevailing sexuality is the series Glandulosi , although the apomictic series Discolores and Radula also retain a high degree of sexuality, which is influenced by environmental conditions and/or pollen donors. The aim of this study is to detect sources of genetic variability, determine the origin of apomictic taxa and validate microsatellite markers by cloning and sequencing.

METHODS

A total of 206 individuals from two central European regions were genotyped for 11 nuclear microsatellite loci and the chloroplast trn L- trn F region. Microsatellite alleles were further sequenced in order to determine the exact repeat number and to detect size homoplasy due to insertions/deletions in flanking regions.

KEY RESULTS

The results confirm that apomictic microspecies of ser. Radula are derived from crosses between sexual series Glandulosi and apomictic series Discolores , whereby the apomict acts as pollen donor. Each apomictic microspecies is derived from a single distinct genotype differing from the parental taxa, suggesting stabilized clonal reproduction. Intraspecific variation within apomicts is considerably low compared with sexual series Glandulosi , and reflects somatic mutation accumulation. While facultative apomicts produce clonal offspring, sexual species are the conduits of origin for new genetically different apomictic lineages.

CONCLUSIONS

One of the main driving forces of evolution and speciation in the highly apomictic subgenus Rubus in central Europe is sexuality in the series Glandulosi . Palaeovegetation data suggest that initial hybridizations took place over different time periods in the two studied regions, and that the successful origin and spread of apomictic microspecies of the series Radula took place over several millennia. Additionally, the cloning and sequencing show that standard evaluations of microsatellite repeat numbers underestimate genetic variability considering homoplasy in allele size.

DNA content variation and its significance in the evolution of the genus Micrasterias (Desmidiales, Streptophyta)

It is now clear that whole genome duplications have occurred in all eukaryotic evolutionary lineages, and that the vast majority of flowering plants have experienced polyploidisation in their evolutionary history. However, study of genome size variation in microalgae lags behind that of higher plants and seaweeds. In this study, we have addressed the question whether microalgal phylogeny is associated with DNA content variation in order to evaluate the evolutionary significance of polyploidy in the model genus Micrasterias. We applied flow-cytometric techniques of DNA quantification to microalgae and mapped the estimated DNA content along the phylogenetic tree. Correlations between DNA content and cell morphometric parameters were also tested using geometric morphometrics. In total, DNA content was successfully determined for 34 strains of the genus Micrasterias. The estimated absolute 2C nuclear DNA amount ranged from 2.1 to 64.7 pg; intraspecific variation being 17.4–30.7 pg in M. truncata and 32.0–64.7 pg in M. rotata. There were significant differences between DNA contents of related species. We found strong correlation between the absolute nuclear DNA content and chromosome numbers and significant positive correlation between the DNA content and both cell size and number of terminal lobes. Moreover, the results showed the importance of cell/life cycle studies for interpretation of DNA content measurements in microalgae.

A novel strategy to study apomixis, automixis, and autogamy in plants

KEY MESSAGE

The combination of a flow cytometric seed screen and genotyping of each single seed offers a cost-effective approach to detecting complex reproductive pathways in flowering plants. Reproduction may be seen as one of the driving forces of evolution. Flow cytometric seed screen and genotyping of parents and progeny are commonly employed techniques to discern various modes of reproduction in flowering plants. Nevertheless, both methods possess limitations constraining their individual capacity to investigate reproductive modes thoroughly. We implemented both methods in a novel manner to analyse reproduction pathways using a carefully selected material of parental individuals and their seed progeny. The significant advantage of this approach lies in its ability to apply both methods to a single seed. The introduced methodology provides valuable insights into discerning the levels of apomixis, sexuality, and selfing in complex Rubus taxa. The results may be explained by the occurrence of automixis in Rubus, which warrants further investigation. The approach showcased its effectiveness in a different apomictic system, specifically in Taraxacum. Our study presents a comprehensive methodological approach for determining the mode of reproduction where flow cytometry loses its potential. It provides a reliable and cost-effective method with significant potential in biosystematics, population genetics, and crop breeding.

Recent Origin of a Range-Restricted Species With Subsequent Introgression in its Widespread Congener in the Phyteuma spicatum Group (Campanulaceae)

Understanding the causes of restricted geographic distributions is of major interest to evolutionary and conservation biologists. Inferring historical factors has often relied on ad hoc interpretations of genetic data, and hypothesis testing within a statistical framework under different demographic scenarios remains underutilised. Using coalescent modelling on RAD-sequencing data, we (i) test hypotheses about the origin of Phyteuma gallicum (Campanulaceae), a range-restricted endemic of central France sympatric with its widespread congener Ph. spicatum, and (ii) date its origin, irrespective of its mode of origin, to test the hypothesis that the restricted range is due to a recent time of origin. The best supported model of origin is one of a dichotomous split of Ph. gallicum, confirmed as distinct species, and the Central European Ph. nigrum with subsequent gene flow between Ph. gallicum and Ph. spicatum. The split of Ph. gallicum and Ph. nigrum is estimated at 45-55,000 years ago. Coalescent modelling on genomic data not only clarified the mode of origin (dichotomous speciation instead of a previously hypothesised hybridogenic origin) but also identified recency of speciation as a sufficient, although likely not the sole, factor to explain the restricted distribution range. Coalescent modelling strongly improves our understanding of the evolution of range-restricted species that are frequently of conservation concern, as is the case for Ph. gallicum.

Festucasilana (Poaceae), a new species from the Sila plateau in Italy

A new hexaploid species of fine-leaved fescue from Festucasect.Festuca (Festucasilana Ardenghi, Pallanza & Foggi, sp. nov.) endemic to the Sila plateau is described. The new taxon shows morphological affinities with species of the F.marginata group from which it can be distinguished by higher ploidy, ecology, and leaf cross section anatomy. ddRADseq data suggests F.silana could be a local hexaploid descendant/derivate of the widespread diploid F.marginata. Its distribution is restricted to several localities in the Sila highlands of the Southern Apennines, Italy.

Plant kleptomaniacs: geographical genetic patterns in the amphi-apomictic Rubus ser. Glandulosi (Rosaceae) reveal complex reticulate evolution of Eurasian brambles

BACKGROUND AND AIMS

Rubus ser. Glandulosi provides a unique model of geographical parthenogenesis on a homoploid (2n = 4x) level. We aim to characterize evolutionary and phylogeographical patterns in this taxon and shed light on the geographical differentiation of apomicts and sexuals. Ultimately, we aim to evaluate the importance of phylogeography in the formation of geographical parthenogenesis.

METHODS

Rubus ser. Glandulosi was sampled across its Eurasian range together with other co-occurring Rubus taxa (587 individuals in total). Double-digest restriction site-associated DNA sequencing (ddRADseq) and modelling of suitable climate were used for evolutionary inferences.

KEY RESULTS

Six ancestral species were identified that contributed to the contemporary gene pool of R. ser. Glandulosi. Sexuals were introgressed from Rubus dolichocarpus and Rubus moschus in West Asia and from Rubus ulmifolius agg., Rubus canescens and Rubus incanescens in Europe, whereas apomicts were characterized by alleles of Rubus subsect. Rubus. Gene flow between sexuals and apomicts was also detected, as was occasional hybridization with other taxa.

CONCLUSIONS

We hypothesize that sexuals survived the last glacial period in several large southern refugia, whereas apomicts were mostly restricted to southern France, whence they quickly recolonized Central and Western Europe. The secondary contact of sexuals and apomicts was probably the principal factor that established geographical parthenogenesis in R. ser. Glandulosi. Sexual populations are not impoverished in genetic diversity along their borderline with apomicts, and maladaptive population genetic processes probably did not shape the geographical patterns.