Microsatellite Content in 397 Nuclear Exons and Their Flanking Regions in the Fern Family Ophioglossaceae

Microsatellites or SSRs are small tandem repeats that are 1–6 bp long. They are usually highly polymorphic and form important portions of genomes. They have been extensively analyzed in humans, animals and model plants; however, information from non-flowering plants is generally lacking. Here, we examined 29 samples of Ophioglossaceae ferns, mainly from the genera Botrychium and Sceptridium. We analyzed the SSR distribution, density and composition in almost 400 nuclear exons and their flanking regions. We detected 45 SSRs in exons and 1475 SSRs in the flanking regions. In the exons, only di-, tri- and tetranucleotides were found, and all of them were 12 bp long. The annotation of the exons containing SSRs showed that they were related to various processes, such as metabolism, catalysis, transportation or plant growth. The flanking regions contained SSRs from all categories, with the most numerous being dinucleotides, followed by tetranucleotides. More than one-third of all the SSRs in the flanking regions were 12 bp long. The SSR densities in the exons were very low, ranging from 0 to 0.07 SSRs/kb, while those in the flanking regions ranged from 0.24 to 0.81 SSRs/kb; and those in the combined dataset ranged from 0.2 to 0.81 SSRs/kb. The majority of the detected SSRs in the flanking regions were polymorphic and present at the same loci across two or more samples but differing in the number of repeats. The SSRs detected here may serve as a basis for further population genetic, phylogenetic or evolutionary genetic studies, as well as for further studies focusing on SSRs in the genomes and their roles in adaptation, evolution and diseases

Phylogenomic evolutionary insights in the fern family Gleicheniaceae

The pantropical fern family Gleicheniaceae comprises approximately 157 species. Seven genera are currently recognized in the family, although their monophyly is still uncertain due to low sampling in phylogenetic studies. We examined the monophyly of the genera through extended sampling, using the first phylogenomic inference of the family including data from both nuclear and plastid genomes. Seventy-six samples were sequenced (70 Gleicheniaceae species and six outgroups) using high throughput sequencing, including all seven currently recognized genera. Plastid and nuclear data were recovered and assembled; the nuclear data was phased to reduce paralogy as well as hybrid noise in the final recovered topology. Maximum likelihood trees were built for each locus, and a concatenated dataset was built for both datasets. A species tree based on a multispecies coalescent model was generated, and divergence time analyses performed. We here present the first genomic phylogenetic inferences concerning Gleicheniaceae, confirming the monophyly of most genera except Sticherus, which we recovered as paraphyletic. Although most of the extant genera of Gleicheniaceae originated during the Mesozoic, several genera show Neogene and even Quaternary diversifications, and our results suggest that reticulation and polyploidy may have played significant roles during this diversification. However, some genera, such as Rouxopteris and Stromatopteris, appear to represent evolutionary relicts

A Global Phylogenomic Study of the Thelypteridaceae

The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, have been gained from recent phylogenetic studies; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. We sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. These were analyzed using both maximum likelihood analysis of a concatenated matrix and multi-species coalescent methods. Our phylogenomic results, informed by recently published morphological evidence, provide the foundation for a generic classification which recircumscribed 14 genera and recognized seven new genera. The 37 monophyletic genera sampled demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile and are thus inadequate for defining genera