Polymorphism at four-fold degenerate site, but not at the intergenic regions, explains nucleotide compositional strand asymmetry in bacteria

We investigated single nucleotide polymorphism in intergenic regions (IRs) and four-fold degenerate sites (FFS) in genomes of three γ-Proteobacteria and two Firmicutes to understand the mechanism of nucleotide compositional asymmetry between the leading and the lagging strands. Pattern of the polymorphism spectra were alike regarding transitions but variable regarding transversions in the IRs of these bacteria. Contrasting trends of complementary polymorphisms such as C->T vs G->A as well as A->G vs T->C in the IRs vindicated similar replication-associated strand asymmetry regarding cytosine and adenine deamination, respectively, across these bacteria. Surprisingly, the polymorphism pattern at FFS was different from that of the IRs and its frequency was always more than the IRs in these bacteria. Further, the polymorphism patterns within a bacterium were inconsistent across the five amino acids, which neither the replication nor the transcription-associated mutations could explain. However, the polymorphism at FFS coincided with amino acid specific codon usage bias in the five bacteria. Further, strand asymmetry in nucleotide composition could be explained by the polymorphism at FFS, not at the IRs. Therefore, polymorphisms at FFS might not be treated as nearly neutral unlike that in IRs in these bacteria.

Ranunculus schmalhausenii (section Batrachium, Ranunculaceae), a neglected water crowfoot endemic to Fennoscandia—a case of rapid hybrid speciation in postglacial environment of North Europe

The taxa of Ranunculus section Batrachium (Ranunculaceae) have been variably and unsatisfactorily treated in North Europe. Since the description of Ranunculus schmalhausenii (Batrachium dichotomum), probably the most common species in the area, its taxonomic status and identity have been unclear and differently implied. In the majority of treatments, individuals of R. schmalhausenii were ascribed to R. peltatus but sometimes also to the other morphologically similar, heterophyllous taxa. Based on detailed morphological study combined with geographical, ecological and biological evaluation the separate species status of this taxon was finally evidenced. The additive ITS polymorphism pattern of R. schmalhausenii confirmed its hybridogenous origin, however identification of the parental species was impeded by the heterogeneous character of the polymorphism detected. Genetic variation expressed by R. schmalhausenii samples may provide evidence of its multiple origin and suggests sexual reproduction of the taxon. Analysis of a sequence variation of two noncoding cpDNA regions, namely psbE-petL and rpl32-trnL, showed that individuals of R. schmalhausenii inherited cpDNA from two lineages of Batrachium, indicating that this taxon was created at least in two separate hybridization events. Ranunculus schmalhausenii may have originated from sexual ancestral species as multiple created hybrids which have been stabilized by polyploidisation. Genetic structure of R. schmalhausenii is somehow similar to also hybridogenous R. penicillatus. In this study, a detailed morphological, geographical, ecological, and biological description of R. schmalhausenii was presented and the differences between this species and similar taxa were outlined. The name was lectotypified and its synonymy was provided. In contrast to many other heterophyllous species of Ranunculus section Batrachium, R. schmalhausenii occurs mainly in young, postglacial landscapes of Fennoscandia, prefering deep and clear waters with current or wave action and a hard bottom, which perfectly corresponds with a relict, postglacial nature of the species. The species probably presents an example of rapid hybrid speciation (less than 10 000 years) in postglacial environment of North Europe and may be considered as endemic to Fennoscandia. Moreover, R. schmalhausenii, as a weak competitor and pollution sensitive taxon, can be regarded as an indicator of clean waters. Phylogenetic relations within section Batrachium indicates convergent evolution of some species and two cases of possible cpDNA capture.

Molecular evidence for the hybrid origin of Potamogeton ×subrufus Hagstr. (Potamogetonaceae)

<em>Potamogeton</em> ×<em>subrufus</em> Hagstr. was described as a hybrid between <em>P. lucens</em> L. and <em>P. nodosus</em> Poir.; however, the taxon had not been widely accepted and regarded as conspecific with <em>P.</em> ×<em>fluitans</em> Roth, the hybrid between <em>P. lucens</em> and P. <em>natans</em> L. The origin of <em>P.</em> ×<em>subrufus</em> had been obscured till 2010, when, based on morpho-anatomical treatment, it was shown that <em>P.</em> ×<em>subrufus</em> displays several characters consistently different from those of <em>P.</em> ×<em>fluitans</em>. Here we report a successful amplification and sequencing of nuclear ribosomal ITS1 region from a 115 year-old herbarium specimen of <em>P.</em> ×<em>subrufus</em>, collected in locus classicus by J. Baagöe and preserved in the Herbarium of the Institute of Botany, Jagiellonian University (KRA). Based on the additive polymorphism pattern expressed in the ITS1 sequences of <em>P.</em> ×<em>subrufus</em>, we demonstrate that one of the parents of this hybrid was <em>P. nodosus</em>, as was claimed by Hagström.

Single Laboratory Validation of a Microsatellite Marker-Based Method in Tomato Variety Identification

The objective of this study was to develop a systematic and flexible method for assembling multiplex simple sequence repeat marker panels for high-throughput genome analysis in the tomato, Solanum lycopersicum, for varietal identification and to demonstrate the technical viability of these genetic markers for use in the enforcement of U.S. Department of Agriculture marketing order-based identity preservation programs. GeneMapper, a semiautomated software tool, was used for designing multiplex panels, allele identification, and polymorphism pattern evaluation of diverse tomato cultivars. Semiautomated genotyping was performed on a set of 12 microsatellite markers providing genome-wide coverage of the tomato chromosomes. Microsatellites were detected with fluorescently labeled primers grouped into five multiplex panels, and each primer pair was assessed in replicated trials for reliability of allele size estimates. Allele sizes for each locus were compared, and a database for 34 tomato varieties was developed. The microsatellite marker set identified distinct allelic peaks and unique genetic fingerprints for each of the studied tomato varieties. A "blind testing" exercise with UglyRipe™ and Vintage Ripe™ tomato varieties, using the above set of markers and database, further established the usefulness of these microsatellite markers for tomato commodity marketing order enforcement.