Evolutionary dynamics of the chloroplast genome sequences of six Colobanthus species.

The complete plastome sequences of six species were sequenced to better understand the evolutionary relationships and mutation patterns in the chloroplast genome of the genus Colobanthus. The length of the chloroplast genome sequences of C. acicularis, C. affinis, C. lycopodioides, C. nivicola, C. pulvinatus and C. subulatus ranged from 151,050 to 151,462 bp. The quadripartite circular structure of these genome sequences has the same overall organization and gene content with 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames. A total of 153 repeat sequences were revealed. Forward repeats were dominant, whereas complementary repeats were found only in C. pulvinatus. The mononucleotide SSRs composed of A/T units were most common, and hexanucleotide SSRs were detected least often. Eleven highly variable regions which could be utilized as potential markers for phylogeny reconstruction, species identification or phylogeography were identified within Colobanthus chloroplast genomes. Seventy-three protein-coding genes were used in phylogenetic analyses. Reconstructed phylogeny was consistent with the systematic position of the studied species, and the representatives of the same genus were grouped in one clade. All studied Colobanthus species formed a single group and C. lycopodioides was least similar to the remaining species.

Retrotransposon-based genetic variation of Poa annua populations from contrasting climate conditions.

BACKGROUND: Poa annua L. is an example of a plant characterized by abundant, worldwide distribution from polar to equatorial regions. Due to its high plasticity and extraordinary expansiveness, P. annua is considered an invasive species capable of occupying and surviving in a wide range of habitats including pioneer zones, areas intensively transformed by human activities, remote subarctic meadows and even the Antarctic Peninsula region. METHODS: In the present study, we evaluated the utility of inter-primer binding site (iPBS) markers for assessing the genetic variation of P. annua populations representing contrasting environments from the worldwide range of this species. The electrophoretic patterns of polymerase chain reaction products obtained for each individual were used to estimate the genetic diversity and differentiation between populations. RESULTS: iPBS genotyping revealed a pattern of genetic variation differentiating the six studied P. annua populations characterized by their different climatic conditions. According to the analysis of molecular variance, the greatest genetic variation was recorded among populations, whereas 41.75% was observed between individuals within populations. The results of principal coordinates analysis (PCoA) and model-based clustering analysis showed a clear subdivision of analyzed populations. According to PCoA, populations from Siberia and the Kola Peninsula were the most different from each other and showed the lowest genetic variability. The application of STRUCTURE software confirmed the unique character of the population from the Kola Peninsula. DISCUSSION: The lowest variability of the Siberia population suggested that it was subjected to genetic drift. However, although demographic expansion was indicated by negative values of Fu's FS statistic and analysis of mismatch distribution, it was not followed by significant traces of a bottleneck or a founder effect. For the Antarctic population, the observed level of genetic variation was surprisingly high, despite the observed significant traces of bottleneck/founder effect following demographic expansion, and was similar to that observed in populations from Poland and the Balkans. For the Antarctic population, the multiple introduction events from different sources are considered to be responsible for such an observation. Moreover, the results of STRUCTURE and PCoA showed that the P. annua from Antarctica has the highest genetic similarity to populations from Europe. CONCLUSIONS: The observed polymorphism should be considered as a consequence of the joint influence of external abiotic stress and the selection process. Environmental changes, due to their ability to induce transposon activation, lead to the acceleration of evolutionary processes through the production of genetic variability.

The complete chloroplast genome of Colobanthus apetalus (Labill.) Druce: genome organization and comparison with related species.

Colobanthus apetalus is a member of the genus Colobanthus, one of the 86 genera of the large family Caryophyllaceae which groups annual and perennial herbs (rarely shrubs) that are widely distributed around the globe, mainly in the Holarctic. The genus Colobanthus consists of 25 species, including Colobanthus quitensis, an extremophile plant native to the maritime Antarctic. Complete chloroplast (cp) genomes are useful for phylogenetic studies and species identification. In this study, next-generation sequencing (NGS) was used to identify the cp genome of C. apetalus. The complete cp genome of C. apetalus has the length of 151,228 bp, 36.65% GC content, and a quadripartite structure with a large single copy (LSC) of 83,380 bp and a small single copy (SSC) of 17,206 bp separated by inverted repeats (IRs) of 25,321 bp. The cp genome contains 131 genes, including 112 unique genes and 19 genes which are duplicated in the IRs. The group of 112 unique genes features 73 protein-coding genes, 30 tRNA genes, four rRNA genes and five conserved chloroplast open reading frames (ORFs). A total of 12 forward repeats, 10 palindromic repeats, five reverse repeats and three complementary repeats were detected. In addition, a simple sequence repeat (SSR) analysis revealed 41 (mono-, di-, tri-, tetra-, penta- and hexanucleotide) SSRs, most of which were AT-rich. A detailed comparison of C. apetalus and C. quitensis cp genomes revealed identical gene content and order. A phylogenetic tree was built based on the sequences of 76 protein-coding genes that are shared by the eleven sequenced representatives of Caryophyllaceae and C. apetalus, and it revealed that C. apetalus and C. quitensis form a clade that is closely related to Silene species and Agrostemma githago. Moreover, the genus Silene appeared as a polymorphic taxon. The results of this study expand our knowledge about the evolution and molecular biology of Caryophyllaceae.

AFLP-profiling of long-term stored and regenerated rye Genebank samples.

The aim of these studies was to analyse the genetic changes induced by natural aging during long-term seed storage of rye. For this purpose, the AFLP (Amplified Fragment Length Polymorphism) technique was applied. In the experiment, DNA variation was demonstrated in seven-day-old seedlings of four seed samples of cv. Dankowskie Zlote, showing different levels of viability following long-term storage. Among the 362 AFLP fragments analysed, 73 had significantly different frequencies in at least one of the series. Principle Coordinate Analysis (PCA) based on molecular data revealed differences between the progenies of naturally aged seed samples with variable initial viability. It was clearly shown that materials with low viability differed in structure from highly viable ones, and that the population changes exhibited in the first case are preserved through regenerations. Although changes that were observed for initially viable samples were not so significant, they still occurred - probably as a result of genetic shift

Studies on changes in specific rye genome regions due to seed aging and regeneration.

The aim of this study was to identify the genetic changes in rye seeds induced by natural aging during long-term storage and successive regeneration cycles under gene bank conditions. Genomic DNA from four rye samples (cv. Dankowskie Zlote), varying in their initial viability and having gone through one or three reproduction cycles, were analysed using specific PCR targeting of a secalin locus, and various repetitive fragments defined by the R173 sequence. A statistical analysis of the band frequencies for both secalin and R173.3 primer pairs revealed no changes in their frequencies. Similar data on R173.1 demonstrated significant changes between samples of different initial viability showing a lack of a band of the expected length (987 bp) in progeny originating from low viability seeds lots. These changes were inherited even after three regeneration cycles. Our results may indicate that long-term storage that leads to loss of viability also generates heritable changes in the preserved germplasm. However, it remains to be discovered where these changes occur and whether they are connected with coding or with non-coding DNA regions.