The analysis of telomere length is an important component of many studies aiming to characterize the role of telomere maintenance mechanisms in cellular lifespan, disease, or in general chromosome protection and DNA replication pathways. Several powerful methods to accurately measure the telomere length from Southern blots have been developed, but their utility for large-scale genomic studies has not been previously evaluated. Here, we performed a comparative analysis of two recently developed programs, TeloTool and WALTER, for the extraction of mean telomere length values from Southern blots. Using both software packages, we measured the telomere length in two extensive experimental datasets for the model plant Arabidopsis thaliana, consisting of 537 natural accessions and 65 T-DNA (transfer DNA for insertion mutagenesis) mutant lines in the reference Columbia (Col-0) genotype background. We report that TeloTool substantially overestimates the telomere length in comparison to WALTER, especially for values over 4500 bp. Importantly, the TeloTool- and WALTER-calculated telomere length values correlate the most in the 2100–3500 bp range, suggesting that telomeres in this size interval can be estimated by both programs equally well. We further show that genome-wide association studies using datasets from both telomere length analysis tools can detect the most significant SNP candidates equally well. However, GWAS analysis with the WALTER dataset consistently detects fewer significant SNPs than analysis with the TeloTool dataset, regardless of the GWAS method used. These results imply that the telomere length data generated by WALTER may represent a more stringent approach to GWAS and SNP selection for the downstream molecular screening of candidate genes. Overall, our work reveals the unanticipated impact of the telomere length analysis method on the outcomes of large-scale genomic screens.

Analysis of telomere length is an important component of many studies aiming to characterize the role of telomere maintenance mechanisms in cellular lifespan, disease, or in general chromosome protection and DNA replication pathways. Several powerful methods to accurately measure telomere length from Southern blots have been developed, but their utility for large-scale genomic studies has not been previously evaluated. Here we performed comparative analysis of two recently developed programs, TeloTool and WALTER, for extracting mean telomere length values from Southern blots. Using both software packages, we measured telomere length in two extensive experimental datasets for the model plant Arabidopsis thaliana, consisting of 537 natural accessions and 65 T-DNA mutant lines in the Col-0 reference background. We report that TeloTool substantially overestimates telomere length in comparison to WALTER, especially for values over 4,500 bp. Importantly, TeloTool and WALTER-calculated telomere length values correlate the most in the 2,100-3,500 bp range, suggesting that telomeres in this size interval can be estimated by both programs equally well. We further show that genome-wide association studies using datasets from both telomere length analysis tools can detect the most significant SNP candidates equally well. However, GWAS analysis with the WALTER dataset consistently detects fewer significant SNPs than analysis with the TeloTool dataset, regardless of the GWAS method used. These results imply that telomere length data generated by WALTER may represent a more stringent approach to GWAS and SNP selection for downstream molecular screening of candidate genes. Overall, our work revealed the unanticipated impact of telomere length analysis method on the outcomes of large-scale genomic screens.

Bryophytes have recently emerged as potentially promising producers of bioactive metabolites with multiple applications in biomedicine and biotechnology. Our previous studies have established that the model moss Ceratodon purpureus produces novel compounds with potent antimicrobial activities against Gram-positive bacteria. Here, we conducted a comparative analysis of metabolites produced by four different natural isolates of C. purpureus and observed considerable variation in the composition of antibacterial compounds. Next, we partially purified bioactive compounds from extracellular exudates produced by the two model C. purpureus lines, GG1 and R40. Untargeted metabolomic analysis revealed that GG1 isolate secreted a much more diverse set of metabolome components, including various amines, fatty acids, lactones, quinones and terpenoids, in comparison to the R40 isolate. However, the relative percentages of nitrogen-, phosphorus- and sulfur-containing compounds were notably similar in both metabolomes. Importantly, our analysis predicted the presence of several classes of potentially bioactive metabolites in metabolomes of both moss isolates. Taken together, our experiments provided an important evidence that extracellular metabolomes of the model moss Ceratodon purpureus are characterized by a remarkable intraspecific variability in the secretion, composition and abundance of different extracellular compounds.

The ends of linear chromosomes of most eukaryotes consist of protein-bound DNA arrays called telomeres, which play essential roles in protecting genome integrity. Despite general evolutionary conservation in function, telomeric DNA is known to drastically vary in length and sequence between different eukaryotic lineages. Bryophytes are a group of early diverging land plants that include mosses, liverworts, and hornworts. This group of ancient land plants recently emerged as a new model for important discoveries in genomics and evolutionary biology, as well as for understanding plant adaptations to a terrestrial lifestyle. We measured telomere length in different ecotypes of model Bryophyte species, including Physcomitrium patens, Marchantia polymorpha, Ceratodon purpureus, and in Sphagnum isolates. Our data indicate that all analyzed moss and liverwort genotypes have relatively short telomeres. Furthermore, all analyzed ecotypes and isolates of model mosses and liverworts display evidence of substantial natural variation in telomere length. Interestingly, telomere length also differs between male and female strains of the dioecious liverwort M. polymorpha and dioecious moss C. purpureus. Given that Bryophytes are extraordinarily well-adapted to different ecological niches from polar to tropical environments, our data will contribute to understanding the impact of natural telomere length variation on evolutionary adaptations in this ancient land plant lineage.