Nuclear ribosomal spacer regions in plant phylogenetics : problems and prospects

Peer reviewe

Plastid trnF pseudogenes are present in Jaltomata, the sister genus of Solanum (Solanaceae) : molecular evolution of tandemly repeated structural mutations

Extensive gene duplication arranged in a tandem array is rare in the plastome of embryophytes. Interestingly, we found pseudogene copies of the trnF gene in the genus Jaltomata, the sister genus of Solanum where such gene duplication has been previously reported. In each Jaltomata sequence available we found two pseudogene copies in close 5’-proximity to the original functional gene. The size of each pseudogene copy ranged between 17 and 48 bp and the anticodon domain was identified as the most conserved element. A common ATT(G)n motif is particularly interesting and its modifications were found to border the 3’ of the duplicated regions. Other motifs were partial residues, or entire parts of the T- and D-domains, and both domains proved to be variable in length among the pseudogenes identified. The residues of the 3’ and 5’ acceptor stem were not found among the copies. We further compared the newly discovered copies of Jaltomata with those ones previously described from Solanum and inferred phylogenetic relationships of the copies aligned. The evolution of Solanum copies, in contrast to Jaltomata, is hard to explain as resulting only in parsimonious changes since reticulate evolutionary patterns were detected among the copies. The dynamic evolutionary patterns of Solanum might be explained by possible inter- or intrachromosomal recombination.Peer reviewe

Complete chloroplast genome sequence of Coyote tobacco (Nicotiana attenuata, Solanaceae)

In this study, we announce the complete chloroplast genome sequence of Nicotiana attenuata. The genome sequence of 155,941 bp consists of two inverted repeat (IRa and IRb) regions of 25,438 bp each, a large single-copy (LSC) region of 86,513 bp and a small single-copy (SSC) region of 18,524 bp. The overall GC content is 37.9% and the GC contents of LSC, IRs, and SSC are 36%, 43.2%, and 32.1%, respectively. The plastome with 129 annotated unique genes includes 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Using the whole chloroplast genome sequences alignment of 16 Solanaceae species a phylogenetic hypothesis is presented validating the position of N. attenuata within Nicotianeae.Peer reviewe

Imre Festetics and the Sheep Breeders’ Society of Moravia: Mendel’s Forgotten “Research Network”

Contemporary science thrives on collaborative networks, but these can also be found elsewhere in the history of science in unexpected places. When Mendel turned his attention to inheritance in peas he was not isolated monk, but rather the latest in a line of Moravian researchers and agriculturalists who had been thinking about inheritance for half a century. Many of the principles of inheritance had already been sketched out by Imre Festetics, a Hungarian sheep breeder active in Brno. Festetics, however, was ultimately hindered by the complex nature of his study traits, aspects of wool quality that we now know to be polygenic. Whether or not Mendel was aware of Festetics’ ideas, both men were products of the same vibrant milieu in 19th century Moravia that combined theory and agricultural practice to eventually uncover the rules of inheritance.Peer reviewe

The plastid genome of Vanillon (Vanilla pompona, Orchidaceae)

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The plastid genome of the invasive plant common ragweed (Ambrosia artemisiifolia, Asteraceae)

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IRscope: An online program to visualize the junction sites of chloroplast genomes

Motivation: Genome plotting is performed using a wide range of visualizations tools each with emphasis on a different informative dimension of the genome. These tools can provide a deeper insight into the genomic structure of the organism. Results: Here, we announce a new visualization tool that is specifically designed for chloroplast genomes. It allows the users to depict the genetic architecture of up to ten chloroplast genomes in the vicinity of the sites connecting the inverted repeats to the short and long single copy regions. The software and its dependent libraries are fully coded in R and the reflected plot is scaled up to realistic size of nucleotide base pairs in the vicinity of the junction sites. We introduce a website for easier use of the program and R source code of the software to be used in case of preferences to be changed and integrated into personal pipelines. The input of the program is an annotation GenBank (.gb) file, the accession or GI number of the sequence or a DOGMA output file. The software was tested using over a 100 embryophyte chloroplast genomes and in all cases a reliable output was obtained.Peer reviewe

Reassessing the role of morphology in bryophyte phylogenetics : combined data improves phylogenetic inference despite character conflict

Morphological data has gained renewed attention and has been shown to be crucial in clarifying the phylogenetic relationship in a wide range of taxa. In the last decades, phylogenetic analyses of sequence-level data have radically modified the systematic schemes within bryophytes (early non-vascular land plants) and have revealed a widespread pattern of conflict with morphology-based classifications. Yet, a comprehensive evaluation of character conflict has not yet been performed in the context of combined matrices. In this study, we evaluate the impact of morphology on bryophyte phylogeny following a total-evidence approach across 10 published matrices. The analysed matrices span a wide range of bryophytes, taxonomic levels, gene sampling and number of morphological characters and taxa. Data conflict was addressed by measuring: (i) the topological congruence between individual partitions, (ii) changes in support values of the combined data relative to the molecular partition and (iii) clade stability. The association between these measures and the number of morphological characters per taxon (Nc/T ratio) and the proportion of non-fixed characters (i.e., inapplicable, polymorphic and missing data) was explored. In the individual partition analyses, the Nc/T ratio correlated positively with the topological congruence in six to seven datasets depending on the weighting scheme. The proportion of non-fixed cells had a minor influence on congruence between data partitions. The number of characters and proportion of non-fixed data varied significantly between morphological datasets that improved congruence between data types. This variation suggests that morphological datasets affect the results of combined analyses in different ways, depending on the taxa studied. Combined analyses revealed that, despite the low congruence values between partitions, integrating data types improves support values and stability. However, while non-fixed data had no negative effect on support values, stability was reduced as the proportion of non-fixed cells increased. Nc/T ratio was negatively associated with support values and it showed ambiguous responses in stability evaluations. Overall, the results indicate that adding morphology may contribute to the inference of phylogenetic relationships of bryophytes despite character conflict. Our findings suggest that merely comparing (a) morphology-based classifications with molecular phylogenies or (b) the outcome from individual data partitions can misestimate data conflict. These findings imply that analyses of combined data may provide conservative assessments of data conflict and, eventually, lead to an improved sampling of morphological characters in large-scale analyses of bryophytes.Peer reviewe

On the origin of Solanum nigrum: can networks help?

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