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

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

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

The plastid genome of Vanillon (Vanilla pompona, Orchidaceae)

Peer reviewe

Development of chloroplast microsatellite markers for giant ragweed (Ambrosia trifida)

Premise Plant invasions are increasing globally, and extensive study of the genetic background of the source and invading populations is needed to understand such biological processes. For this reason, chloroplast microsatellite markers were identified to explore the genetic diversity of the noxious weed Ambrosia trifida (Asteraceae). Methods and Results The complete chloroplast genome of A. trifida was mined for microsatellite loci, and 15 novel chloroplast primers were identified to assess the genetic diversity of 49 Ambrosia samples. The number of alleles amplified ranged from two to six, with an average of 3.2 alleles per locus. Shannon's information index varied from 0.305 and 1.467, expected heterozygosity ranged from 0.178 to 0.645, and the polymorphism information content value ranged from 0.211 to 0.675 (average 0.428). The cross-species transferability of the 15 microsatellite loci was also evaluated in four related Ambrosia species (A. artemisiifolia, A. maritima, A. psilostachya, and A. tenuifolia). Conclusions The novel chloroplast microsatellite markers developed in the current study demonstrate substantial cross-species transferability and will be helpful in future genetic diversity studies of A. trifida and related species.Peer reviewe

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

Peer reviewe

Exploring phylogeny of the microsoroid ferns (Polypodiaceae) based on six plastid DNA markers

The microsoroid ferns are one of the largest subfamilies of the Polypodiaceae with over 180 species mainly found in the humid forests of tropical Australasia. The phylogenetic relationships are still unclear, especially the delimitation of the genus Microsorum which has been recognized to be non-monophyletic. We analysed the microsoroid ferns using six chloroplast DNA regions (rbcL, rps4+rps4-trnS, trnL+trnL-trnF, atpA, atpB and matK) in order to present a robust hypothesis of their phylogeny. Our results suggest that they comprise up to 17 genera; of them, 12 agree with a previously accepted generic classification. Five tribes are proposed based on the phylogenetic relationships. Most of the species traditionally included in the genus Microsorum are found in six genera belonging to two tribes. In addition to the commonly used DNA markers, the additional atpA and matK are helpful to provide information about the phylogenetic relationships of the microsoroid ferns.Peer reviewe

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