Die mitochondriale DNA basaler Tracheophyten : Molekulare Evolution komplexer Genomstrukturen

Aufgrund ihrer hohen Komplexität ist die Anzahl vollständig sequenzierter pflanzlicher mitochondrialer Genome (Chondrome) noch gering. Sie beschränkt sich auf die vollständig ermittelten mtDNA-Sequenzen einiger Angiospermen und einzelner Arten der Leber-, Laub- und Hornmoose und lediglich einer Art der Gymnospermen. Aus den basalen Gefäßpflanzengruppen (Tracheophyten), also den Bärlappgewächsen (Lycophyten) und den Farnen (Monilophyten), lagen bislang sogar noch gar keine vollständigen mtDNA-Sequenzen vor. Die Evolution der vielen molekularen Besonderheiten in den Chondromen der Landpflanzen war somit nur lückenhaft nachvollziehbar. Im Rahmen dieser Arbeit wurde diese phylogenetische Lücke durch die vollständige mtDNA-Sequenzierung des Lycophyten Isoetes engelmannii begleitet durch eine umfassende Analyse seines mitochondrialen Transkriptoms und eine weitgehende Untersuchung der mtDNA des Monilophyten Gleichenia dicarpa gefüllt. Darüber hinaus wurde im Rahmen einer begleitenden Diplomarbeit das komplette mitochondriale Genom und Transkriptom des Lycophyten Selaginella moellendorffii ermittelt. Das Chondrom von I. engelmannii zeigt einen individuellen Trend zu einer kompakten genomischen Struktur mit extrem kleinen Introns und intergenischen Regionen, wohingegen die mtDNA des Schwestertaxons S. moellendorffii völlig gegensätzlich mit großen intergenischen Bereichen und Introns ausgestattet ist. In beiden Lycophyten allerdings wurden hoch rekombinante mitochondriale Genome gefunden. Diese führen zur Entstehung neuer mitochondrialer Eigenheiten, beispielsweise neuer trans-spleißender Introns - auch Gruppe I Introns in beiden Lycophyten - und dem Einbau "promisker" DNA aus dem Zellkern oder den Chloroplasten. Anhand der vollständigen mitochondrialen Transkriptomanalysen konnten in I. engelmannii über 1700 und in S. moellendorffii sogar über 2000 RNA Editing-Positionen identifiziert werden. Während in S. moellendorffii ausschließlich Cytidin-zu-Uridin-Konversionen zu finden sind, handelt es sich bei 20 % der Editing-Ereignisse in I. engelmannii um Austausche in Gegenrichtung von Uridin zu Cytidin. Als weitere Besonderheit wurde massives RNA Editing in I. engelmannii nicht nur in mRNAs sondern auch in tRNAs gefunden, während in der mtDNA von S. moellendorffii als völligem Novum für pflanzliche Chondrome alle Gene für tRNAs verloren gegangen sind. Die chondromale Komplexität ist offenbar in den Monilophyten noch weiter gesteigert. Große Regionen der mtDNA von G. dicarpa bestehen aus integrierten mobilen Elementen, u.a. acht "promisker" Retrotransposons. Diese wurden offenbar als kollaterales Ereignis massiver Transpositionen im Kerngenom auch in die mtDNA eingebaut

Diversidad de especies de Xanthoparmelia (Parmeliaceae) en la vegetación de matorrales xerofíticos mexicanos, evidenciada por datos moleculares, morfológicos y químicos

The genus Xanthoparmelia is the largest genus of lichen- forming fungi with about 800 species worldwide. Xanthoparmelia is also common in the deserts of central Mexico, but only a few molecular studies exist on its species’ diversity in this region. In this study, we sampled 38 Xanthoparmelia species from around the world including species from the xerophytic scrubs of central Mexico to assess the diversity using an integrative approach. Molecular phylogenetic analyses were performed using a combination of the ITS, mtSSU and nuLSU genetic markers. We evaluated our phylogenetic results in a context of traditional morphological and chemical characters. The combined evidence of molecular, morphological, and chemical data identified a total of 18 Xanthoparmelia species-level lineages occurring in central Mexico. However, numerous traditionally circumscribed species did not form monophyletic groups in the molecular phylogenetic reconstructions. This conflict indicates that taxonomy and species delimitation in the genus Xanthoparmelia requires revision and emphasizes the importance of molecular evidence for more robust species delimitations in this genus.Xanthoparmelia es el género más grande de hongos liquenizados, con alrededor de 800 especies en todo el mundo. Xanthoparmelia es común en los desiertos del centro de México, pero existen pocos estudios moleculares sobre la diversidad de especies en esta región. En este estudio, muestreamos 38 especies de Xanthoparmelia de diferentes partes del mundo, incluidas especies de los matorrales xerófilos del centro de México, para evaluar la diversidad usando una aproximación integrativa. Los análisis filogenéticos moleculares se realizaron combinando los marcadores genéticos ITS, mtSSU y nuLSU. Además, evaluamos nuestros resultados filogenéticos en un contexto de caracteres morfológicos y químicos usados en la taxonomía tradicional. Teniendo en cuenta las evidencias obtenidas a partir de caracteres moleculares, morfológicos y químicos se identificaron un total de 18 linajes de Xanthoparmelia con categoría de especie que aparecen en el centro de México. Sin embargo, muchas especies tradicionalmente circunscritas no formaron grupos monofiléticos. Este conflicto indica que la taxonomía y delimitación de especies en el género Xanthoparmelia requiere revisión y enfatiza la importancia de los datos moleculares para una delimitación más robusta de especies en este género

Surfactant gels with vesicular structure

Surfactants are an important class of chemicals, which are used not only as detergents but also in many other areas, such as cosmetics, pharmacy, and the food industry. In aqueous solution, surfactants form aggregates due to their amphiphilic character. This self-assembly leads to micelles and liquid crystalline phases with a variety of structures. Furthermore, non-equilibrium structures, such as vesicles, can be formed, for example, due to shear forces applied when mixing formulations. The structure of a surfactant solution has a large influence on its rheological properties. In particular, vesicular structures often show gel-like properties. We have investigated mixtures of surfactant, fatty alcohol, and water, which show gel-like properties even at high dilution. A system containing sodium dodecyl sulfate (SDS) and cetyl alcohol (CA) [1] with a combined mass fraction of 3 % at varying SDS/CA ratio was studied in detail in order to explore the origin of the gel-like behavior observed at low SDS/CA ratios. The chain melting temperatures of the surfactant/cosurfactant aggregates were determined by proton NMR and differential scanning calorimetry, while the phase structure was investigated by neutron and x-ray scattering as well as by cryo-transmission electron microscopy. Using pulsed field gradient NMR the diffusivity of water in the different samples could be obtained. Gel-like samples were found to show a large fraction of water that has an apparent diffusion coefficient up to three orders of magnitude lower than the one of free water. Combining the results obtained by the different methods a structural model which can explain the gel-like properties could be developed [2]. The gel character is due to large jammed uni- and multilamellar vesicles. As the SDS/CA ratio increases the stacked bilayer membranes cannot be swollen by water any more and a dispersion with a low volume fraction of small compact aggregates results. Please click Additional Files below to see the full abstract

Complete plastid genomes from \u3ci\u3eOphioglossum californicum, Psilotum nudum,\u3c/i\u3e and \u3ci\u3eEquisetum hyemale\u3c/i\u3e reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

Background: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. Results: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. Conclusions: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

Complete plastid genomes from Ophioglossum californicum, Psilotum nudum, and Equisetum hyemale reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

BACKGROUND: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. RESULTS: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. CONCLUSIONS: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

Complete plastid genomes from \u3ci\u3eOphioglossum californicum, Psilotum nudum,\u3c/i\u3e and \u3ci\u3eEquisetum hyemale\u3c/i\u3e reveal an ancestral land plant genome structure and resolve the position of Equisetales among monilophytes

Background: Plastid genome structure and content is remarkably conserved in land plants. This widespread conservation has facilitated taxon-rich phylogenetic analyses that have resolved organismal relationships among many land plant groups. However, the relationships among major fern lineages, especially the placement of Equisetales, remain enigmatic. Results: In order to understand the evolution of plastid genomes and to establish phylogenetic relationships among ferns, we sequenced the plastid genomes from three early diverging species: Equisetum hyemale (Equisetales), Ophioglossum californicum (Ophioglossales), and Psilotum nudum (Psilotales). A comparison of fern plastid genomes showed that some lineages have retained inverted repeat (IR) boundaries originating from the common ancestor of land plants, while other lineages have experienced multiple IR changes including expansions and inversions. Genome content has remained stable throughout ferns, except for a few lineage-specific losses of genes and introns. Notably, the losses of the rps16 gene and the rps12i346 intron are shared among Psilotales, Ophioglossales, and Equisetales, while the gain of a mitochondrial atp1 intron is shared between Marattiales and Polypodiopsida. These genomic structural changes support the placement of Equisetales as sister to Ophioglossales + Psilotales and Marattiales as sister to Polypodiopsida. This result is augmented by some molecular phylogenetic analyses that recover the same relationships, whereas others suggest a relationship between Equisetales and Polypodiopsida. Conclusions: Although molecular analyses were inconsistent with respect to the position of Marattiales and Equisetales, several genomic structural changes have for the first time provided a clear placement of these lineages within the ferns. These results further demonstrate the power of using rare genomic structural changes in cases where molecular data fail to provide strong phylogenetic resolution

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/1/nph15650_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/2/nph15650.pd

Lycophyte plastid genomics: extreme variation in GC, gene and intron content and multiple inversions between a direct and inverted orientation of the rRNA repeat

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/1/nph15650_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/148375/2/nph15650.pd

Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired short, novel IRs, some of which also exhibit recombinational activity to generate genomic structural diversity. This diversity has been shown to exist between, and occasionally within, cupressophyte species, but it is not known whether multiple genomic forms coexist within individual plants. To examine the recombinational potential of the novel cupressophyte IRs within individuals and between species, we sequenced the plastomes of four closely related species of Juniperus. The four plastomes have identical gene content and genome organization except for a large 36 kb inversion between approximately 250 bp IR containing trnQ-UUG. Southern blotting showed that different isomeric versions of the plastome predominate among individual junipers, whereas polymerase chain reaction and high-throughput read-pair mapping revealed the substoichiometric presence of the alternative isomeric form within each individual plant. Furthermore, our comparative genomic studies demonstrate that the predominant and substoichiometric arrangements of this IR have changed several times in other cupressophytes as well. These results provide compelling evidence for substoichiometric shifting of plastomic forms during cupressophyte evolution and suggest that substoichiometric shifting activity in plastid genomes may be adaptive

Predominant and Substoichiometric Isomers of the Plastid Genome Coexist within Juniperus Plants and Have Shifted Multiple Times during Cupressophyte Evolution

Abstract Most land plant plastomes contain two copies of a large inverted repeat (IR) that promote high-frequency homologous recombination to generate isomeric genomic forms. Among conifer plastomes, this canonical IR is highly reduced in Pinaceae and completely lost from cupressophytes. However, both lineages have acquired short, novel IRs, some of which also exhibit recombinational activity to generate genomic structural diversity. This diversity has been shown to exist between, and occasionally within, cupressophyte species, but it is not known whether multiple genomic forms coexist within individual plants. To examine the recombinational potential of the novel cupressophyte IRs within individuals and between species, we sequenced the plastomes of four closely related species of Juniperus. The four plastomes have identical gene content and genome organization except for a large 36 kb inversion between approximately 250 bp IR containing trnQ-UUG. Southern blotting showed that different isomeric versions of the plastome predominate among individual junipers, whereas polymerase chain reaction and high-throughput read-pair mapping revealed the substoichiometric presence of the alternative isomeric form within each individual plant. Furthermore, our comparative genomic studies demonstrate that the predominant and substoichiometric arrangements of this IR have changed several times in other cupressophytes as well. These results provide compelling evidence for substoichiometric shifting of plastomic forms during cupressophyte evolution and suggest that substoichiometric shifting activity in plastid genomes may be adaptive