Genetic variation of introduced red oak (Quercus rubra) stands in Germany compared to North American populations

Although Northern red oak (Quercus rubra L.) is the most important introduced deciduous tree species in Germany, only little is known about its genetic variation. For the frst time, we describe patterns of neutral and potentially adaptive nuclear genetic variation in Northern red oak stands across Germany. For this purpose, 792 trees were genotyped including 611 trees from 12 stands in Germany of unknown origin and 181 trees from four populations within the natural distribution area in North America. Our marker set included 12 potentially adaptive (expressed sequence tag-derived simple sequence repeat=EST SSR) and 8 putatively selectively neutral nuclear microsatellite (nSSR) markers. Our results showed that German stands retain comparatively high levels of genetic variation at both EST-SSRs and nSSRs, but are more similar to each other than to North American populations. These fndings are in agreement with earlier chloroplast DNA analyses which suggested that German populations originated from a limited geographic area in North America. The comparison between potentially adaptive and neutral microsatellite markers did not reveal diferences in the analyzed diversity and diferentiation measures for most markers. However, locus FIR013 was identifed as a potential outlier locus. Due to the absence of signatures of selection in German stands, we suggest that introduced populations were established with material from provenances that were adapted to environmental conditions similar to those in Germany. However, we analyzed only a limited number of loci which are unlikely to be representative of adaptive genetic diferences among German stands. Our results suggest that the apparent introduction from a limited geographic range in North America may go along with a reduced adaptive potential

Development of novel Quercus rubra chloroplast genome CAPS markers for haplotype identification : научное издание

Статья из журнала. Научное издание.Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markers, we sequenced 87-97 % of the entire chloroplast genome (except the second inverted repeat) of 8 trees representing different regions of the Quercus rubra L natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of Quercus rubra L. as a reference. In total, 118 single nucleotide polymorphisms (SNPs) and 107 insertions or deletions (indels) were detected, and 15 cleaved amplified polymorphic sequence (CAPS) markers were developed for Q. rubra. Using these new markers together with five chloroplast microsatellite or simple sequence repeat (cpSSR) markers, we identified 10 haplotypes in our diversity panel of 19 Q. rubra populations. Specifically, two haplotypes based only on the cpSSR markers could now be separated in five haplotypes. These markers are useful to assess haplotype diversity with high resolution and are also transferable to a closely related species, Quercus ellipsoidalis E. J. Hill. Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markersOur main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA marker

Development of novel quercus rubra chloroplast genome caps markers for haplotype identification

Our main objective was to generate cost-effective chloroplast (cp) DNA markers that are easy to apply and to score. In combination with already published cpSSR markers they should increase haplotype resolution in populations. To discover new cpDNA markers, we sequenced 87-97 % of the entire chloroplast genome (except the second inverted repeat) of 8 trees representing different regions of the Quercus rubra L. natural range with 4,030X-6,297X coverage and assembled the genome sequences using the publicly available chloroplast genome of Quercus rubra L. as a reference. In total, 118 single nucleotide polymorphisms (SNPs) and 107 insertions or deletions (indels) were detected, and 15 cleaved amplified polymorphic sequence (CAPS) markers were developed for Q. rubra. Using these new markers together with five chloroplast microsatellite or simple sequence repeat (cpSSR) markers, we identified 10 haplotypes in our diversity panel of 19 Q. rubra populations. Specifically, two haplotypes based only on the cpSSR markers could now be separated in five haplotypes. These markers are useful to assess haplotype diversity with high resolution and are also transferable to a closely related species, Quercus ellipsoidalis E. J. Hill

Genetic variation of introduced red oak (Quercus rubra) stands in Germany compared to North American populations

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Genetic variation of introduced red oak (Quercus rubra) stands in Germany compared to North American populations : научное издание

Статья из журнала. Научное издание.Although Northern red oak (Quercus rubra L.) is the most important introduced deciduous tree species in Germany, only little is known about its genetic variation. For the first time, we describe patterns of neutral and potentially adaptive nuclear genetic variation in Northern red oak stands across Germany. For this purpose, 792 trees were genotyped including 611 trees from 12 stands in Germany of unknown origin and 181 trees from four populations within the natural distribution area in North America. Our marker set included 12 potentially adaptive (expressed sequence tag-derived simple sequence repeat = EST SSR) and 8 putatively selectively neutral nuclear microsatellite (nSSR) markers. Our results showed that German stands retain comparatively high levels of genetic variation at both EST-SSRs and nSSRs, but are more similar to each other than to North American populations. These findings are in agreement with earlier chloroplast DNA analyses which suggested that German populations originated from a limited geographic area in North America. The comparison between potentially adaptive and neutral microsatellite markers did not reveal differences in the analyzed diversity and differentiation measures for most markers. However, locus FIR013 was identified as a potential outlier locus. Due to the absence of signatures of selection in German stands, we suggest that introduced populations were established with material from provenances that were adapted to environmental conditions similar to those in Germany. However, we analyzed only a limited number of loci which are unlikely to be representative of adaptive genetic differences among German stands. Our results suggest that the apparent introduction from a limited geographic range in North America may go along with a reduced adaptive potential

Genetic diversity and differentiation of introduced red oak (Quercus rubra) in Germany in comparison with reference native North American populations

Northern red oak (Quercus rubra) was introduced to Europe in the late seventeenth century and has since become the most important deciduous non-native tree species in Germany. Despite its importance, little is known about the origin and patterns of genetic variation in German red oak stands. To be able to make recommendations regarding the adaptive potential of red oak stands, which might be related to their origin and the selection of provenances, with respect to climate change, a better understanding of the genetic diversity and structure of German red oak stands is needed. Individuals from 62 populations in Germany and North America were genotyped at five chloroplast microsatellite loci to characterize chloroplast haplotype diversity and geographic structure. Compared to reference populations from the natural distribution range, German red oak stands demonstrated a relatively low genetic differentiation among populations and represented only a fraction of the haplotype diversity found in North America. For several stands located in southern Germany, considerably higher haplotype diversity than in other German stands was found. While most German stands showed signatures of founder effects, the diversity of stands in southern Germany might have been increased due to admixture and multiple introductions of different North American provenances. Overall, we conclude that German stands originated from a limited geographic area, possibly located in the northern part of the native distribution range

Genetic diversity and differentiation of introduced red oak (Quercus rubra) in Germany in comparison with reference native North American populations.

Northern red oak (Quercus rubra) was introduced to Europe in the late 17th century and is today the most important deciduous foreign tree species in Germany. Despite its importance little is known about the origin of local red oak stands and patterns of genetic variation in German red oak stands. To be able to make recommendations regarding the adaptive potential of red oak and the selection of provenances with respect to climate change, a better understanding of the genetic diversity and structure of German red oak stands is needed. Therefore, individuals from 62 stands in Germany and North America were genotyped at five chloroplast microsatellite loci to characterize chloroplast haplotype diversity and geographical structure. Compared to reference stands from the natural distribution range, German stands demonstrated a relatively low genetic differentiation among populations and represented only a fraction of the haplotype diversity found in North America. For several stands located in the south of Germany a considerably higher haplotype diversity was found. Therefore, we conclude that German stands originated from a limited geographic range within the natural distribution, which was possibly located in the northern part of the native distribution range. While most German stands showed signatures of founder effects due to originating from a small number of individuals within a limited range, particularly stands in the south of Germany could have benefited from admixture and multiple introductions of different North American provenances

Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota

Mucispirillum schaedleri is an abundant inhabitant of the intestinal mucus layer of rodents and other animals and has been suggested to be a pathobiont, a commensal that plays a role in disease. In order to gain insights into its lifestyle, we analyzed the genome and transcriptome of M. schaedleri ASF 457 and performed physiological experiments to test traits predicted by its genome. Although described as a mucus inhabitant, M. schaedleri has limited capacity for degrading host-derived mucosal glycans and other complex polysaccharides. Additionally, M. schaedleri reduces nitrate and expresses systems for scavenging oxygen and reactive oxygen species in vivo, which may account for its localization close to the mucosal tissue and expansion during inflammation. Also of note, M. schaedleri harbors a type VI secretion system and putative effector proteins and can modify gene expression in mucosal tissue, suggesting intimate interactions with its host and a possible role in inflammation. The M. schaedleri genome has been shaped by extensive horizontal gene transfer, primarily from intestinal Epsilon- and Deltaproteobacteria, indicating that horizontal gene transfer has played a key role in defining its niche in the gut ecosystem. IMPORTANCE Shifts in gut microbiota composition have been associated with intestinal inflammation, but it remains unclear whether inflammation-associated bacteria are commensal or detrimental to their host. Here, we studied the lifestyle of the gut bacterium Mucispirillum schaedleri, which is associated with inflammation in widely used mouse models. We found that M. schaedleri has specialized systems to handle oxidative stress during inflammation. Additionally, it expresses secretion systems and effector proteins and can modify the mucosal gene expression of its host. This suggests that M. schaedleri undergoes intimate interactions with its host and may play a role in inflammation. The insights presented here aid our understanding of how commensal gut bacteria may be involved in altering susceptibility to disease.Copyright © 2017 Loy et al