The Experts below are selected from a list of 1410 Experts worldwide ranked by ideXlab platform
Joachim Messing - One of the best experts on this subject based on the ideXlab platform.
-
plant evolution and environmental adaptation unveiled by long read whole genome sequencing of Spirodela
Proceedings of the National Academy of Sciences of the United States of America, 2019Co-Authors: Dong An, Yongrui Wu, Qiao Wen-xiao, Daiyin Chao, Yubin Li, Yating Zhang, Changsheng Li, Yong Zhou, Joachim MessingAbstract:Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retrotranspositions occur early in monocot evolution, featured with both prokaryote-like gene-rich regions and eukaryotic repeat islands. Protein-coding genes are reduced to 18,708 gene models supported by 492,435 high-quality full-length PacBio complementary DNA (cDNA) sequences. Different from land plants, the primitive architecture of Spirodela’s adventitious roots and lack of lateral roots and root hairs are consistent with dispensable functions of nutrient absorption. Disease-resistant genes encoding antimicrobial peptides and dirigent proteins are expanded by tandem duplications. Remarkably, disease-resistant genes are not only amplified, but also highly expressed, consistent with low levels of 24-nucleotide (nt) small interfering RNA (siRNA) that silence the immune system of land plants, thereby protecting Spirodela against a wide spectrum of pathogens and pests. The long-read sequence information not only sheds light on plant evolution and adaptation to the environment, but also facilitates applications in bioenergy and phytoremediation.
-
genome wide analysis of pentatricopeptide repeat proteins of an aquatic plant
Planta, 2016Co-Authors: Wenqin Wang, Joachim MessingAbstract:A large proportion of genes in plant genomes are organized as gene families. Whereas most gene families in the aquative plant Spirodela are reduced in their copy number, the PPR gene family is expanded, which match the RNA editing sites in organelles, providing us with new insights in the evolution of flowering plants. Pentatricopeptide-repeat proteins (PPRs) are nuclear-encoded proteins that are targeted to mitochondria and plastids to stabilize and edit mRNA transcribed from organellar genomes. They have been described for many terrestrial plant species from a diverse spectrum of sequenced genomes. To further increase our understanding of the evolution of this gene family across angiosperms, we analyzed the PPR genes in the aquatic species Spirodela polyrhiza in the order of the Alismatales (monocotyledonous plants). Because we had generated next generation sequencing data from transcripts and had sequenced the genome of Spirodela polyrhiza, we were able to identify its PPR genes and determine the level of their expression. In total, we could identify 556 PPR proteins, of which 238 members belong to the P (P motif) subfamily that is mainly involved in RNA stabilization and 318 ones to the PLS (P, Longer P, shorter P motif) subfamily responsible for RNA editing. Compared to other angiosperms, this is a large increase in the copy number of the PLS-PPRs subfamily and the expansion correlates with the increase of the number of RNA editing sites of organellar transcripts. Expression of PPR was generally stable even during growing and dormant stages, indicating that their function was critical throughout development. However, PPRs, especially those of the PLS subfamily, were expressed at relatively low levels, suggesting a delicate fine-tuning of its trans-acting function in the post-transcriptional regulation of gene expression. Thus, understanding PPR evolution and expression will help decipher the PPR code for their binding sites, which could genetically engineer RNA-binding proteins toward desired sequence.
-
RNA editing in chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species
PLoS ONE, 2015Co-Authors: Wenqin Wang, Yongrui Wu, Pál Maliga, Wei Zhang, Joachim MessingAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
-
Phylogenetic tree of monocot representatives based on rbcL sequences.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:The tree was drawn by MEGA 6 maximum likelihood by using rbcL sequences of Spirodela, coconut, rice and maize. In the ndh gene family, Spirodela shares more RNA editing sites with coconut (81%) than rice (42%) and maize (38%).
-
List of RNA editing sites in the chloroplast of Spirodela.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:List of RNA editing sites in the chloroplast of Spirodela.
Wenqin Wang - One of the best experts on this subject based on the ideXlab platform.
-
Genomes and Transcriptomes of Duckweeds
Frontiers Media S.A., 2018Co-Authors: Yong Zhou, Wenqin WangAbstract:Duckweeds (Lemnaceae family) are the smallest flowering plants that adapt to the aquatic environment. They are regarded as the promising sustainable feedstock with the characteristics of high starch storage, fast propagation, and global distribution. The duckweed genome size varies 13-fold ranging from 150 Mb in Spirodela polyrhiza to 1,881 Mb in Wolffia arrhiza. With the development of sequencing technology and bioinformatics, five duckweed genomes from Spirodela and Lemna genera are sequenced and assembled. The genome annotations discover that they share similar protein orthologs, whereas the repeat contents could mainly explain the genome size difference. The gene families responsible for cell growth and expansion, lignin biosynthesis, and flowering are greatly contracted. However, the gene family of glutamate synthase has experienced expansion, indicating their significance in ammonia assimilation and nitrogen transport. The transcriptome is comprehensively sequenced for the genera of Spirodela, Landoltia, and Lemna, including various treatments such as abscisic acid, radiation, heavy metal, and starvation. The analysis of the underlying molecular mechanism and the regulatory network would accelerate their applications in the fields of bioenergy and phytoremediation. The comparative genomics has shown that duckweed genomes contain relatively low gene numbers and more contracted gene families, which may be in parallel with their highly reduced morphology with a simple leaf and primary roots. Still, we are waiting for the advancement of the long read sequencing technology to resolve the complex genomes and transcriptomes for unsequenced Wolffiella and Wolffia due to the large genome sizes and the similarity in their polyploidy
-
genome wide analysis of pentatricopeptide repeat proteins of an aquatic plant
Planta, 2016Co-Authors: Wenqin Wang, Joachim MessingAbstract:A large proportion of genes in plant genomes are organized as gene families. Whereas most gene families in the aquative plant Spirodela are reduced in their copy number, the PPR gene family is expanded, which match the RNA editing sites in organelles, providing us with new insights in the evolution of flowering plants. Pentatricopeptide-repeat proteins (PPRs) are nuclear-encoded proteins that are targeted to mitochondria and plastids to stabilize and edit mRNA transcribed from organellar genomes. They have been described for many terrestrial plant species from a diverse spectrum of sequenced genomes. To further increase our understanding of the evolution of this gene family across angiosperms, we analyzed the PPR genes in the aquatic species Spirodela polyrhiza in the order of the Alismatales (monocotyledonous plants). Because we had generated next generation sequencing data from transcripts and had sequenced the genome of Spirodela polyrhiza, we were able to identify its PPR genes and determine the level of their expression. In total, we could identify 556 PPR proteins, of which 238 members belong to the P (P motif) subfamily that is mainly involved in RNA stabilization and 318 ones to the PLS (P, Longer P, shorter P motif) subfamily responsible for RNA editing. Compared to other angiosperms, this is a large increase in the copy number of the PLS-PPRs subfamily and the expansion correlates with the increase of the number of RNA editing sites of organellar transcripts. Expression of PPR was generally stable even during growing and dormant stages, indicating that their function was critical throughout development. However, PPRs, especially those of the PLS subfamily, were expressed at relatively low levels, suggesting a delicate fine-tuning of its trans-acting function in the post-transcriptional regulation of gene expression. Thus, understanding PPR evolution and expression will help decipher the PPR code for their binding sites, which could genetically engineer RNA-binding proteins toward desired sequence.
-
RNA editing in chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species
PLoS ONE, 2015Co-Authors: Wenqin Wang, Yongrui Wu, Pál Maliga, Wei Zhang, Joachim MessingAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
-
Phylogenetic tree of monocot representatives based on rbcL sequences.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:The tree was drawn by MEGA 6 maximum likelihood by using rbcL sequences of Spirodela, coconut, rice and maize. In the ndh gene family, Spirodela shares more RNA editing sites with coconut (81%) than rice (42%) and maize (38%).
-
List of RNA editing sites in the chloroplast of Spirodela.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:List of RNA editing sites in the chloroplast of Spirodela.
Pál Maliga - One of the best experts on this subject based on the ideXlab platform.
-
RESEARCH ARTICLE RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species
2016Co-Authors: Wei Zhang, Pál MaligaAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chlo-roplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocoty-ledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were rel-atively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor
-
RNA editing in chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species
PLoS ONE, 2015Co-Authors: Wenqin Wang, Yongrui Wu, Pál Maliga, Wei Zhang, Joachim MessingAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
-
Phylogenetic tree of monocot representatives based on rbcL sequences.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:The tree was drawn by MEGA 6 maximum likelihood by using rbcL sequences of Spirodela, coconut, rice and maize. In the ndh gene family, Spirodela shares more RNA editing sites with coconut (81%) than rice (42%) and maize (38%).
-
List of RNA editing sites in the chloroplast of Spirodela.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:List of RNA editing sites in the chloroplast of Spirodela.
-
Alignment of editing sites in the ndhB gene.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:There were 14 edited sites identified in Spirodela ndhB coding region, plus another one from an intron which was not shown here. The amino acid substitutions caused by the editing events were marked with arrows. The locations in the CDS were listed on the top of alignment. All aligned sequences were obtained from the chloroplast genome sequence before RNA editing.
Klaus J. Appenroth - One of the best experts on this subject based on the ideXlab platform.
-
Duckweed for Human Nutrition: No Cytotoxic and No Anti-Proliferative Effects on Human Cell Lines
Plant Foods for Human Nutrition, 2019Co-Authors: K. Sowjanya Sree, Hans-martin Dahse, Jima N. Chandran, Bernd Schneider, Gerhard Jahreis, Klaus J. AppenrothAbstract:Duckweeds (Lemnaceae) possess good qualitative and quantitative profiles of nutritional components for its use as human food. However, no studies have been conducted on the probable presence or absence of any adverse effects. The extracts from seven duckweed species ( Spirodela polyrhiza, Landoltia punctata, Lemna gibba, Lemna minor, Wolffiella hyalina, Wolffia globosa , and Wolffia microscopica ) covering all five genera of the plant family were herewith tested for cytotoxic effects on the human cell lines HUVEC, K-562, and HeLa and for anti-proliferative activity on HUVEC and K-562 cell lines. From these assays, it is evident that duckweeds do not possess any detectable anti-proliferative or cytotoxic effects, thus, the high nutritional value is not diminished by such detrimental factors. The present result is a first step to exclude any harmful effects of highly nutritious duckweed for human.
-
low genetic variation is associated with low mutation rate in the giant duckweed
bioRxiv, 2018Co-Authors: Shuqing Xu, Jessica Stapley, Saskia Gablenz, Justin Boyer, Sowjanya K Sree, Alex Widmer, Klaus J. Appenroth, Meret HuberAbstract:Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. We investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals revealed extremely low within-species genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels, and accurate estimates of mutation rate can help to explain seemingly counter-intuitive patterns of genome-wide variation.
-
effects of nickel on the chloroplasts of the duckweeds Spirodela polyrhiza and lemna minor and their possible use in biomonitoring and phytoremediation
Chemosphere, 2010Co-Authors: Klaus J. Appenroth, Aron Keresztes, K Krech, Wolfgang Fischer, H KoloczekAbstract:Abstract Toxic effects of Ni 2+ on the chloroplasts of the two duckweed species Spirodela polyrhiza , clone SJ and Lemna minor , clone St were investigated according to the ISO 20079 protocol. Ni 2+ induced a transition from chloroplasts to chloro-amyloplasts and amylo-chloroplasts, but not to gerontoplasts, as shown by electron microscopy. The contents of the chlorophylls a and b decreased strongly, whereas that of carotenoids remained approximately constant. Most striking was, however, the accumulation of transitory starch. Bell-shaped dose–response curves showed that Spirodela and Lemna amassed maximum starch contents of approximately 10% and 7%, respectively, on a fresh weight basis. Because Ni 2+ in the concentrations applied does not stimulate photosynthesis, the Ni 2+ -induced starch accumulation indicates that the export of carbohydrates out of the plastids decreased, most probably due to the lower demand of the rest of the cells as a result of the Ni 2+ -dependent inhibition of growth. The half-maximal concentrations for inhibition of the fresh weight increase over the 7-day test period were 3.7 μM and 6.6 μM for Spirodela and Lemna , respectively: Spirodela was thus somewhat more sensitive to the heavy metal. Both species accumulated approximately 3 g of Ni 2+ per kg of dry weight after application of 100 μM NiCl 2 . Because of their high sensitivity to phytotoxic effects, however, Spirodela and Lemna do not appear to be particularly suitable for phytoremediation of Ni 2+ -contaminated waste water. The high sensitivity to Ni 2+ makes them instead a suitable system for ecotoxicological testing in accordance with the ISO 20079 protocol.
Wei Zhang - One of the best experts on this subject based on the ideXlab platform.
-
RESEARCH ARTICLE RNA Editing in Chloroplasts of Spirodela polyrhiza, an Aquatic Monocotelydonous Species
2016Co-Authors: Wei Zhang, Pál MaligaAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chlo-roplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocoty-ledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were rel-atively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor
-
RNA editing in chloroplasts of Spirodela polyrhiza, an aquatic monocotelydonous species
PLoS ONE, 2015Co-Authors: Wenqin Wang, Yongrui Wu, Pál Maliga, Wei Zhang, Joachim MessingAbstract:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
-
Phylogenetic tree of monocot representatives based on rbcL sequences.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:The tree was drawn by MEGA 6 maximum likelihood by using rbcL sequences of Spirodela, coconut, rice and maize. In the ndh gene family, Spirodela shares more RNA editing sites with coconut (81%) than rice (42%) and maize (38%).
-
List of RNA editing sites in the chloroplast of Spirodela.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:List of RNA editing sites in the chloroplast of Spirodela.
-
Alignment of editing sites in the ndhB gene.
2015Co-Authors: Wenqin Wang, Pál Maliga, Wei Zhang, Joachim MessingAbstract:There were 14 edited sites identified in Spirodela ndhB coding region, plus another one from an intron which was not shown here. The amino acid substitutions caused by the editing events were marked with arrows. The locations in the CDS were listed on the top of alignment. All aligned sequences were obtained from the chloroplast genome sequence before RNA editing.
