Wojciech Pląder | Warsaw University of Life Sciences (original) (raw)

Papers by Wojciech Pląder

Research paper thumbnail of miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)

International Journal of Molecular Sciences

The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during... more The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA’s target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analys...

Research paper thumbnail of The metabolic profiles of transgenic cucumber lines vary with different chromosomal locations of the transgene

Cellular & molecular biology letters, 2005

The metabolic profiles of five transgenic cucumber lines were compared taking into consideration ... more The metabolic profiles of five transgenic cucumber lines were compared taking into consideration their transgene integration sites. The plants analyzed were homozygous and contained transgenes integrated in a single locus on chromosomes I, II, III or IV. The transgenes were preferentially located in the euchromatic regions. Each of these locations possessed a specific metabolic profile. The number of altered compounds in the transgenic lines varied between 9 and 23 of the 47 metabolites identified. These alterations seem to be specific for each independent transgene integration. However, some changes are common: a decrease in the levels of phenylalanine, aspartate, ethanolamine and pipecolate, and an increase in the level of benzoic acid. The observed effects of transgene introduction are discussed in this paper.

Research paper thumbnail of Karyotype Analysis and Chromosomal Distribution of Repetitive DNA Sequences of Cucumis metuliferus Using Fluorescence in situ Hybridization

Cytogenetic and Genome Research, 2014

Cucumis metuliferus (2n = 24) is a cultivated species of the Cucumis genus which is a potential g... more Cucumis metuliferus (2n = 24) is a cultivated species of the Cucumis genus which is a potential genetic resource for Cucumis crops. Although some cytogenetic research has been reported, there is no study of karyotyping in this species. Here, we used 4',6-diamidino-2-phenylindole and chromomycin A3 staining to identify 12 pairs of chromosomes in early-metaphase cells. Fluorescence in situ hybridization revealed the chromosomal distribution patterns of the 5S and 45S ribosomal DNA (rDNA) genes, telomeres, and 3 different satellite repeats. The 2 major signals of the 45S rDNA were located on the satellite of chromosome 11, and the 2 signals of the 5S rDNA and 2 minor signals of the 45S rDNA were located on chromosome 12. The telomere probes hybridized to the ends of all chromosomes. The 3 satellite DNAs were localized at the ends of chromosomes 1, 2, 4-10, and at the end of the short arm of chromosome 3. In summary, we reported the identification of all chromosomes of C. metuliferus. We also depicted the location of 5S and 45S rDNA, the telomere motif sequence, CmetSat1, CmetSatT2, and CmetmSat1 in an ideogram. © 2014 S. Karger AG, Basel.

Research paper thumbnail of 12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome – the most efficient way to begin post genomic era

Nature Precedings, 2011

New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the... more New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length and N50 2’324 Kbp. In the Celera/Arachne method contigs after prior pyrosequencing reads assembly (in the form of ~ 800 nt reads) were used together with the STCs as the input to Arachne assembler. Number of contigs were 15’764 of the length 193 Mbp with N50 23’280 bp. Number of super...

Research paper thumbnail of Xyloglucan endotransglucosylase/hydrolase genes in cucumber (Cucumis sativus) - differential expression during somatic embryogenesis+

Physiologia Plantarum, 2004

Defined changes in the cell wall directed by many proteins accompany every morphogenetic process ... more Defined changes in the cell wall directed by many proteins accompany every morphogenetic process in plants. Xyloglucan endotransglucosylase/hydrolase proteins (XTH; EC 2.4.1.207) have the potential to modify the hemicellulose matrix within the cell wall. Cs-XTH1 and Cs-XTH3 genes, which encode XTH proteins, were found among numerous genes that are differentially expressed after the induction of cucumber somatic embryogenesis. The expression of these genes increased during somatic embryogenesis. The Cs-XTH1 gene was localized on the second chromosome near the centromere region, whereas Cs-XTH3 was found in the middle of the fifth chromosome's longer arm. Northern blot hybridization showed that both genes were preferentially expressed in roots. We also observed higher accumulation of both transcripts in somatic embryos than in the proembryogenic mass. The localization of mRNA by in situ hybridization revealed that the Cs-XTH1 transcripts were largely accumulated in the presumptive cotyledon primordia of somatic embryos. The XTH gene family consists of a number of genes with a high degree of structural similarity. Screening a cucumber genomic library has identified other members of this gene family. The intron/exon structure, sequence similarities and the close chromosomal distance between some members suggest their common evolutionary origin. The involvement of XTH-related genes in somatic embryo formation is discussed.

Research paper thumbnail of The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

PLoS ONE, 2011

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas an... more Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar-Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration-and ethylene-responsive cisregulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.

Research paper thumbnail of Influence of transgenesis on genome variability in cucumber lines with a thaumatin II gene

Physiology and Molecular Biology of Plants, 2021

The development of new plant varieties by genetic modification aims at improving their features o... more The development of new plant varieties by genetic modification aims at improving their features or introducing new qualities. However, concerns about the unintended effects of transgenes and negative environmental impact of genetically modified plants are an obstacle for the use of these plants in crops. To analyze the impact of transgenesis on plant genomes, we analyze three cucumber transgenic lines with an introduced thaumatin II gene. After genomes sequencing, we analyzed the transgene insertion site and performed variant prediction. As a result, we obtained similar number of variants for all analyzed lines (average of 4307 polymorphisms), with high abundance in one region of chromosome 4. According to SnpEff analysis, the presence of genomic variants generally does not influence the genome functionality, as less than 2% of polymorphisms have high impact. Moreover, analysis indicates that these changes were more likely induced by in vitro culture than by the transgenesis itself....

Research paper thumbnail of The construction of genomic libraries in BAC and its practical application and bioinformatic usage

Libraries constructed in bacterial artificial chromosome (BAC) vectors are essential in modern ge... more Libraries constructed in bacterial artificial chromosome (BAC) vectors are essential in modern genomics for all organisms such as plants, animals, insects, algae and microbes. Cloning using a bacterial artificial chromosome (BAC) allows to obtain high quality genomic libraries that are used for physical mapping, cytogenetic research, identification and isolation of genes, as well as for gene sequencing and genomic assembly. Here we describe the methodology of BAC library construction, characterization and the newest application and bioinformatics usage in the post-genomic era.

Research paper thumbnail of The Effects of DNA Synthesis Inhibitors on Cell Cycle Synchronization in Cucumber (Cucumis sativus L.) Root Meristems

The effects of hydroxyurea (HU) and aphidicolin (APD) on cell cycle synchronization in cucumber r... more The effects of hydroxyurea (HU) and aphidicolin (APD) on cell cycle synchronization in cucumber root meristems were studied. A 10 times lower HU concentration was effective for cucumber synchronization compared to that used as a typical treatment in Vicia faba or Triticum aestivum, and the peak mitotic index (MI) was 5 h after inhibitor removal. Higher APD concentrations (15 mM and above) caused the accumulation of M phase cells, and the peak MI was 4 h after its removal. After release from the HU block, the use of Hoagland's nutrient solution on cell cycle synchronization resulted in a considerable increase in MI. The efficiency of colchicine was also very high, and cells at anaphase or telophase were observed at very low frequencies. The highest MI (39%) was obtained 4 h after an 18 h APD block at 15 mM followed by 0.05% colchicine treatment for 2 h. Our synchronizing procedure in C. sativus would be very helpful for flow-sorting of mitotic chromosomes, karyomorphological analysis, and genetic analysis.

Research paper thumbnail of Comparison of bioinformatics programs for analysis of single nucleotide variants

Changes in genomic sequence might influence the gene expression, protein function and, what is re... more Changes in genomic sequence might influence the gene expression, protein function and, what is related to phenotype of the organism. The Next Generation Sequencing provides a big amount of data that could be used in predicting the single nucleotide variants between analyzed and reference genome. Herein we compare three tools for predicting the structural variants: Freebayes, GATK toolkit and DeepVariant. Predictions with usage of each program were made on cucumber lines and the results were compared. Our analysis indicates that in order to obtain more precise and reliable variant predictions it is worth to use more than one program for detecting polymorphisms and cross-check the results.

Research paper thumbnail of Effect of Transgenesis on mRNA and miRNA Profiles in Cucumber Fruits Expressing Thaumatin II

Genes, Mar 20, 2020

Transgenic plants are commonly used in breeding programs because of the various features that can... more Transgenic plants are commonly used in breeding programs because of the various features that can be introduced. However, unintended effects caused by genetic transformation are still a topic of concern. This makes research on the nutritional safety of transgenic crop plants extremely interesting. Cucumber (Cucumis sativus L.) is a crop that is grown worldwide. The aim of this study was to identify and characterize differentially expressed genes and regulatory miRNAs in transgenic cucumber fruits that contain the thaumatin II gene, which encodes the sweet-tasting protein thaumatin II, by NGS sequencing. We compared the fruit transcriptomes and miRNomes of three transgenic cucumber lines with wild-type cucumber. In total, we found 47 differentially expressed genes between control and all three transgenic lines. We performed the bioinformatic functional analysis and gene ontology classification. We also identified 12 differentially regulated miRNAs, from which three can influence the two targets (assigned as DEGs) in one of the studied transgenic lines (line 224). We found that the transformation of cucumber with thaumatin II and expression of the transgene had minimal impact on gene expression and epigenetic regulation by miRNA, in the cucumber fruits.

Research paper thumbnail of Characterization of Lebanese Germplasm of Snake Melon (Cucumis melo subsp. melo var. flexuosus) Using Morphological Traits and SSR Markers

Agronomy

Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditiona... more Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditional crop in the Mediterranean region. Nevertheless, there has been poor interest in assessing snake melon germplasm where its genetic resources have not been surveyed before despite their potential in adaptation to environmental changes. In this study, we assess the genetic diversity of snake melon landraces collected from different Lebanese regions at both morphological and molecular levels. Morphological characterization using a set of 18 descriptors revealed an important phenotypic variability among the landraces studied. Principle component analysis indicated that fruit hair and its consistency, fruit size, and skin color pattern were good criteria for discriminating among landraces. Based on the scatter plot diagram, landraces of snake melon formed five different groups with one being defined as typical var. flexuosus. Ten simple sequence repeat (SSR) markers were used for the molecul...

Research paper thumbnail of Genome-wide discovery of DNA variants in cucumber somaclonal lines

Research paper thumbnail of Correction to: A high-quality cucumber genome assembly enhances computational comparative genomics

Molecular Genetics and Genomics

Research paper thumbnail of Biological significance, computational analysis, and applications of plant microRNAs

Acta Physiologiae Plantarum

Research paper thumbnail of Genetic and molecular bases of cucumber (Cucumis sativus L.) sex determination

Research paper thumbnail of The utility of optical detection system (qPCR) and bioinformatics methods in reference gene expression analysis

Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2016

Research paper thumbnail of Detection of genomic rearrangements in cucumber using genomecmp software

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017

Research paper thumbnail of Bioinformatics and expressional analysis of cDNA clones from floral buds

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017

Research paper thumbnail of Assembly of cucumber (Cucumis sativus L.) somaclones

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017

Research paper thumbnail of miRNA Profiling and Its Role in Multi-Omics Regulatory Networks Connected with Somaclonal Variation in Cucumber (Cucumis sativus L.)

International Journal of Molecular Sciences

The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during... more The role of miRNAs in connection with the phenomenon of somaclonal variation, which occurs during plant in vitro culture, remains uncertain. This study aims to investigate the possible role of miRNAs in multi-omics regulatory pathways in cucumber somaclonal lines. For this purpose, we performed sRNA sequencing (sRNA-seq) from cucumber fruit samples identified 8, 10 and 44 miRNAs that are differentially expressed between somaclones (S1, S2, S3 lines) and the reference B10 line of Cucumis sativus. For miRNA identification, we use ShortStack software designed to filter miRNAs from sRNAs according to specific program criteria. The identification of predicted in-silico targets revealed 2,886 mRNAs encoded by 644 genes. The functional annotation of miRNA’s target genes and gene ontology classification revealed their association with metabolic processes, response to stress, multicellular organism development, biosynthetic process and catalytic activity. We checked with bioinformatic analys...

Research paper thumbnail of The metabolic profiles of transgenic cucumber lines vary with different chromosomal locations of the transgene

Cellular & molecular biology letters, 2005

The metabolic profiles of five transgenic cucumber lines were compared taking into consideration ... more The metabolic profiles of five transgenic cucumber lines were compared taking into consideration their transgene integration sites. The plants analyzed were homozygous and contained transgenes integrated in a single locus on chromosomes I, II, III or IV. The transgenes were preferentially located in the euchromatic regions. Each of these locations possessed a specific metabolic profile. The number of altered compounds in the transgenic lines varied between 9 and 23 of the 47 metabolites identified. These alterations seem to be specific for each independent transgene integration. However, some changes are common: a decrease in the levels of phenylalanine, aspartate, ethanolamine and pipecolate, and an increase in the level of benzoic acid. The observed effects of transgene introduction are discussed in this paper.

Research paper thumbnail of Karyotype Analysis and Chromosomal Distribution of Repetitive DNA Sequences of Cucumis metuliferus Using Fluorescence in situ Hybridization

Cytogenetic and Genome Research, 2014

Cucumis metuliferus (2n = 24) is a cultivated species of the Cucumis genus which is a potential g... more Cucumis metuliferus (2n = 24) is a cultivated species of the Cucumis genus which is a potential genetic resource for Cucumis crops. Although some cytogenetic research has been reported, there is no study of karyotyping in this species. Here, we used 4',6-diamidino-2-phenylindole and chromomycin A3 staining to identify 12 pairs of chromosomes in early-metaphase cells. Fluorescence in situ hybridization revealed the chromosomal distribution patterns of the 5S and 45S ribosomal DNA (rDNA) genes, telomeres, and 3 different satellite repeats. The 2 major signals of the 45S rDNA were located on the satellite of chromosome 11, and the 2 signals of the 5S rDNA and 2 minor signals of the 45S rDNA were located on chromosome 12. The telomere probes hybridized to the ends of all chromosomes. The 3 satellite DNAs were localized at the ends of chromosomes 1, 2, 4-10, and at the end of the short arm of chromosome 3. In summary, we reported the identification of all chromosomes of C. metuliferus. We also depicted the location of 5S and 45S rDNA, the telomere motif sequence, CmetSat1, CmetSatT2, and CmetmSat1 in an ideogram. © 2014 S. Karger AG, Basel.

Research paper thumbnail of 12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome – the most efficient way to begin post genomic era

Nature Precedings, 2011

New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the... more New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length and N50 2’324 Kbp. In the Celera/Arachne method contigs after prior pyrosequencing reads assembly (in the form of ~ 800 nt reads) were used together with the STCs as the input to Arachne assembler. Number of contigs were 15’764 of the length 193 Mbp with N50 23’280 bp. Number of super...

Research paper thumbnail of Xyloglucan endotransglucosylase/hydrolase genes in cucumber (Cucumis sativus) - differential expression during somatic embryogenesis+

Physiologia Plantarum, 2004

Defined changes in the cell wall directed by many proteins accompany every morphogenetic process ... more Defined changes in the cell wall directed by many proteins accompany every morphogenetic process in plants. Xyloglucan endotransglucosylase/hydrolase proteins (XTH; EC 2.4.1.207) have the potential to modify the hemicellulose matrix within the cell wall. Cs-XTH1 and Cs-XTH3 genes, which encode XTH proteins, were found among numerous genes that are differentially expressed after the induction of cucumber somatic embryogenesis. The expression of these genes increased during somatic embryogenesis. The Cs-XTH1 gene was localized on the second chromosome near the centromere region, whereas Cs-XTH3 was found in the middle of the fifth chromosome's longer arm. Northern blot hybridization showed that both genes were preferentially expressed in roots. We also observed higher accumulation of both transcripts in somatic embryos than in the proembryogenic mass. The localization of mRNA by in situ hybridization revealed that the Cs-XTH1 transcripts were largely accumulated in the presumptive cotyledon primordia of somatic embryos. The XTH gene family consists of a number of genes with a high degree of structural similarity. Screening a cucumber genomic library has identified other members of this gene family. The intron/exon structure, sequence similarities and the close chromosomal distance between some members suggest their common evolutionary origin. The involvement of XTH-related genes in somatic embryo formation is discussed.

Research paper thumbnail of The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants

PLoS ONE, 2011

Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas an... more Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sort of evolutionary molecular mechanisms regulate genetic adaptation of plants to different ecosystems and organism biodiversity. Here we present the draft genome sequence of the Cucumis sativus genome of the North-European Borszczagowski cultivar (line B10) and comparative genomics studies with the known genomes of: C. sativus (Chinese cultivar-Chinese Long (line 9930)), Arabidopsis thaliana, Populus trichocarpa and Oryza sativa. Cucumber genomes show extensive chromosomal rearrangements, distinct differences in quantity of the particular genes (e.g. involved in photosynthesis, respiration, sugar metabolism, chlorophyll degradation, regulation of gene expression, photooxidative stress tolerance, higher non-optimal temperatures tolerance and ammonium ion assimilation) as well as in distributions of abscisic acid-, dehydration-and ethylene-responsive cisregulatory elements (CREs) in promoters of orthologous group of genes, which lead to the specific adaptation features. Abscisic acid treatment of non-acclimated Arabidopsis and C. sativus seedlings induced moderate freezing tolerance in Arabidopsis but not in C. sativus. This experiment together with analysis of abscisic acid-specific CRE distributions give a clue why C. sativus is much more susceptible to moderate freezing stresses than A. thaliana. Comparative analysis of all the five genomes showed that, each species and/or cultivars has a specific profile of CRE content in promoters of orthologous genes. Our results constitute the substantial and original resource for the basic and applied research on environmental adaptations of plants, which could facilitate creation of new crops with improved growth and yield in divergent conditions.

Research paper thumbnail of Influence of transgenesis on genome variability in cucumber lines with a thaumatin II gene

Physiology and Molecular Biology of Plants, 2021

The development of new plant varieties by genetic modification aims at improving their features o... more The development of new plant varieties by genetic modification aims at improving their features or introducing new qualities. However, concerns about the unintended effects of transgenes and negative environmental impact of genetically modified plants are an obstacle for the use of these plants in crops. To analyze the impact of transgenesis on plant genomes, we analyze three cucumber transgenic lines with an introduced thaumatin II gene. After genomes sequencing, we analyzed the transgene insertion site and performed variant prediction. As a result, we obtained similar number of variants for all analyzed lines (average of 4307 polymorphisms), with high abundance in one region of chromosome 4. According to SnpEff analysis, the presence of genomic variants generally does not influence the genome functionality, as less than 2% of polymorphisms have high impact. Moreover, analysis indicates that these changes were more likely induced by in vitro culture than by the transgenesis itself....

Research paper thumbnail of The construction of genomic libraries in BAC and its practical application and bioinformatic usage

Libraries constructed in bacterial artificial chromosome (BAC) vectors are essential in modern ge... more Libraries constructed in bacterial artificial chromosome (BAC) vectors are essential in modern genomics for all organisms such as plants, animals, insects, algae and microbes. Cloning using a bacterial artificial chromosome (BAC) allows to obtain high quality genomic libraries that are used for physical mapping, cytogenetic research, identification and isolation of genes, as well as for gene sequencing and genomic assembly. Here we describe the methodology of BAC library construction, characterization and the newest application and bioinformatics usage in the post-genomic era.

Research paper thumbnail of The Effects of DNA Synthesis Inhibitors on Cell Cycle Synchronization in Cucumber (Cucumis sativus L.) Root Meristems

The effects of hydroxyurea (HU) and aphidicolin (APD) on cell cycle synchronization in cucumber r... more The effects of hydroxyurea (HU) and aphidicolin (APD) on cell cycle synchronization in cucumber root meristems were studied. A 10 times lower HU concentration was effective for cucumber synchronization compared to that used as a typical treatment in Vicia faba or Triticum aestivum, and the peak mitotic index (MI) was 5 h after inhibitor removal. Higher APD concentrations (15 mM and above) caused the accumulation of M phase cells, and the peak MI was 4 h after its removal. After release from the HU block, the use of Hoagland's nutrient solution on cell cycle synchronization resulted in a considerable increase in MI. The efficiency of colchicine was also very high, and cells at anaphase or telophase were observed at very low frequencies. The highest MI (39%) was obtained 4 h after an 18 h APD block at 15 mM followed by 0.05% colchicine treatment for 2 h. Our synchronizing procedure in C. sativus would be very helpful for flow-sorting of mitotic chromosomes, karyomorphological analysis, and genetic analysis.

Research paper thumbnail of Comparison of bioinformatics programs for analysis of single nucleotide variants

Changes in genomic sequence might influence the gene expression, protein function and, what is re... more Changes in genomic sequence might influence the gene expression, protein function and, what is related to phenotype of the organism. The Next Generation Sequencing provides a big amount of data that could be used in predicting the single nucleotide variants between analyzed and reference genome. Herein we compare three tools for predicting the structural variants: Freebayes, GATK toolkit and DeepVariant. Predictions with usage of each program were made on cucumber lines and the results were compared. Our analysis indicates that in order to obtain more precise and reliable variant predictions it is worth to use more than one program for detecting polymorphisms and cross-check the results.

Research paper thumbnail of Effect of Transgenesis on mRNA and miRNA Profiles in Cucumber Fruits Expressing Thaumatin II

Genes, Mar 20, 2020

Transgenic plants are commonly used in breeding programs because of the various features that can... more Transgenic plants are commonly used in breeding programs because of the various features that can be introduced. However, unintended effects caused by genetic transformation are still a topic of concern. This makes research on the nutritional safety of transgenic crop plants extremely interesting. Cucumber (Cucumis sativus L.) is a crop that is grown worldwide. The aim of this study was to identify and characterize differentially expressed genes and regulatory miRNAs in transgenic cucumber fruits that contain the thaumatin II gene, which encodes the sweet-tasting protein thaumatin II, by NGS sequencing. We compared the fruit transcriptomes and miRNomes of three transgenic cucumber lines with wild-type cucumber. In total, we found 47 differentially expressed genes between control and all three transgenic lines. We performed the bioinformatic functional analysis and gene ontology classification. We also identified 12 differentially regulated miRNAs, from which three can influence the two targets (assigned as DEGs) in one of the studied transgenic lines (line 224). We found that the transformation of cucumber with thaumatin II and expression of the transgene had minimal impact on gene expression and epigenetic regulation by miRNA, in the cucumber fruits.

Research paper thumbnail of Characterization of Lebanese Germplasm of Snake Melon (Cucumis melo subsp. melo var. flexuosus) Using Morphological Traits and SSR Markers

Agronomy

Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditiona... more Snake melon (Cucumis melo subsp. melo L. var. flexuosus (L.) Naudin) is an ancient and traditional crop in the Mediterranean region. Nevertheless, there has been poor interest in assessing snake melon germplasm where its genetic resources have not been surveyed before despite their potential in adaptation to environmental changes. In this study, we assess the genetic diversity of snake melon landraces collected from different Lebanese regions at both morphological and molecular levels. Morphological characterization using a set of 18 descriptors revealed an important phenotypic variability among the landraces studied. Principle component analysis indicated that fruit hair and its consistency, fruit size, and skin color pattern were good criteria for discriminating among landraces. Based on the scatter plot diagram, landraces of snake melon formed five different groups with one being defined as typical var. flexuosus. Ten simple sequence repeat (SSR) markers were used for the molecul...

Research paper thumbnail of Genome-wide discovery of DNA variants in cucumber somaclonal lines

Research paper thumbnail of Correction to: A high-quality cucumber genome assembly enhances computational comparative genomics

Molecular Genetics and Genomics

Research paper thumbnail of Biological significance, computational analysis, and applications of plant microRNAs

Acta Physiologiae Plantarum

Research paper thumbnail of Genetic and molecular bases of cucumber (Cucumis sativus L.) sex determination

Research paper thumbnail of The utility of optical detection system (qPCR) and bioinformatics methods in reference gene expression analysis

Photonics Applications in Astronomy, Communications, Industry, and High-Energy Physics Experiments 2016

Research paper thumbnail of Detection of genomic rearrangements in cucumber using genomecmp software

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017

Research paper thumbnail of Bioinformatics and expressional analysis of cDNA clones from floral buds

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017

Research paper thumbnail of Assembly of cucumber (Cucumis sativus L.) somaclones

Photonics Applications in Astronomy, Communications, Industry, and High Energy Physics Experiments 2017