cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14157109.v1
title: Transcriptome analysis of ionic-liquid tolerant <i>Bacillus amyloliquefaciens</i> CMW1 and identification of a novel efflux pump

description: Bacteria that exhibit ionic-liquid (IL) tolerance are useful in chemical industries using renewable carbon sources pre-treated by ILs to produce biofuels and fine chemicals. An IL, 1-butyl-3-methylimidazolium chloride ([BMIM]Cl), has a remarkable ability to solubilize wood components, whereas [BMIM]Cl inhibits the growth of various bacterial hosts useful for bioconversion. We previously isolated a 10% [BMIM]Cl-tolerant bacterium <i>Bacillus amyloliquefaciens</i> CMW1. Here we report novel mechanisms of tolerance to [BMIM]Cl in strain CMW1 and a novel major facilitator superfamily transporter coded by an ionic-liquid tolerance (ILT) gene. First, using CMW1 cells grown in the presence or absence of 10% [BMIM]Cl, whole-transcriptome analysis and differentially expressed gene analysis were performed. Probable mechanisms of tolerance to [BMIM]Cl include the uptake of osmoprotectants from the culture medium toward CMW1 cells and the export of [BMIM] cations that accumulated in CMW1 cells. The finding represents a first step in elucidation of the mechanisms of IL resistance in Gram-positive bacteria. Second, we conferred tolerance to 5% [BMIM]Cl on [BMIM]Cl-susceptible <i>Brevibacillus choshinensis</i> using ILT gene. This finding provides a notable basis for engineering IL-tolerant bacterial hosts that are applicable for the effective and sustainable production of industrially important chemicals.
DOI: 10.6084/m9.figshare.16990096
title: Morphological variation, genetic diversity and phylogenetic relationships of <i>Hypericum triquetrifolium</i> Turra populations from Tunisia

description: <i>Hypericum triquetrifolium</i> Turra is an ecologically, medicinally and economically important species in Tunisia. Thirty-six <i>Hypericum</i> individuals sampled from 6 northern Tunisian locations were investigated for their diversity and relationships using 10 inter-simple sequence repeats (ISSR) markers and 10 morphological features at vegetative stage. The phylogenetic analysis, using 308 bp of sequenced ITS1 region, identified the <i>Hypericum</i> individuals as <i>H. triquetrifolium</i> that clustered with members of genus <i>Hypericum</i> section 9, 9a, 9b and 27, in agreement with the previous molecular classification of the genus. Among the 10 ISSR markers tested, 7 were scorable and yielded 91 loci with 94.5% of polymorphism. UBC848 and UBC836 were the most polymorphic ISSR markers. The level of genetic diversity (HT = 0.247) and gene flow between the six populations (<i>N</i><sub>m</sub> = 1.169) were moderate. The structure analysis revealed three genetic subpopulations: individuals of Le Krib location formed a subpopulation divergent from two other subpopulations, probably due to its northwestern and high-altitude geographic barriers, and its sub-humid microclimate. Zaghouan, northeastern location in the lower semi-arid, with the highest genetic (<i>I</i> = 0.370) and morphological (<i>I</i> = 0.631) Shannon’s information indices and, regrouping two out of the three genetic subpopulations, is the most probable zone of origin for <i>H. triquetrifolium.</i> In addition, morphological data showed higher diversity than ISSR data; however, no evidence of correlation between genetic and morphologic traits could be suggested in this study. These results on the genetic diversity and phylogenetic analysis will contribute to the conservation of the gene pool of <i>H. triquetrifolium</i> in Tunisia.
DOI: 10.6084/m9.figshare.16923559
title: Phytochemical investigation, antioxidant and antibacterial activities of the fruit extracts of <i>Solanum anguivi</i>

description: <i>Solanum anguivi</i> Lam. is an ethnomedicinal plant. Local traditional practitioners believe that it reduces the risk of diabetes and atherosclerosis diseases. The present study was intended to conduct qualitative phytochemical analysis, determine the total flavonoid and phenolic contents, estimate the antioxidant capacity and antibacterial activities of the extracts of the fruits of this plant. The antioxidant activity was determined by analyzing the radical scavenging activity (RSA) using 2,2-diphenyl-1-picryhydrazyl (DPPH), and ferric reducing antioxidant power (FRAP) assays. The antibacterial activities were determined by the agar well diffusion method. Qualitative phytochemical screening of the crude extracts obtained from the fruits of the plant indicated the presence of alkaloids, flavonoids, phenols, glycosides, steroids, terpenoids, saponins and tannins. The highest total phenolic and total flavonoid content were obtained in the ethanol extract of the fruits, followed by dichloromethane and <i>n</i>-hexane extract. The total phenolic content (in gallic acid equivalents, GAE) ranged from 113.3 to 202.72 mg GAE/g. The total flavonoid content (in catechin equivalent, CE) varied from 61.72 to 142.64 mg (CE)/g. All fruit extracts of <i>S. anguivi</i> exhibited antioxidant activity as revealed by DPPH and FRAP assays. The DPPH RSA (% inhibition) of the fruit extract varied from 35.11 to 80.13. The total phenolic and Flavonoid contents showed alinear correlation with RSA. Furthermore, all fruit extracts showed antibacterial activity against gram-positive and gram-negative bacteria varying from 12.5 to 16.75 mm. The result showed that the extracts of the plant exerted stronger bactericidal effect on gram-positive bacteria than on gram-negative bacteria. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1993087 .
DOI: 10.6084/m9.figshare.16923559.v1
title: Phytochemical investigation, antioxidant and antibacterial activities of the fruit extracts of <i>Solanum anguivi</i>

description: <i>Solanum anguivi</i> Lam. is an ethnomedicinal plant. Local traditional practitioners believe that it reduces the risk of diabetes and atherosclerosis diseases. The present study was intended to conduct qualitative phytochemical analysis, determine the total flavonoid and phenolic contents, estimate the antioxidant capacity and antibacterial activities of the extracts of the fruits of this plant. The antioxidant activity was determined by analyzing the radical scavenging activity (RSA) using 2,2-diphenyl-1-picryhydrazyl (DPPH), and ferric reducing antioxidant power (FRAP) assays. The antibacterial activities were determined by the agar well diffusion method. Qualitative phytochemical screening of the crude extracts obtained from the fruits of the plant indicated the presence of alkaloids, flavonoids, phenols, glycosides, steroids, terpenoids, saponins and tannins. The highest total phenolic and total flavonoid content were obtained in the ethanol extract of the fruits, followed by dichloromethane and <i>n</i>-hexane extract. The total phenolic content (in gallic acid equivalents, GAE) ranged from 113.3 to 202.72 mg GAE/g. The total flavonoid content (in catechin equivalent, CE) varied from 61.72 to 142.64 mg (CE)/g. All fruit extracts of <i>S. anguivi</i> exhibited antioxidant activity as revealed by DPPH and FRAP assays. The DPPH RSA (% inhibition) of the fruit extract varied from 35.11 to 80.13. The total phenolic and Flavonoid contents showed alinear correlation with RSA. Furthermore, all fruit extracts showed antibacterial activity against gram-positive and gram-negative bacteria varying from 12.5 to 16.75 mm. The result showed that the extracts of the plant exerted stronger bactericidal effect on gram-positive bacteria than on gram-negative bacteria. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1993087 .
DOI: 10.6084/m9.figshare.16911985
title: Initial sample processing can influence the soil microbial metabarcoding surveys, revealed by <i>Leucocalocybe mongolica</i> fairy ring ecosystem

description: In this study, we aimed to investigate the influence of soil preservation approaches, especially cryopreservation and high temperature-drying on the sequencing quality of its microbial community and the background microbial diversity information of fairy ring soil from <i>Leucocalocybe mongolica</i>. Through DNA metabarcoding surveys based on 16S rDNA and ITS (Internal Transcribed Spacer) barcodes, we observed that the bacterial abundance was notably changed when the soil samples were exposed in room temperature for 4 h, whereas the fungal composition was not significantly changed. Moreover, the soil samples preserved their major microbial structures even after high temperature-drying for 12 h, whereas their microbial diversity was influenced. Overall, a total of 9283 and 1871 OTUs (Operational Taxonomic Units) were obtained from soil bacteria and fungi, respectively, and we observed that <i>Chthoniobacteraceae</i> and <i>Tricholomataceae</i> were the dominant bacterial and fungal families in the fairy ring soil, respectively. Our study reveals the impact of soil processing methods on the microbial community compositions contributes to the understanding of fairy ring ecology. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1996272 .
DOI: 10.6084/m9.figshare.16911985.v1
title: Initial sample processing can influence the soil microbial metabarcoding surveys, revealed by <i>Leucocalocybe mongolica</i> fairy ring ecosystem

description: In this study, we aimed to investigate the influence of soil preservation approaches, especially cryopreservation and high temperature-drying on the sequencing quality of its microbial community and the background microbial diversity information of fairy ring soil from <i>Leucocalocybe mongolica</i>. Through DNA metabarcoding surveys based on 16S rDNA and ITS (Internal Transcribed Spacer) barcodes, we observed that the bacterial abundance was notably changed when the soil samples were exposed in room temperature for 4 h, whereas the fungal composition was not significantly changed. Moreover, the soil samples preserved their major microbial structures even after high temperature-drying for 12 h, whereas their microbial diversity was influenced. Overall, a total of 9283 and 1871 OTUs (Operational Taxonomic Units) were obtained from soil bacteria and fungi, respectively, and we observed that <i>Chthoniobacteraceae</i> and <i>Tricholomataceae</i> were the dominant bacterial and fungal families in the fairy ring soil, respectively. Our study reveals the impact of soil processing methods on the microbial community compositions contributes to the understanding of fairy ring ecology. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1996272 .
DOI: 10.6084/m9.figshare.16782950
title: Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan <i>Capsicum annuum</i> germplasm

description: Pepper (<i>Capsicum annuum</i> L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for <i>C. annuum</i>, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 <i>C. annuum</i> accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (&lt;5%). The mean He, Ho and PIC for the 21 SSR loci in the whole set were 0.531, 0.249 and 0.483, respectively. Model-based structure analysis divided the collection into 3 main clusters (<i>K</i> = 3) that grouped accessions with distinct fruit traits like shape, size, pungency. Further genetic structure analysis at increasing <i>K</i>s suggested the presence of sub-clustering within the three main clusters. A Balkan <i>C. annuum</i> mini core collection was constructed based on the allelic diversity and the inferred genetic structure. As far as the mini core collection captured substantial part of the allele richness, genetic and phenotypic diversity of the analysed 176 non-redundant accessions, while maintaining good representativeness, we believe it will be of high interest to pepper breeders and germplasm conservation specialists. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1946428 .
DOI: 10.6084/m9.figshare.16782950.v2
title: Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan <i>Capsicum annuum</i> germplasm

description: Pepper (<i>Capsicum annuum</i> L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for <i>C. annuum</i>, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 <i>C. annuum</i> accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (&lt;5%). The mean He, Ho and PIC for the 21 SSR loci in the whole set were 0.531, 0.249 and 0.483, respectively. Model-based structure analysis divided the collection into 3 main clusters (<i>K</i> = 3) that grouped accessions with distinct fruit traits like shape, size, pungency. Further genetic structure analysis at increasing <i>K</i>s suggested the presence of sub-clustering within the three main clusters. A Balkan <i>C. annuum</i> mini core collection was constructed based on the allelic diversity and the inferred genetic structure. As far as the mini core collection captured substantial part of the allele richness, genetic and phenotypic diversity of the analysed 176 non-redundant accessions, while maintaining good representativeness, we believe it will be of high interest to pepper breeders and germplasm conservation specialists. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1946428 .
DOI: 10.6084/m9.figshare.16782950.v1
title: Genetic diversity and population structure analysis – a prerequisite for constructing a mini core collection of Balkan <i>Capsicum annuum</i> germplasm

description: Pepper (<i>Capsicum annuum</i> L.) is one of the most important vegetable crops worldwide. The Balkans, including Bulgaria, are considered as the secondary centre of pepper diversity especially for <i>C. annuum</i>, where local forms with diverse phenotypes and qualities have formed due to the specific agro-climatic conditions and breeding traditions. Evaluation of the genetic diversity and structure of a pepper collection is an important tool for further development of new varieties and the maintenance of sustainable agriculture. In this study, a set of 179 <i>C. annuum</i> accessions collected from different locations in the Balkan Peninsula was genotyped with 21 simple sequence repeat (SSR; microsatellite) markers. In total, 146 alleles were amplified among which the majority were with low frequencies (&lt;5%). The mean He, Ho and PIC for the 21 SSR loci in the whole set were 0.531, 0.249 and 0.483, respectively. Model-based structure analysis divided the collection into 3 main clusters (<i>K</i> = 3) that grouped accessions with distinct fruit traits like shape, size, pungency. Further genetic structure analysis at increasing <i>K</i>s suggested the presence of sub-clustering within the three main clusters. A Balkan <i>C. annuum</i> mini core collection was constructed based on the allelic diversity and the inferred genetic structure. As far as the mini core collection captured substantial part of the allele richness, genetic and phenotypic diversity of the analysed 176 non-redundant accessions, while maintaining good representativeness, we believe it will be of high interest to pepper breeders and germplasm conservation specialists. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1946428 .
DOI: 10.6084/m9.figshare.17059748
title: SSR and morphological traits based fingerprints and DNA barcodes for varietal identification in rice

description: Varietal identification has attained prime importance at a global level particularly in the context of plant variety protection. In this study, forty-six traits were characterized for the establishment of the sheer distinctness among eighteen rice varieties. Morphologically, out of forty-six traits, twenty-five traits did not display any variation among the varieties studied. Significant variations were observed for 21 traits which are relatively more informative in the identification/characterization. Distinctness, uniformity and stability-based fingerprints specific to the studied varieties were developed based on the variations. A total of 175 simple sequence repeat (SSR) markers were screened for polymorphism; 53 hypervariable polymorphic SSR markers were utilized for fingerprinting of rice varieties. A total of 151 alleles were detected in these 53 SSR markers with an amplification size ranging from 120 to 750 bp and the allelic range of 2–4. The average number of alleles observed was 2.84 per locus. The PIC values of 53 SSRs ranged from 0.03 (RM 12983) to 0.64 (RM 11449) with an average of 0.40. The generated allelic variations of 53 SSR markers for the varieties were translated into DNA barcode profiles by separating the allele size from each SSR locus. Multiplex polymerase chain reaction (PCR) with five markers (RM 21392, RM 1388, RM 6699, RM 25754 and RM 16913) was used to identify rice varieties based on the band positions. This study classifies and identifies rice varieties and is an important reference to test the authenticity and varietal purity of other rice varieties in the future. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1987324 .
DOI: 10.6084/m9.figshare.17059748.v1
title: SSR and morphological traits based fingerprints and DNA barcodes for varietal identification in rice

description: Varietal identification has attained prime importance at a global level particularly in the context of plant variety protection. In this study, forty-six traits were characterized for the establishment of the sheer distinctness among eighteen rice varieties. Morphologically, out of forty-six traits, twenty-five traits did not display any variation among the varieties studied. Significant variations were observed for 21 traits which are relatively more informative in the identification/characterization. Distinctness, uniformity and stability-based fingerprints specific to the studied varieties were developed based on the variations. A total of 175 simple sequence repeat (SSR) markers were screened for polymorphism; 53 hypervariable polymorphic SSR markers were utilized for fingerprinting of rice varieties. A total of 151 alleles were detected in these 53 SSR markers with an amplification size ranging from 120 to 750 bp and the allelic range of 2–4. The average number of alleles observed was 2.84 per locus. The PIC values of 53 SSRs ranged from 0.03 (RM 12983) to 0.64 (RM 11449) with an average of 0.40. The generated allelic variations of 53 SSR markers for the varieties were translated into DNA barcode profiles by separating the allele size from each SSR locus. Multiplex polymerase chain reaction (PCR) with five markers (RM 21392, RM 1388, RM 6699, RM 25754 and RM 16913) was used to identify rice varieties based on the band positions. This study classifies and identifies rice varieties and is an important reference to test the authenticity and varietal purity of other rice varieties in the future. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1987324 .
DOI: 10.6084/m9.figshare.16826324
title: Uncovering ceRNA integrated networks that associate with fertility in a photoperiod and temperature sensitive male sterile wheat line

description: The pollen fertility of photoperiod/temperature sensitive genic male sterile (P/TGMS) wheat is controlled by light and/or temperature. Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in the development of anthers in plants, but their impact on male sterility in the P/TGMS line is not well understood. In this study, we carried out high-throughput sequencing to investigate the differential expression of lncRNAs and circRNAs and their biological functions in anthers of photo-thermosensitive genic male sterile (PTGMS) wheat line BS366-42L during the transition phase of male fertility under four different photoperiod and temperature treatments. Eight lncRNAs, 40 mRNAs and three circRNAs were screened out and thought as essential candidates that closely related to male sterility. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the potential functions of differentially expressed RNAs. The results indicated that carbohydrate-related metabolism was important for male sterility in the wheat PTGMS line BS366-42L. lncRNA/circRNA-mRNA-miRNA (ceRNA) integrate networks were constructed to reflect their complex inner association with male sterility. Our study provides a systematic perspective on the potential function of RNAs in male fertility in PTGMS lines of wheat.
DOI: 10.6084/m9.figshare.16826324.v2
title: Uncovering ceRNA integrated networks that associate with fertility in a photoperiod and temperature sensitive male sterile wheat line

description: The pollen fertility of photoperiod/temperature sensitive genic male sterile (P/TGMS) wheat is controlled by light and/or temperature. Circular RNA (circRNA) and long non-coding RNA (lncRNA) are known to participate in the development of anthers in plants, but their impact on male sterility in the P/TGMS line is not well understood. In this study, we carried out high-throughput sequencing to investigate the differential expression of lncRNAs and circRNAs and their biological functions in anthers of photo-thermosensitive genic male sterile (PTGMS) wheat line BS366-42L during the transition phase of male fertility under four different photoperiod and temperature treatments. Eight lncRNAs, 40 mRNAs and three circRNAs were screened out and thought as essential candidates that closely related to male sterility. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to predict the potential functions of differentially expressed RNAs. The results indicated that carbohydrate-related metabolism was important for male sterility in the wheat PTGMS line BS366-42L. lncRNA/circRNA-mRNA-miRNA (ceRNA) integrate networks were constructed to reflect their complex inner association with male sterility. Our study provides a systematic perspective on the potential function of RNAs in male fertility in PTGMS lines of wheat.