cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.22140541
title: Genome-wide <i>in silico</i> and <i>in vitro</i> mining to develop a novel cyclotide-based marker system in plants

description: Cyclotides are cysteine-rich cyclic peptides that have various activities and applications. Mining at the whole-genome scale facilitates the profiling and development of cyclotide-based markers. However, the characterization of cyclotide subfamilies at a genome-scale in plants is an untapped area that needs more studies. Here we developed four degenerate cyclotide subfamily-specific (CSS) markers based on their subfamily’s semi-conserved sequence for identifying each subfamily separately. Initially, an <i>in silico</i> cyclotide mining analysis was performed on 15 plant genomes/transcriptomes. The <i>in silico</i> PCR produced 476 amplicons in the Bracelet, Moebius, Hybrid and Trypsin Inhibitor (TI) subfamilies. <i>In silico</i> profiling results identified 903 cyclotide mature domains (CMDs) in the analyzed genomes/transcriptomes for the four subfamilies. In addition, the prevalence of each subfamily correlated positively with the genome size, particularly in Hybrid, followed by TI and Bracelet subfamilies. The CSS markers were validated <i>in vitro</i> on 19 genotypes/cultivars. The CSS markers generated a total of 175 bands, with a polymorphic percentage of 98%–100%. Cluster analysis showed distinct clusters for cultivars/genotypes of each plant species. The marker efficiency parameters demonstrated the capability of CSS markers to determine the genetic diversity among the studied plant species. This study represents the first report to perform genome/transcriptome-wide mining to characterize the Cyclotide subfamilies in plants. This study proposed potential applications of the novel CSS markers as an effective system for screening cyclotide subfamilies across multiple plant species with no prior sequencing knowledge requirement. Additionally, it proposes an innovative approach for identifying the appropriate cyclotide subfamily used in drug design.
DOI: 10.6084/m9.figshare.22140541.v1
title: Genome-wide <i>in silico</i> and <i>in vitro</i> mining to develop a novel cyclotide-based marker system in plants

description: Cyclotides are cysteine-rich cyclic peptides that have various activities and applications. Mining at the whole-genome scale facilitates the profiling and development of cyclotide-based markers. However, the characterization of cyclotide subfamilies at a genome-scale in plants is an untapped area that needs more studies. Here we developed four degenerate cyclotide subfamily-specific (CSS) markers based on their subfamily’s semi-conserved sequence for identifying each subfamily separately. Initially, an <i>in silico</i> cyclotide mining analysis was performed on 15 plant genomes/transcriptomes. The <i>in silico</i> PCR produced 476 amplicons in the Bracelet, Moebius, Hybrid and Trypsin Inhibitor (TI) subfamilies. <i>In silico</i> profiling results identified 903 cyclotide mature domains (CMDs) in the analyzed genomes/transcriptomes for the four subfamilies. In addition, the prevalence of each subfamily correlated positively with the genome size, particularly in Hybrid, followed by TI and Bracelet subfamilies. The CSS markers were validated <i>in vitro</i> on 19 genotypes/cultivars. The CSS markers generated a total of 175 bands, with a polymorphic percentage of 98%–100%. Cluster analysis showed distinct clusters for cultivars/genotypes of each plant species. The marker efficiency parameters demonstrated the capability of CSS markers to determine the genetic diversity among the studied plant species. This study represents the first report to perform genome/transcriptome-wide mining to characterize the Cyclotide subfamilies in plants. This study proposed potential applications of the novel CSS markers as an effective system for screening cyclotide subfamilies across multiple plant species with no prior sequencing knowledge requirement. Additionally, it proposes an innovative approach for identifying the appropriate cyclotide subfamily used in drug design.
DOI: 10.6084/m9.figshare.22769239
title: Structural implications of SARS-CoV-2 Surface Glycoprotein N501Y mutation within receptor-binding domain [499-505] – computational analysis of the most frequent Asn501 polar uncharged amino acid mutations

description: The aim of this study was to evaluate the impact of the most frequent Asn501 polar uncharged amino acid mutations upon important structural properties of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) Surface Glycoprotein RBD – hACE2 (human angiotensin-converting enzyme 2) heterodimer. Mutations N501Y, N501T and N501S were considered and their impact upon complex solubility, secondary motifs formation and intermolecular hydrogen bonding interface was analyzed. Results and findings are reported based on 50 ns run in Gromacs molecular dynamics simulation software. Special attention is paid on the biomechanical shifts in the receptor-binding domain (RBD) [499-505]: ProThrAsn(Tyr)GlyValGlyTyr, having substituted Asparagine to Tyrosine at position 501. The main findings indicate that the N501S mutation increases SARS-CoV-2 S-protein RBD – hACE2 solubility over N501T, N501 (wild type): SASAN501S=364.66±3.2842 nm2, SASAN501T=360±3.4156 nm2, SASAN501=359.56±3.6473 nm2. The N501Y mutation shifts α-helix S-protein RBD [366-370]: SerValLeuTyrAsn into π-helix for <i>t</i> &gt; 38.5 ns. An S-protein RBD [503-505]: ValGlyTyr shift from 310-helix into a turn is observed due to the N501Y mutation in <i>t</i> &gt; 33 ns. An empirical proof for the presence of a Y501-binding pocket, based on RBD [499-505]: PTYGVGY Cα’s RMSF peak formation is presented. There is enhanced electrostatic interaction between Tyr505 (RBD) phenolic -OH group and Glu37 (hACE2) side chain oxygen atoms due to the N501Y mutation. The N501Y mutation shifts the Gly502S-ProteinN-H…O=CLys353hACE2 hydrogen bond into permanent polar contact; E(Gly502S-ProteinN-H…O=CLys353hACE2)N501Y=4.816210332kcal/mol; E(Gly502S-ProteinN-H…O=CLys353hACE2)N501=3.909532232kcal/mol.
DOI: 10.6084/m9.figshare.23936019
title: <i>In silico</i> analysis of Hsp70 genes in <i>Ctenopharyngodon idella</i> and their expression profiles in response to environmental stresses

description: Heat shock protein 70 (Hsp70) is a crucial member of the Hsp family, which is present in many animals, and acts as a chaperone to protect the organism from damage caused by various environmental stresses, particularly unfavorable temperatures. In this study, we used homologous gene search and domain analysis to identify sixteen Hsp70 genes (named as CiHSP genes) from the genome of grass carp (<i>Ctenopharyngodon idella</i>). These genes were classified into ten subfamilies based on their conserved structures and phylogenetic analysis. To investigate the biological functions of CiHSP genes in grass carp, we analyzed public RNA-Seq data, and found that most members of the CiHSP gene family were highly expressed in the brain and kidney, suggesting potential roles in protecting brain cells and participating in fish immunological processes. Additionally, these CiHSP genes were characterized as responding to high density and high temperature stress, with most members significantly upregulated under high temperature conditions. These findings demonstrate the critical roles of CiHSP genes in grass carp development and their response to environmental stress, which will provide valuable insights for determining their function and potential application in fish production in the future.
DOI: 10.6084/m9.figshare.23936019.v1
title: <i>In silico</i> analysis of Hsp70 genes in <i>Ctenopharyngodon idella</i> and their expression profiles in response to environmental stresses

description: Heat shock protein 70 (Hsp70) is a crucial member of the Hsp family, which is present in many animals, and acts as a chaperone to protect the organism from damage caused by various environmental stresses, particularly unfavorable temperatures. In this study, we used homologous gene search and domain analysis to identify sixteen Hsp70 genes (named as CiHSP genes) from the genome of grass carp (<i>Ctenopharyngodon idella</i>). These genes were classified into ten subfamilies based on their conserved structures and phylogenetic analysis. To investigate the biological functions of CiHSP genes in grass carp, we analyzed public RNA-Seq data, and found that most members of the CiHSP gene family were highly expressed in the brain and kidney, suggesting potential roles in protecting brain cells and participating in fish immunological processes. Additionally, these CiHSP genes were characterized as responding to high density and high temperature stress, with most members significantly upregulated under high temperature conditions. These findings demonstrate the critical roles of CiHSP genes in grass carp development and their response to environmental stress, which will provide valuable insights for determining their function and potential application in fish production in the future.
DOI: 10.6084/m9.figshare.24781458.v1
title: Identification of QTL controlling the ratio of linalool to linalyl acetate in the flowers of <i>Lavandula angustifolia</i> Mill var. Hemus

description: The content of linalyl acetate and the ratio of linalool to linalyl acetate (L/LA ratio) are one of the important parameters that determine the quality of lavender oil. The characterization of a segregating population derived from a self-pollinated <i>Lavandula angustifolia</i> var. Hemus resulted in the identification of a single quantitative trait locus controlling the L/LA ratio (L/LA-QTL) and located on chromosome 8 of the lavender reference genome. The L/LA data analysis demonstrated that plants homozygous for one of the L/LA-QTL alleles had significantly higher linalool content, lower linalyl acetate content and higher L/LA ratio, than the plants which were either heterozygous or homozygous for the other allele. No significant difference was observed for the sum of linalool and linalyl acetate content among these three groups of plants, suggesting that the identified L/LA-QTL is related to an enzyme conversion of linalool to linalyl acetate. The BLAST search revealed that the L/LA-QTL region included a sequence of the <i>LiAAT4</i> gene of monoterpene acetyltransferase, considered as a candidate gene for the L/LA-QTL locus. Sequence analysis of the <i>LiAAT4</i> gene of var. Hemus revealed the presence of two alleles differing in two nucleotides and predicted amino acid substitutions. The comparison of the allele configurations of SSR, SRAP and <i>LiAAT4</i> loci and the L/LA ratio of plants showing recombination in the L/LA-QTL region provided further support that <i>LiAAT4</i> is a candidate gene underlying the identified L/LA-QTL and controlling the L/LA ratio. The application of molecular markers for the identified L/LA-QTL is discussed.
DOI: 10.6084/m9.figshare.21842063
title: Systematic identification and characterization of the soybean (<i>Glycine max</i>) B-box transcription factor family

description: In plants, the B-box (BBX) transcription factors (TFs) are a subfamily of zinc-finger TFs that act to regulate diverse plant growth and development processes. The BBX TFs have been the subject of considerable attention, and are well characterized in diverse plant species, including in rice (<i>Oryza sativa</i>) and <i>Arabidopsis thaliana</i>, but less so in the economically important soybean (<i>Glycine max</i>). In this work, we systematically identified and characterized 57 soybean BBX genes (<i>GmBBX1</i> to <i>GmBBX57</i>). These genes were mapped to all 20 soybean chromosomes and were divided into five clades with high intra-clade intron–exon similarity. The majority of <i>GmBBX</i> gene promoter <i>cis</i>-acting elements were responsive to light, abscisic acid, salicylic acid and methyl jasmonate, as well as a diverse array of other stimuli. Quantitative RT-PCR indicated that several <i>GmBBX</i> genes exhibited tissue-specific and phytohormone- and abiotic stress-responsiveness. The results of this study will be useful in the continued characterization of soybean BBX gene functions and provide new ideas for soybean breeding.
DOI: 10.6084/m9.figshare.21842122
title: Incidence of ancient variants associated with oncological diseases in modern populations

description: Publicly available genome-wide data, sequenced from 2730 ancient human samples were analyzed for genetic predisposition to malignancy. The temporal and spatial incidence of risk variants for cancer diseases in ancient genomes was recorded, allowing for estimates of their frequencies in ancient human communities. We identified 55 risk alleles associated with oncological conditions in the screened ancient samples. For further analysis, we selected three variants conclusively deemed to entail pathogenic effect, the <i>VHL</i> gene’s rs28940298, the <i>TP53</i> gene’s rs78378222 and the <i>BRCA2</i> gene’s rs11571833. The contemporary population frequency of these three variants is lower, or similar, to their estimated frequency in ancient human communities, indicating that they might have been subject to negative selection. This is also suggested by their temporal dynamics during the last 10000 years, which show an overall temporal decrease in population frequency. The oldest samples in which these three variants were established testify their ancient origin, including the presence of <i>TP53</i> gene’s rs78378222 variant in 50000 BP old Neanderthal and Denisovan genomes. Our results demonstrate the presence of cancer-causing mutations in ancient human communities and suggest that they differed in frequency among ancient populations as they do among contemporary ones. Data on germline mutations in tumour suppressor genes in ancient human genomes are scarce and their historic prevalence gives insights into the evolution of predisposition to cancer disease and hence helps advance paleogenomic medicine.
DOI: 10.6084/m9.figshare.21842122.v1
title: Incidence of ancient variants associated with oncological diseases in modern populations

description: Publicly available genome-wide data, sequenced from 2730 ancient human samples were analyzed for genetic predisposition to malignancy. The temporal and spatial incidence of risk variants for cancer diseases in ancient genomes was recorded, allowing for estimates of their frequencies in ancient human communities. We identified 55 risk alleles associated with oncological conditions in the screened ancient samples. For further analysis, we selected three variants conclusively deemed to entail pathogenic effect, the <i>VHL</i> gene’s rs28940298, the <i>TP53</i> gene’s rs78378222 and the <i>BRCA2</i> gene’s rs11571833. The contemporary population frequency of these three variants is lower, or similar, to their estimated frequency in ancient human communities, indicating that they might have been subject to negative selection. This is also suggested by their temporal dynamics during the last 10000 years, which show an overall temporal decrease in population frequency. The oldest samples in which these three variants were established testify their ancient origin, including the presence of <i>TP53</i> gene’s rs78378222 variant in 50000 BP old Neanderthal and Denisovan genomes. Our results demonstrate the presence of cancer-causing mutations in ancient human communities and suggest that they differed in frequency among ancient populations as they do among contemporary ones. Data on germline mutations in tumour suppressor genes in ancient human genomes are scarce and their historic prevalence gives insights into the evolution of predisposition to cancer disease and hence helps advance paleogenomic medicine.
DOI: 10.6084/m9.figshare.23633793.v1
title: Oligo-dT anchored cDNA-SRAP and cDNA-SCoT aided identification of transcripts differentially expressed during the early stages of recovery of resurrection plant <i>Haberlea rhodopensis</i> Friv. from freezing-induced desiccation

description: Resurrection plants are a unique group of flora showing an extraordinary ability to survive extreme water shortages. Among them, the Bulgarian endemic plant <i>Haberlea rhodopensis</i> Friv. has been used as a model to study the mechanisms underlying desiccation tolerance induced by water and low temperature stress. Although extensive transcriptome data, including two RNAseq experiments, are available for drought induced desiccation and recovery, the gene expression during recovery after freezing-induced desiccation (RAF) remains largely unexplored. In this study we performed a differential screening using a new approach, based on oligo-dT anchored cDNA-SRAP (copy DNA sequence-related amplified polymorphism) and a modified oligo-dT anchored cDNA-SCoT (copy DNA start codon targeted) assays to provide new information on genes involved in the tolerance to low temperature stress and the recovery of <i>H. rhodopensis</i>. The putative functions of 19 identified transcript derived fragments were established by searching for homology with known sequences in public databases and the expression of 10 of them during the early stages of recovery was confirmed by quantitative reverse transcription polymerase chain reaction. Some of the identified genes have known functions in the response to abiotic stress in other plant species including resurrection plants, which confirms the effectiveness of the approach used in the present study. The results of this study will contribute to obtaining new information on the defence mechanisms in the recovery process of <i>H. rhodopensis</i>, especially at the early stages of recovery, which is the most vulnerable period for plants.
DOI: 10.6084/m9.figshare.24781458
title: Identification of QTL controlling the ratio of linalool to linalyl acetate in the flowers of <i>Lavandula angustifolia</i> Mill var. Hemus

description: The content of linalyl acetate and the ratio of linalool to linalyl acetate (L/LA ratio) are one of the important parameters that determine the quality of lavender oil. The characterization of a segregating population derived from a self-pollinated <i>Lavandula angustifolia</i> var. Hemus resulted in the identification of a single quantitative trait locus controlling the L/LA ratio (L/LA-QTL) and located on chromosome 8 of the lavender reference genome. The L/LA data analysis demonstrated that plants homozygous for one of the L/LA-QTL alleles had significantly higher linalool content, lower linalyl acetate content and higher L/LA ratio, than the plants which were either heterozygous or homozygous for the other allele. No significant difference was observed for the sum of linalool and linalyl acetate content among these three groups of plants, suggesting that the identified L/LA-QTL is related to an enzyme conversion of linalool to linalyl acetate. The BLAST search revealed that the L/LA-QTL region included a sequence of the <i>LiAAT4</i> gene of monoterpene acetyltransferase, considered as a candidate gene for the L/LA-QTL locus. Sequence analysis of the <i>LiAAT4</i> gene of var. Hemus revealed the presence of two alleles differing in two nucleotides and predicted amino acid substitutions. The comparison of the allele configurations of SSR, SRAP and <i>LiAAT4</i> loci and the L/LA ratio of plants showing recombination in the L/LA-QTL region provided further support that <i>LiAAT4</i> is a candidate gene underlying the identified L/LA-QTL and controlling the L/LA ratio. The application of molecular markers for the identified L/LA-QTL is discussed.
DOI: 10.6084/m9.figshare.21792466
title: QTL for yield per plant under water deficit and well-watered conditions and drought susceptibility index in soybean (<i>Glycine max</i> (L.) Merr.)

description: Drought has historically represented the greatest abiotic stress to adversely affect the stability of soybean (<i>Glycine max</i> (L.) Merr.) yields in non-irrigated field conditions. To investigate the genetic basis underlying drought tolerance in soybean, we screened the seed yield per plant (YP) in a natural diversity panel of 149 accessions under both water deficit (drought-stressed; YP-S) and well-watered (full irrigation; YP-W) conditions in field and greenhouse trials and calculated a drought susceptibility index (DSI) based on the differences in yield between treatments within each accession. A total of 19 quantitative trait loci (QTLs) were identified: eight were significantly associated with YP-W, 10 were associated with YP-S, 2 were associated with DSI and one QTL was associated with both YP-S and DSI. We then compared QTLs identified here with previously reported markers and found that these loci were located in regions associated with yield-related and other agronomic traits. In particular, YP-S-associated single nucleotide polymorphism (SNP) ss246509299 in chromosome (Chr.) 8, and YP-W-associated ss249310678 on Chr. 17 were both previously correlated with canopy wilt. Eight significant QTLs were located within eight genes. <i>Glyma.18g092200</i>, contained ss249600231 and annotated as <i>GmWRKY168</i>, is reportedly responsive to cadmium. This study helps to resolve which loci contribute to yield under drought stress in soybean, and can potentially serve as markers for selection of elite, high-yield and drought tolerant varieties.
DOI: 10.6084/m9.figshare.21792466.v1
title: QTL for yield per plant under water deficit and well-watered conditions and drought susceptibility index in soybean (<i>Glycine max</i> (L.) Merr.)

description: Drought has historically represented the greatest abiotic stress to adversely affect the stability of soybean (<i>Glycine max</i> (L.) Merr.) yields in non-irrigated field conditions. To investigate the genetic basis underlying drought tolerance in soybean, we screened the seed yield per plant (YP) in a natural diversity panel of 149 accessions under both water deficit (drought-stressed; YP-S) and well-watered (full irrigation; YP-W) conditions in field and greenhouse trials and calculated a drought susceptibility index (DSI) based on the differences in yield between treatments within each accession. A total of 19 quantitative trait loci (QTLs) were identified: eight were significantly associated with YP-W, 10 were associated with YP-S, 2 were associated with DSI and one QTL was associated with both YP-S and DSI. We then compared QTLs identified here with previously reported markers and found that these loci were located in regions associated with yield-related and other agronomic traits. In particular, YP-S-associated single nucleotide polymorphism (SNP) ss246509299 in chromosome (Chr.) 8, and YP-W-associated ss249310678 on Chr. 17 were both previously correlated with canopy wilt. Eight significant QTLs were located within eight genes. <i>Glyma.18g092200</i>, contained ss249600231 and annotated as <i>GmWRKY168</i>, is reportedly responsive to cadmium. This study helps to resolve which loci contribute to yield under drought stress in soybean, and can potentially serve as markers for selection of elite, high-yield and drought tolerant varieties.