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Brassica

Brassica is a genus of plants in the mustard family, Brassicaceae, that includes several economically important crops such as broccoli, cabbage, cauliflower, kale, and Brussels sprouts.
These plants are known for their nutritional value, containing high levels of vitamins, minerals, and antioxidants.
Brassica species are widely cultivated around the world and are an integral part of many cuisines.
They have also been the subject of extensive scientific research due to their potential health benefits and diverse genetic characteristics.
The PubComapre.ai platform can help researchers streamline their Brassica studies by providing access to reliable protocols and enhancing reproducibility and accuracy.

Most cited protocols related to «Brassica»

1
Brassica Genotyping via Infinium Array
The cluster file for B. napus was generated at AAFC through analysis of 437 genotypes and at TraitGenetics through the analysis of 432 genotypes. The cluster files for B. oleracea and B. rapa were generated with 129 and 121 samples, respectively. In both laboratories, DNA was extracted from young leaf tissue of greenhouse grown plants using a cetyltrimethylammonium bromide (CTAB)-based method (Murray and Thompson 1980 (link)). DNA was quantified and 200 ng were hybridised to the Brassica 60 K Infinium array as described in the manufacturer’s protocol (Illumina Inc., San Diego, CA). The arrays were scanned using an Illumina HiScan or BeadArray Reader, and SNP data were analysed using the Genotyping module of the GenomeStudio software package with the setting for the No Call threshold set to 0.05.
Clarke W.E., Higgins E.E., Plieske J., Wieseke R., Sidebottom C., Khedikar Y., Batley J., Edwards D., Meng J., Li R., Lawley C.T., Pauquet J., Laga B., Cheung W., Iniguez-Luy F., Dyrszka E., Rae S., Stich B., Snowdon R.J., Sharpe A.G., Ganal M.W, & Parkin I.A. (2016). A high-density SNP genotyping array for Brassica napus and its ancestral diploid species based on optimised selection of single-locus markers in the allotetraploid genome. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 129(10), 1887-1899.
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Publication 2016
5-fluoro-2,2'-cyclocytidine Brassica Cetrimonium Bromide Plant Leaves Tissues
2
Metabolite Extraction from Plant Tissues
All solvents used for sample preparation and analyses were of LC/MS-grade quality (CHROMASOLV, Fluka). A list of standard compounds used for the recovery experiment including sum formulas, molar masses, PubChem IDs and suppliers can be found in the Supplemental Information S3. L-Tryptophan-2′,4′,5′,6′,7′-D5 (98%) was purchased from Cambridge Isotope Laboratories. Arabidopsis thaliana (ecotype Col-0) was grown for six weeks on a soil/vermiculite mixture (3/2) in a growth cabinet with 8 h light ( 150 μE m−2s−1) at 22°C and 16 h dark at 20°C. Seeds of Brassica napus, Brassica oleracera and Brassica rapa were kindly provided by D. Strack, Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Halle. All other seeds were obtained from local distributors. Procedures for extraction of leaf and seed material are provided in Supplemental Information S4.
Kuhl C., Tautenhahn R., Böttcher C., Larson T.R, & Neumann S. (2011). CAMERA: An integrated strategy for compound spectra extraction and annotation of LC/MS data sets. Analytical chemistry, 84(1), 283-289.
Publication 2011
11-dehydrocorticosterone Arabidopsis thalianas Brassica Brassica napus Brassica rapa Diet, Formula Ecotype Isotopes Light Molar Plant Leaves Plants Secondary Metabolism Solvents Tryptophan vermiculite
3
Annotating Brassica rapa Reference Genome
We named the newly annotated gene models following the standards of gene model nomenclature for Brassica reference genomes (http://www.brassica.info/info/genome_annotation.php): Bra (for Brassica rapa) followed by the chromosome number and letter “g” (for gene). Genes from the top to the bottom of chromosomes were assigned numbers (in steps of 10) with five digits with leading zero integers. To distinguish the genes in v3.0 from the other lines of B. rapa, the number “3” (for the third version of B. rapa reference genome) and a single capital letter “C” (for variety Chiifu-401-42) were assigned after a “.” following the gene numbers; for example, BraA05g036760.3C.
After gene prediction, gene functions were assigned according to the best match of the alignments against various protein databases using BLAST v2.2.31 (E-value = 1e-5), including the KEGG33 (link), Swiss-Prot, and TrEMBL databases34 (link). GO terms for each gene were obtained from the corresponding InterPro entries35 (link). Overall, we inferred 44,539 (96.86%) genes that were annotated based on the results from searching the protein databases (Supplementary Table S18).
Intact LTR-RTs were identified using LTR_finder36 (link) and classified the intact LTR-RTs by predicting the RT domains using the Pfam database (version 26.0) and HMMER software37 . Muscle38 (link) was then employed to perform multiple RT sequence alignments, and RAxML39 was adopted to construct maximum likelihood (ML) trees based on the sequence alignments with 500 bootstrap replications. Finally, the interactive tree of life (iTOL)40 (link) was used to plot the ML trees. The analysis of LTR insertion time was performed as previously reported4 (link).
We also performed noncoding RNA annotation for our assembly. tRNA annotation was conducted using tRNAscan-SE (v1.3.1)41 (link) according to its structural characteristics. Homology-based rRNAs were localized by mapping known full-length plant rRNAs to the B. rapa genome v3.0. snRNAs were predicted by Infenal (v1.1)42 (link) using the Rfam database43 . miRNA annotation was performed as previously described44 (link).
Zhang L., Cai X., Wu J., Liu M., Grob S., Cheng F., Liang J., Cai C., Liu Z., Liu B., Wang F., Li S., Liu F., Li X., Cheng L., Yang W., Li M.H., Grossniklaus U., Zheng H, & Wang X. (2018). Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. Horticulture Research, 5, 50.
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Publication 2018
Brassica Brassica rapa Chromosomes DNA Replication FCER2 protein, human Fingers Genes Genome MicroRNAs Operator, Genetic Plants Ribosomal RNA RNA, Untranslated Sequence Alignment Small Nuclear RNA Term Birth Transfer RNA Trees
4
Comparative Analysis of Trait-Related Genes
We performed comparative analysis of trait-related gene families. Genes from
grape, papaya and Arabidopsis were downloaded from the GenoScope database
( http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/), the
Hawaii Papaya Genome Project ( http://asgpb.mhpcc.hawaii.edu/papaya/), and the Arabidopsis
Information Resource ( http://www.arabidopsis.org/). Previously reported
Arabidopsis and Brassica gene sequences were downloaded from
TAIR ( http://www.arabidopsis.org/) and BRAD ( http://brassicadb.org/brad/).
The protein sequences of the genes were used to determine homologues in grape,
papaya, Arabidopsis, B. oleracea and B. rapa by performing
blast comparisons with an E-value 1e–10. The Clustal61 (link) programs were used for multiple sequence alignment. Alignment of
the small family of GI genes was performed using MEGA562 (link) to
conduct neighbour-joining analysis with default parameters and subjected to
careful manual checks to remove highly divergent sequences from further
analysis. While for other genes, often found in families of tens of genes, the
phylogenetic analysis were performed by PhyML63 (link), which can
accommodate quite divergent sequences by implementing a maximal likelihood
approach with initial analysis based on neighbour-joining method. During these
analyses, we constructed trees using both CDS and protein sequence, and the
protein-derived tree was used to show the phylogeny if not much incongruity was
found. Bootstrapping was performed using 100 repetitive samplings for each gene
family. All the inferred trees were displayed using MEGA5 (ref. 62 (link)). The multiple sequence alignment of these families
was provided as Supplementary Data
3.
Liu S., Liu Y., Yang X., Tong C., Edwards D., Parkin I.A., Zhao M., Ma J., Yu J., Huang S., Wang X., Wang J., Lu K., Fang Z., Bancroft I., Yang T.J., Hu Q., Wang X., Yue Z., Li H., Yang L., Wu J., Zhou Q., Wang W., King G.J., Pires J.C., Lu C., Wu Z., Sampath P., Wang Z., Guo H., Pan S., Yang L., Min J., Zhang D., Jin D., Li W., Belcram H., Tu J., Guan M., Qi C., Du D., Li J., Jiang L., Batley J., Sharpe A.G., Park B.S., Ruperao P., Cheng F., Waminal N.E., Huang Y., Dong C., Wang L., Li J., Hu Z., Zhuang M., Huang Y., Huang J., Shi J., Mei D., Liu J., Lee T.H., Wang J., Jin H., Li Z., Li X., Zhang J., Xiao L., Zhou Y., Liu Z., Liu X., Qin R., Tang X., Liu W., Wang Y., Zhang Y., Lee J., Kim H.H., Denoeud F., Xu X., Liang X., Hua W., Wang X., Wang J., Chalhoub B, & Paterson A.H. (2014). The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications, 5, 3930.
Publication 2014
Amino Acid Sequence Arabidopsis Brassica Carica papaya Genes Genome Grapes Sequence Alignment Toxic Epidermal Necrolysis Trees Vitis
5
Genome Assembly and Validation of Brassica oleracea
We took a series of checking and filtering measures on reads following the
Illumina-Pipeline, and low-quality reads, adaptor sequences and duplicates were
removed (Supplementary Methods).
The reads after the above filtering and correction steps were used to perform
assembly including contig construction, scaffold construction and gap filling
using SOAPdenovo1.04 ( http://soap.genomics.org.cn/) (Supplementary Methods). Finally, we used
20-kb-span paired-end data generated from the 454 platform and 105-kb-span
BAC-end data downloaded from NCBI ( http://www.ncbi.nlm.nih.gov/nucgss?term=BOT01) to extend scaffold
length (Supplementary Methods). The
B. oleracea genome size was estimated using the distribution curve of
17-mer frequency (Supplementary
Methods).
To anchor the assembled scaffolds onto pseudo-chromosomes, we developed a genetic
map using a double haploid population with 165 lines derived from a F1 cross
between two homozygous lines 02–12 (sequenced) and 0188
(re-sequenced). The genetic map contains 1,227 simple sequence repeat markers
and single nucleotide polymorphism markers in nine linkage groups, which span a
total of 1,180.2 cM with an average of 0.96 cM between the
adjacent loci16 (link). To position these markers to the scaffolds,
marker primers were compared with the scaffold sequences using e-PCR (parameters
-n2 -g1 –d 400–800), with the best-scoring match chosen in
case of multiple matches.
We validated the B. oleracea genome assembly by comparing it with the
published physical map constructed using 73,728 BAC clones ( http://lulu.pgml.uga.edu/fpc/WebAGCoL/brassica/WebFPC/)17 (link) and a genetic map from B. napus18 (link) (Supplementary Methods). Eleven
Sanger-sequenced B. oleracea BAC sequences were used to assess the
assembled genome using MUMmer-3.22 ( http://mummer.sourceforge.net/) (Supplementary Methods).
Liu S., Liu Y., Yang X., Tong C., Edwards D., Parkin I.A., Zhao M., Ma J., Yu J., Huang S., Wang X., Wang J., Lu K., Fang Z., Bancroft I., Yang T.J., Hu Q., Wang X., Yue Z., Li H., Yang L., Wu J., Zhou Q., Wang W., King G.J., Pires J.C., Lu C., Wu Z., Sampath P., Wang Z., Guo H., Pan S., Yang L., Min J., Zhang D., Jin D., Li W., Belcram H., Tu J., Guan M., Qi C., Du D., Li J., Jiang L., Batley J., Sharpe A.G., Park B.S., Ruperao P., Cheng F., Waminal N.E., Huang Y., Dong C., Wang L., Li J., Hu Z., Zhuang M., Huang Y., Huang J., Shi J., Mei D., Liu J., Lee T.H., Wang J., Jin H., Li Z., Li X., Zhang J., Xiao L., Zhou Y., Liu Z., Liu X., Qin R., Tang X., Liu W., Wang Y., Zhang Y., Lee J., Kim H.H., Denoeud F., Xu X., Liang X., Hua W., Wang X., Wang J., Chalhoub B, & Paterson A.H. (2014). The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nature Communications, 5, 3930.
Publication 2014
Brassica Chromosome Mapping Chromosomes Clone Cells Genome Homozygote Oligonucleotide Primers Physical Examination Short Tandem Repeat Single Nucleotide Polymorphism

Most recents protocols related to «Brassica»

1
Brassica Seed Coat Transcriptome Analysis
Transcriptome data of all eight periods of seed coat development of six Brassica species were used to analyze the expression patterns and trends of TT2 and MYB5. The R package ggplot2 (v3.3.6) was used to draw the expression pattern of TT2 and MYB5, and R package ggridges (v0.5.3) was used to draw the expression trends of TT2 and MYB5.
Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.
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Publication 2023
Brassica Transcriptome
2
Transcriptome Analysis of Brassica Seed Development
The raw data of 144 seed coats RNA-seq data of six Brassica species, B. rapa (Parkland-R), B. oleracea (Chinese Kale-O), B. nigra (CR2748-N), B. napus (DH12075-P), B. juncea (AC Vulcan-J), B. carinata (C901163-C) with eight developmental stages (Unfertilized ovule integuments (UO; no embryo), 1- to 2-cell zygote stage (S1), 4- to 8-cell stage (S2, 8-cell stage shown), 16- to 64-cell stage (S3, globular stage shown), heart stage(S4), torpedo stage(S5), bent stage(S6), and mature (S7) stage of seed formation) were collected from Gene Expression Omnibus under accession no. GSE153257. Low-quality reads were removed from the raw reads using Cutadapt and Trimmomatic software to get clean reads [39 , 2 ]. Clean reads were mapped to the corresponding reference genome using HISAT2 software [51 (link)]. Gene expression levels of each gene were calculated using StringTie and Ballgown software [51 (link)]. The read counts of each gene were calculated using the htseq-count function in htseq software [1 (link)]. The R package DEseq2 (v1.16.1) was used to identify the differentially expressed genes (DEGs) between leaves of different colors based on the following criteria: padj < 0.05 & log2FoldChange > 2 [5 (link)].
Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.
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Publication 2023
Brassica Cells Chinese Embryo Eye Gene Expression Genes Heart Kale Ovule RNA-Seq Substantia Nigra System, Integumentary Torpedo Zygote
3
Mapping and Collinearity Analysis of Anthocyanin Genes in Arabidopsis and Brassica
The genome annotation data were collected and mapped on the chromosomes using the TBtools software (v0.67) to identify the physical chromosomal location of all anthocyanin-related genes in Arabidopsis and six Brassica species [4 ]. The collinearity of intraspecific and interspecific genes was determined using the BLASTP (E-value: 1e-10, max_target_seqs:1) and Multiple Collinearity Scan toolkit (MCSscanX, gap_penalty: -1, E-value: 1e-10) [71 (link)], SynOrths software (E-value < 1e-20, Query gene = 20, Reference gene = 100) has been used to determining the collinear orthologous [8 (link)], TBtools software (v0.67) was used to drop the collinearity genes on each chromosome [4 ].
Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.
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Publication 2023
Anthocyanins Arabidopsis Base Sequence Brassica Chromosomes Colinearity, Chromosomal Genes Genome Physical Examination Radionuclide Imaging
4
Identification of Brassica Anthocyanin Genes
In this study, the genome and protein sequences of the B. rapa (Chiifu-401–42 v3.0), B. oleracea (HDEM), B. nigra (Ni100-LR), B. napus (Darmor-bzh v10) were downloaded from the BRAD database [7 ]; http://brassicadb.cn), B. juncea (SCYZ) genome sequence from NCBI PRJNA615316 [22 ] (https://www.ncbi.nlm.nih.gov/), B. carinata (zd-1) genome sequence from GenBank JAAMPC000000000 [66 ] (https://www.ncbi.nlm.nih.gov/), and the anthocyanin-related genes genome and protein sequences were downloaded from the Arabidopsis database (TAIR; http://www.arabidopsis.org/index.jsp). In order to accurately identify anthocyanin-related genes, we mainly divide it into the following steps: Firstly, local BLASTP has been used to search anthocyanin-related genes with E-value < 1e-20, 55 anthocyanin-related genes protein sequences were derived from Arabidopsis. Secondly, the candidate anthocyanin-related genes in the six Brassica species were identified by a local BLASTN search with 55 anthocyanin-related genes coding sequence from Arabidopsis to identify candidates with E-value < 1e-20, identity > 70%, coverage > 60%. Thirdly, SynOrths software [8 (link)] has been used to determining the collinear orthologous of two genes based on their own sequence similarity and the homology of their flanking genes, and then extracting the colinear genes of anthocyanin-related genes. Finally, the BLASTP, BLASTN and SynOrths software identified results were pooled and deduplicated, and determined in conjunction with PFAM protein family database (https://pfam.xfam.org/).
Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.
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Publication 2023
Amino Acid Sequence Anthocyanins Arabidopsis Base Sequence Brassica Genes Genome Open Reading Frames Substantia Nigra
5
Comparative Analysis of TT2 and MYB5 in Brassica
The TT2 and MYB5 protein sequences of the six Brassica species and Arabidopsis were used to generate phylogenetic trees via ClustalX [26 (link)] and MAFFT sofaware (Katoh and Standley, 2013) multiple sequence alignments with the default parameters. A maximum likelihood (ML) phylogenetic tree was constructed using FastTree2 software (v2.1.11), in which JTT (Jones-Taylor-Thornton) model was the best substitution model [52 (link)]. The TT2 and MYB5 promoter regions of 2000 bp regions upstream of the translational start sites ATG were examined based on their positions in the genomes of six Brassica species and Arabidopsis using Samtools software (v 1.8), which was used to identify the cis-elements in the promoters according to the online PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/). The gene structures of TT2 and MYB5 were analyzed according to the GFF annotation file of the gene position information in the six Brassica crops and Arabidopsis database. The MEME online tool (https://meme-suite.org/meme/) was used to investigate conserved domains, and the WEBLoGo online tool (https://weblogo.berkeley.edu/) and SWISS-MODEL online tool (https://swissmodel.expasy.org/) was used to draw spatial structure. TBtools software (v0.67) was used to draw the TT2 and MYB5 to the different copies of each Brassica species, including phylogenetic, promoter characteristics, gene structure, conserved motifs [4 ].
Chen D., Chen H., Dai G., Zhang H., Liu Y., Shen W., Zhu B., Cui C, & Tan C. (2023). Genome-wide identification and expression analysis of the anthocyanin-related genes during seed coat development in six Brassica species. BMC Genomics, 24, 103.
Full text: Click here
Publication 2023
Amino Acid Sequence Arabidopsis Brassica Crop, Avian Gene Order Genes Genetic Structures Genome Protein Biosynthesis Sequence Alignment

Top products related to «Brassica»

1
Brassica 60k infinium snp array by Illumina
Sourced in United States, Germany
The Brassica 60K Illumina Infinium SNP array is a high-throughput genotyping platform designed for the analysis of single nucleotide polymorphisms (SNPs) in Brassica species. It provides a comprehensive and efficient tool for genome-wide genetic analysis, enabling researchers to explore genetic diversity, identify markers associated with traits of interest, and conduct genomic studies.
2
Beadstudio genotyping software by Illumina
BeadStudio genotyping software is a data analysis application designed for use with Illumina's microarray and sequencing platforms. It provides tools for processing, analyzing, and visualizing genomic data generated from these technologies.
3
Hiseq 2000 by Illumina
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The HiSeq 2000 is a high-throughput DNA sequencing system designed by Illumina. It utilizes sequencing-by-synthesis technology to generate large volumes of sequence data. The HiSeq 2000 is capable of producing up to 600 gigabases of sequence data per run.
4
Infinium brassica 60 k snp array by Illumina
The Infinium Brassica 60 K SNP array is a high-density genotyping microarray designed for the analysis of genetic variation in Brassica species. The array contains probes targeting approximately 60,000 single nucleotide polymorphisms (SNPs) distributed across the Brassica genome. This tool enables researchers to perform comprehensive genome-wide association studies, genetic diversity analyses, and marker-assisted breeding applications in Brassica crops.
5
Primescript rt reagent kit by Takara Bio
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The PrimeScript RT reagent kit is a reverse transcription kit designed for the synthesis of first-strand cDNA from RNA templates. The kit includes RNase-free reagents and enzymes necessary for the reverse transcription process.
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TRIzol is a monophasic solution of phenol and guanidine isothiocyanate that is used for the isolation of total RNA from various biological samples. It is a reagent designed to facilitate the disruption of cells and the subsequent isolation of RNA.
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GenomeStudio v2011.1 is a data analysis software developed by Illumina for processing and analyzing data generated from Illumina's microarray platforms. The software provides a suite of tools for data visualization, quality control, and downstream analysis.
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Gallic acid is a naturally occurring organic compound that can be used as a laboratory reagent. It is a white to light tan crystalline solid with the chemical formula C6H2(OH)3COOH. Gallic acid is commonly used in various analytical and research applications.
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The PMD18-T vector is a plasmid used for cloning and maintaining DNA sequences in Escherichia coli. It contains a multiple cloning site for inserting target DNA, an ampicillin resistance gene for selection, and a pUC origin of replication for high-copy number propagation in bacteria.

More about "Brassica"

Brassica is a diverse genus of plants within the mustard family, Brassicaceae, which encompasses several economically important crops like broccoli, cabbage, cauliflower, kale, and Brussels sprouts.
These nutrient-dense plants are known for their high levels of vitamins, minerals, and antioxidants, making them an integral part of many cuisines around the world.
Brassica species have been the subject of extensive scientific research due to their potential health benefits and diverse genetic characteristics.
Researchers leveraging tools like the Brassica 60K Illumina Infinium SNP array, BeadStudio genotyping software, and HiSeq 2000 platforms have delved deeper into the genomics and molecular biology of these crops.
The Infinium Brassica 60 K SNP array, PrimeScript RT reagent kit, and TRIzol have become essential tools in Brassica research, enabling scientists to analyze genetic variation, gene expression, and other crucial aspects of these plants.
Complementary software like GenomeStudio v2011.1 and the PubCompare.ai platform have further streamlined data analysis and protocol optimization, enhancing the reproducibility and accuracy of Brassica studies.
Compounds like Gallic acid, found in Brassica species, have also garnered attention for their potential health benefits and their role in the plants' defense mechanisms.
Researchers can leverage the PubCompare.ai tool to effortlessly locate the most reliable protocols and products, such as the PMD18-T vector, to study these compounds and their impact on Brassica plants.
By harnessing the power of these cutting-edge technologies and resources, scientists can delve deeper into the diverse world of Brassica, unlocking new insights and driving breakthroughs in agriculture, nutrition, and beyond.