Euchromatic regions of the dm3/BDGP release 5 Drosophila melanogaster genome were indexed as in Iseli et al. (2007) (link). PHP code was developed to (1) parse user-inputted DNA sequence to detect CRISPR targets on both strands, (2) execute fetchGWI (Iseli et al. 2007 (link)) to identify similar sequences elsewhere in the genome, (3) employ algorithms based on empirical rules and user-selected parameters to identify potential off-target cleavage sites, and (4) return CRISPR target sites ranked by specificity along with location information and a Gbrowse link for each potential off-target site. The following invertebrate genomes were processed identically: D. simulans (annotation DroSim1), D. yakuba (DroYak2), D. sechellia (DroSec1), D. virilis (DroVir3), two strains of Anopheles gambiae (AgamM1 and AgamS1), Aedes aegypti (AaegL1), Apis mellifera (apiMel3), Tribolium castaneum (TriCas2), and Caenorhabditis elegans (ce10). A detailed user manual is available at http://tools.flycrispr.molbio.wisc.edu/targetFinder/CRISPRTargetFinderManual.pdf .
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Tribolium, monocots
Tribolium, monocots
Tribolium, also known as the red flour beetle, is a genus of beetles in the family Tenebrionidae.
These insects are commonly used as model organisms in biological research, particularly in the study of genetics and developmental biology.
Tribolium species are known for their role in food spoilage, as they can infest stored grains and flour.
Monocots, or monocotyledonous plants, are a group of flowering plants characterized by their single seed leaf (cotyledon) and the arrangement of their vascular bundles.
This diverse group includes many economically important crops such as grasses, cereals, and some ornamental plants.
Monocots are distinct from dicots, which have two seed leaves and a different vascular bundle arrangement.
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These insects are commonly used as model organisms in biological research, particularly in the study of genetics and developmental biology.
Tribolium species are known for their role in food spoilage, as they can infest stored grains and flour.
Monocots, or monocotyledonous plants, are a group of flowering plants characterized by their single seed leaf (cotyledon) and the arrangement of their vascular bundles.
This diverse group includes many economically important crops such as grasses, cereals, and some ornamental plants.
Monocots are distinct from dicots, which have two seed leaves and a different vascular bundle arrangement.
PubCompare.ai is an innovative AI-driven platform that enhances reproducibility and research accuracy by facilitating comparative analysis of scientific protocols from literature, preprints, and patents.
This tool can help researchers identify the best protocols and products, streamlining the research process and improving the quality of their findings.
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Most cited protocols related to «Tribolium, monocots»
Aedes
Anopheles gambiae
Apis
Caenorhabditis elegans
Clustered Regularly Interspaced Short Palindromic Repeats
Cytokinesis
Drosophila melanogaster
Drosophila simulans
Genome
Invertebrates
Strains
Tribolium, monocots
In HomeoDB2, we used genome sequence data of Homo sapiens Build 37.2 (GRCh37.p2), Mus musculus Build 37.1 (C57BL/6J), Gallus gallus Build 2.1 (Gallus_gallus-2.1), Danio rerio (Zv9), Xenopus (Silurana) tropicalis Build 1.1 (v4.2), Drosophila melanogaster (Release 5.30), Tribolium castaneum (Tcas_3.0), and Apis mellifera (Amel_4.5) from NCBI FTP server (ftp://ftp.ncbi.nih.gov/genomes/ ); Caenorhabditis elegans (WS220) from WormBase (http://www.wormbase.org/ ); Branchiostoma floridae (v2.0) from JGI (http://genome.jgi-psf.org/Brafl1/Brafl1.home.html ). Sequence searches and locus identification followed Zhong and Holland (2011 (link)). The HomeoReg dataset was collected from the literature; models of hybridization were edited from results of RNAhybrid (Rehmsmeier et al. 2004). HomeoDB2 was recoded through an Apache+Perl+MySQL web application technology base on Model-View-Controller design pattern.
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Apis
Branchiostoma floridae
Caenorhabditis elegans
Chickens
Crossbreeding
Drosophila melanogaster
Genome
Genome, Human
Mice, House
Tribolium, monocots
Xenopus
Zebrafish
We reconstructed the complete collection of phylogenetic trees, also known as the Phylome, for all A. pisum protein-coding genes with homologs in other sequenced insect genomes. For this we used a similar automated pipeline to that described earlier for the human genome [43] (link). A database was created containing the pea aphid proteome and that of 16 other species. These include 12 other insects (Tribolium castaneum, Nasonia vitripennis, Apis mellifera [from NCBI database], Drosophila pseudoobscura, Drosophila melanogaster, Drosophila mojavensis, Drosophila yakuba [from FlyBase], Pediculus humanus, Culex pipiens [from VectorBase], Anopheles gambiae, Aedes aegypti [from Ensembl], and Bombyx mori [from SILKDB]) and four outgroups (the crustacean Daphnia pulex [the GNOMON predicted set provided by the JGI], the nematode Caenorhabditis elegans, and two chordates, Ciona intestinalis and Homo sapiens [from Ensembl]). For each protein encoded in the pea aphid genome, a Smith-Waterman [106] (link) search (e-val 10−3) was performed against the above mentioned proteomes. Sequences that aligned with a continuous region longer than 50% of the query sequence were selected and aligned using MUSCLE 3.6 [107] with default parameters. Gappy positions were removed using trimAl v1.0 (http://trimal.cgenomics.org ), using a gap threshold of 25% and a conservation threshold of 50%. Phylogenetic trees were estimated with Neighbor Joining (NJ) trees using scoredist distances as implemented in BioNJ [108] (link) and by ML as implemented in PhyML v2.4.4 [105] (link), using JTT as an evolutionary model and assuming a discrete gamma-distribution model with four rate categories and invariant sites, where the gamma shape parameter and the fraction of invariant sites were estimated from the data. Support for the different partitions was computed by approximate likelihood ratio test as implemented in PhymL (aLRT) [109] (link). All trees and alignments have been deposited in PhylomeDB [110] (link) (http://phylomedb.org ). Additional details for this analysis can be found in [110] (link).
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Aedes
Anopheles gambiae
Aphids
Apis
Biological Evolution
Bombyx mori
Caenorhabditis elegans
Chordata
Ciona intestinalis
Crustacea
Culex
Daphnia
Drosophila
Drosophila melanogaster
Gamma Rays
Genes
Genes, vif
Genome
Genome, Human
Genome, Insect
Homo sapiens
Insecta
Lice, Body
Muscle Tissue
Nematoda
Pisum
Proteins
Proteome
Staphylococcal Protein A
Trees
Tribolium, monocots
Adult
Drosophila
Hyperostosis, Diffuse Idiopathic Skeletal
Insecta
Larva
Tribolium, monocots
To identify open reading frames (ORFs) encoding putative ABC transporters, we conducted tblastn searches on the Tribolium castaneum 3.0 genome assembly (Tcas 3.0) using the orthologous groups protein database at BeetleBase (http://BeetleBase.org ) [25 (link)]. As a query, we used highly conserved NBDs from the Drosophila, Anopheles, Bombyx and Daphnia genomes, whose ABC transporter superfamilies were characterized previously [19 (link)-21 (link),26 (link),27 (link)]. Hits from individual subfamilies were only considered when the E-values were less than 10-6. The sequences were re-evaluated with NCBI’s CDS and CDART programs (http://www.ncbi.nlm.nih.gov ), as well as the probabilistic profile hidden Markov models (HMMs) using the HMMER webserver (http://hmmer.janelia.org ). To assign putative Tribolium ABC genes to ABC subfamilies, the NBDs of the corresponding GLEAN models were extracted and used in ClustalW alignments. Next, phylogenetic trees were reconstructed with the maximum-likelihood method (5000 replicates for bootstrapping) using the MEGA 5.03 software [28 (link)]. Subfamily-specific clustering was then compared with that of previous phylogenetic analyses of ABC transporters from Drosophila, Anopheles, Bombyx and Daphnia. The GLEAN models were refined on the basis of homology, EST support and sequence analysis of PCR fragments. The organization of ABC genes and frequent gene duplications in Tribolium impeded the correct prediction of gene models. Therefore, we manually corrected the predicted exon/intron boundaries for some GLEAN models. The subfamily assignment of Tribolium ABC proteins was confirmed by blastp analyses at the NCBI webserver (http://www.ncbi.nlm.nih.gov/blast ). This procedure allowed unequivocal assignment of Tribolium ABC transporters to respective ABCA-H subfamilies. Based on our data we reassessed a previous phylogenetic analysis of the Tribolium ABC transporter superfamily, which was published recently in the scope of the characterization of the silkworm ABC gene superfamily [20 (link)].
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Anopheles
ATP-Binding Cassette Transporters
Bombyx
Bombyx mori
Daphnia
Drosophila
Exons
Gene Duplication
Genes
Genome
Introns
Open Reading Frames
Proteins
Sequence Analysis
Tribolium, monocots
Most recents protocols related to «Tribolium, monocots»
The genome sequence of Leptinotarsa decemlineata (assembly GCA_000500325.2 Ldec_2.0) used as a reference for alignment was split into 31-nucleotide long k-mers and analyzed using the BLASTn tool against the NCBI Nucleotide database. Similarly, other reference genomes of Coleoptera obtained from the NCBI Genome database were examined: Diabrotica virgifera (GCA_003013835.2 Dvir_v2. 0), Oryzaephilus surinamensis (GCA_004796505.1 ASM479650v1), Coccinella septempunctata (GCA_003568925.1 Csep_MD8_v1), Harmonia axyridis (GCA_011033045. 1), Aleochara bilineata (GCA_003054995.1 ASM305499v1), Aethina tumida (GCA_001937115.1 Atum_1.0), Oryctes borbonicus (GCA_902654985. 1), Nicrophorus vespilloides (GCA_001412225.1 Nicve_v1.0), Asbolus verrucosus (GCA_004193795.1 BDFB_1.0), Protaetia brevitarsis (GCA_004143645. 1 ASM414364v1), Popillia japonica (GCA_004785975.1 GSC_JBeet_1), Anoplophora glabripennis (GCA_000390285.2 Agla_2. 0), Pogonus chalceus (GCA_002278615.1 Pchal_1.0), Agrilus planipennis (GCA_000699045.2 Apla_2.0), Sitophilus oryzae (GCA_002938485.2 Soryzae_2. 0), Onthophagus taurus (GCA_000648695.2 Otau_2.0), Dendroctonus ponderosae (GCA_000355655.1), and Tribolium castaneum (GCA_000002335.3 Tcas5.2).
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Beetles
Genome
GPER protein, human
Nucleotides
Tribolium, monocots
Repeat sequences were masked, and the repeat-masked genome was used for gene set annotation with three methods: ab initio annotation, RNA‐seq‐based annotation, and homologue‐based annotation.
In the ab initio method, the software packages Augustus (v2.5.5) and SNAP (v2006‐07‐28) were employed with default settings. Genes with incomplete open reading frames (ORFs) or a protein‐coding length less than 300 bp were filtered out. In the RNA-seq-based method, published gene sets from Aedes aegypti (GCF_002204515.2; from NCBI), Spodoptera frugiperda (GCF_011064685.1; from NCBI), P. japonica (GCA_013421045.1; from NCBI), Anoplophora glabripennis (GCF_000390285.2; from NCBI), Drosophila melanogaster (GCF_000001215.4; from NCBI), Bombyx mori (GCF_014905235.1; from NCBI), Photinus pyralis (GCF_008802855.1; from NCBI), Diabrotica virgifera (GCF_003013835.1; from NCBI), Apis mellifera (GCF_003254395.2; from NCBI), Tribolium castaneum (GCF_000002335.3; from NCBI), and H. axyridis (GCA_011033045.1; from NCBI) were downloaded from NCBI or their own databases and used for homology-based annotation. The longest transcript of each protein-coding gene was aligned to the H. vigintioctomaculata genome using BLAST (tblastn, v2.6.0) with an e-value of 1 × 10−5, and gene structures were predicted using GeneWise (v2.2.0).52 (link) In the RNA‐seq‐based gene approach, the de novo assembled transcripts were aligned to the H. vigintioctomaculata genome using BLAT (v35),45 (link) and PASA (v2.1.0)53 (link) was used to link the spliced alignments. Finally, the gene prediction results were integrated into a final gene set using EVidenceModeler (v1.1.1) software.54 (link)For gene function annotation, the predicted protein-coding genes were searched against the following public databases: Gene Ontology (http://geneontology.org/ ), the Integrated Resource of Protein Domains and Functional Sites (InterPro: https://www.ebi.ac.uk/interpro/ ), Kyoto Encyclopedia of Genes and Genomes (KEGG: https://www.kegg.jp/ ), Clusters of Orthologous Groups of proteins (COG: https://www.ncbi.nlm.nih.gov/COG/ ), Swiss-Prot (www.uniprot.org ), TrEMBL (www.uniprot.org ), and NCBI non-redundant proteins database (NR: https://ftp.ncbi.nlm.nih.gov/blast/db ).
In the ab initio method, the software packages Augustus (v2.5.5) and SNAP (v2006‐07‐28) were employed with default settings. Genes with incomplete open reading frames (ORFs) or a protein‐coding length less than 300 bp were filtered out. In the RNA-seq-based method, published gene sets from Aedes aegypti (GCF_002204515.2; from NCBI), Spodoptera frugiperda (GCF_011064685.1; from NCBI), P. japonica (GCA_013421045.1; from NCBI), Anoplophora glabripennis (GCF_000390285.2; from NCBI), Drosophila melanogaster (GCF_000001215.4; from NCBI), Bombyx mori (GCF_014905235.1; from NCBI), Photinus pyralis (GCF_008802855.1; from NCBI), Diabrotica virgifera (GCF_003013835.1; from NCBI), Apis mellifera (GCF_003254395.2; from NCBI), Tribolium castaneum (GCF_000002335.3; from NCBI), and H. axyridis (GCA_011033045.1; from NCBI) were downloaded from NCBI or their own databases and used for homology-based annotation. The longest transcript of each protein-coding gene was aligned to the H. vigintioctomaculata genome using BLAST (tblastn, v2.6.0) with an e-value of 1 × 10−5, and gene structures were predicted using GeneWise (v2.2.0).52 (link) In the RNA‐seq‐based gene approach, the de novo assembled transcripts were aligned to the H. vigintioctomaculata genome using BLAT (v35),45 (link) and PASA (v2.1.0)53 (link) was used to link the spliced alignments. Finally, the gene prediction results were integrated into a final gene set using EVidenceModeler (v1.1.1) software.54 (link)For gene function annotation, the predicted protein-coding genes were searched against the following public databases: Gene Ontology (
Aedes
Apis
Bombyx mori
Drosophila melanogaster
Gene Annotation
Gene Products, Protein
Genes
Genetic Structures
Genome
Open Reading Frames
Photinus
Protein Domain
Proteins
Repetitive Region
RNA-Seq
Spodoptera frugiperda
Staphylococcal Protein A
Tribolium, monocots
The honeybees used in this study were derived from feral Apis mellifera carnica colonies. Female embryos (which are diploid) were collected from eggs laid by naturally mated queens. Haploid male eggs were collected from non-mated queens treated with CO2, which induces the laying of unfertilized eggs. Embryos were collected using a Jenter egg collection box (Jenter Queen Rearing Kit, Karl Jenter GmbH, Frickenhausen, Germany) and were either injected or left in the incubator at 34 °C until the targeted stage55 (link). Wild type pupae and adults were collected from bee colonies. Wild type Cimex lectularius adult males and females were purchased from Insect Services GmbH (Berlin, Germany). Drosophila melanogaster adults from the isogenic strain w1118 were a gift from Hermann Aberle (Heinrich-Heine University Düsseldorf, Germany). Adult Tribolium castaneum males and females were a gift from Gregor Bucher (University of Göttingen, Germany). The laboratory AsymCx strain of Nasonia vitripennis was cured of Wolbachia infection and continuously reared on Calliphora sp. hosts at 25 °C. Male and female wasps were separated based on the sex-specific forewing size before eclosion. Male-only offspring were generated by offering hosts to virgin females. To produce female offspring, a virgin female was paired with a single male and allowed to mate for one day. Two hosts per day were provided to individual females to initiate oviposition.
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Adult
Apis
Cimex lectularius
Diploidy
Drosophila melanogaster
Eggs
Embryo
Females
feral
Infection
Insecta
Males
Oviposition
Pupa
Strains
Tribolium, monocots
Wasps
Wolbachia
Phylogenetic analysis and amino acid alignment analysis were performed using MEGA 7 [64 (link)]. For phylogenetic analysis, evolutionary history was inferred using the neighbor-joining method [65 (link)]. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) were determined as previously described [66 (link)]. The evolutionary distances were computed using the Poisson correction method and are in units of the number of amino acid substitutions per site. Protein sequence of Vasa were downloaded from National Center for Biotechnology Information. The accession numbers are as follows: Plutella xylostella, XP_037961717.1; D. rerio, CAA72735.1; M. musculus, EDL18409.1; Tribolium castaneum, NP_001034520.2; B. mori, NP_001037347.1; Manduca sexta, NP_001037347.1; X. laevis, NP_001081728.1; C. elegans, NP_491113.1; D. melanogaster, NP_723899.1; Nasonia vitripennis, XP_001603956.3; Amyelois transitella, XP_013187571.1; Helicoverpa armigera, XP_021190483.1; Aedes aegypti, XP_021700879.1; Bicyclus anynana, XP_023939227.1; and Danaus plexippus, XP_032519693.1.
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Aedes
Amino Acids
Amino Acid Sequence
Amino Acid Substitution
Biological Evolution
Caenorhabditis elegans
DNA Replication
Drosophila melanogaster
Muscle Tissue
Tobacco Hornworm
Trees
Tribolium, monocots
Xenopus laevis
Zebrafish
Putative NRs were retrieved from the chromosome-level P. pseudoannulata genome using orthologs of Drosophila melanogaster (King-Jones & Thummel, 2005 ), Anopheles gambiae (Bertrand et al., 2004 (link)), Tribolium castaneum (Bonneton et al., 2008 (link); Tan & Palli, 2008 (link)), Bombyx mori (Cheng et al., 2008 (link)), Aedes aegypti (Cruz et al., 2009 (link)), Acyrthosiphon pisum (Christiaens et al., 2010 (link)), Nilaparvata lugens (Xu et al., 2017 (link)), Bactrocera dorsalis (Yang et al., 2020 (link)), Tetranychus urticae (Grbić et al., 2011 (link)), and Panonychus citri (Li et al., 2017 (link)) as queries using the BLAST tool (v2.7.1, downloaded from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/). A neighbor-joining phylogenetic tree of NRs was constructed with 1 000 bootstraps in MEGA X (v10.0.5) (Kumar et al., 2018 (link)). The conserved domains of NRs were predicted using the NCBI Conserved Domain Database (Lu et al., 2020 (link)) and their structures were drawn using the Illustrator for Biological Sequences (IBS, v1.0.3) tool (Liu et al., 2015 (link)).
Aedes
Anopheles gambiae
Bactrocera
Biopharmaceuticals
Bombyx mori
Chromosomes
Drosophila melanogaster
Genome
Pisum
Tribolium, monocots
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More about "Tribolium, monocots"
Tribolium, also known as the red flour beetle, is a genus of beetles in the family Tenebrionidae.
These insects, commonly used as model organisms in biological research, are particularly valuable for studying genetics and developmental biology.
Tribolium species are notorious for their role in food spoilage, as they can infest and contaminate stored grains and flour.
Monocots, or monocotyledonous plants, represent a diverse group of flowering plants characterized by their single seed leaf (cotyledon) and unique vascular bundle arrangement.
This group includes many economically important crops such as grasses, cereals, and some ornamental plants.
Monocots are distinct from dicots, which have two seed leaves and a different vascular bundle structure.
PubCompare.ai is an innovative AI-driven platform that enhances reproducibility and research accuracy by facilitating comparative analysis of scientific protocols from literature, preprints, and patents.
This tool can help researchers identify the best protocols and products, streamlining the research process and improving the quality of their findings.
Experince the future of scientific discovery todday with PubCompare.ai.
Researchers can leverage PubCompare.ai to access a wealth of information related to Tribolium and monocots.
This includes insights into the use of PCRII vector, FBS, In-Fusion HD Cloning Kit, EX-CELL 420, TRIzol reagent, Amphotericin B, TRIzol, and NanoDrop 2000c spectrophotometer in studies involving these organisms.
Additionally, the platform can provide information on the use of Aspergillus oryzae and Tyramide signal amplification system in relevant research applications.
These insects, commonly used as model organisms in biological research, are particularly valuable for studying genetics and developmental biology.
Tribolium species are notorious for their role in food spoilage, as they can infest and contaminate stored grains and flour.
Monocots, or monocotyledonous plants, represent a diverse group of flowering plants characterized by their single seed leaf (cotyledon) and unique vascular bundle arrangement.
This group includes many economically important crops such as grasses, cereals, and some ornamental plants.
Monocots are distinct from dicots, which have two seed leaves and a different vascular bundle structure.
PubCompare.ai is an innovative AI-driven platform that enhances reproducibility and research accuracy by facilitating comparative analysis of scientific protocols from literature, preprints, and patents.
This tool can help researchers identify the best protocols and products, streamlining the research process and improving the quality of their findings.
Experince the future of scientific discovery todday with PubCompare.ai.
Researchers can leverage PubCompare.ai to access a wealth of information related to Tribolium and monocots.
This includes insights into the use of PCRII vector, FBS, In-Fusion HD Cloning Kit, EX-CELL 420, TRIzol reagent, Amphotericin B, TRIzol, and NanoDrop 2000c spectrophotometer in studies involving these organisms.
Additionally, the platform can provide information on the use of Aspergillus oryzae and Tyramide signal amplification system in relevant research applications.