48 research outputs found

    Phylogenetic tree of the TRAFs and diagrams of their protein domain structure

    No full text
    <p><b>Copyright information:</b></p><p>Taken from "Conservation and divergence of gene families encoding components of innate immune response systems in zebrafish"</p><p>http://genomebiology.com/2007/8/11/R251</p><p>Genome Biology 2007;8(11):R251-R251.</p><p>Published online 27 Nov 2007</p><p>PMCID:PMC2258186.</p><p></p> Details are as in Figure 2, except that the scale shows 0.2 amino acid substitutions. TRAF, tumor necrosis factor receptor-associated factor

    Datasets

    No full text
    This .zip files contains two folders. The folder "Control" contains the 15 raw 454 sequence files generated from the "Test Pools" analysis detailed in Table 2 of the manuscript, and a file of 27 Sanger sequences listed in Table S1. The folder "Tenerife" contains the 6 raw 454 sequence files associated generated from the "Tenerife Forest Samples" analysis detailed in Table 3 of the manuscript

    Regression analyses of the percentage of collembolan mtDNA COI sequences within an MID tag pool (<i>y</i> axis) against the percentage of genomic template from which they are derived within an experimental genomic pool (<i>x</i> axis).

    No full text
    <p>Data come from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone.0057615.s003" target="_blank">Table S1</a>. The panels from top to bottom are MID1 against pool 1, MID4 against pool 2, and MID7 against pool 3.</p

    Primers, MIDs, sequence formats and consensus reference sequence used in this study.

    No full text
    <p>ColFol-for ColFol-rev are the Sanger primers. 454-ColFol-for and 454-Col307-rev are the primers for mass amplification. Adaptors A and B are used by the ‘454’ sequencer to attach individual DNA molecules to microscopic beads, for subsequent sequencing. MIDs (Multiplex Identifiers) are 7 bp sequences that allow different samples to be sequenced together on a single ‘454’ plate and then separated bioinformatically for downstream analysis. There is no MID with 454-Col307-rev because we only pyrosequenced from the forward direction. Row 5 is an example of a 454 read after demultiplexing with the Roche tools. The forward primer is underlined, and the reverse primer dashed underlined. The MID tag is removed during demultiplexing. Row 6 is an example of a sequence after processing of sequences to produce a file of unique sequences.</p

    Heat map of the percentage representation of the 27 Collembola genomes within each of the 5 genomic pools, and within each of the three MID tag pools derived from each of the 5 genomic pools.

    No full text
    <p>For visual clarity, percentage representation of 2% or more is presented as maximum representation. See Supplementary <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057615#pone-0057615-t001" target="_blank">Table 1</a> to see the actual percentages of each sequence found, and species names.</p

    Denoising of mtDNA COI amplicons generated from community samples of Collembola from two forest sites on the island of Tenerife with the pipeline of Yu <i>et al.</i> (2012).

    No full text
    <p>Steps 1–3 represent reduction of unique sequence volume by denoising, while steps 4 and 5 further reduce unique sequence volume by the creation of summary clusters of sequences. See Yu <i>et al.</i> (2012) for a detailed explanation of each of the steps. Bracketed values in step 2 represent sequences inferred to be chimeras with the <i>de novo</i> chimera detection function UCHIME in USEARCH, all of which were removed in step 4 of PyroClean.</p

    Neighbour joining tree of PyroCleaned sequences derived from two forest sampling sites in the island of Tenerife, and 21 taxonomically identified Sanger sequences samples from Tenerife (in bold).

    No full text
    <p>Sequence identifiers represent MID tag, the name of the sequence, and the frequency representation of the sequence. Sequences were assessed for taxonomic identity against the BOLD Identification Database, and we report closest matches for Collembola, and non-Collembola if matching is higher. Letters in bold represent sequence matches to Collembola of 99% or higher: <b>A</b> – <i>Tetrodontophora bielanensis</i> (88%), <i>Pelosia muscerda</i> (Lepidoptera, 91%), <b>B</b> – <i>Tetrodontophora bielanensis</i> (89%), <i>Myotis ikonnikova</i> (Chiroptera, 91%); <b>C</b> – <i>Tetrodontophora bielanensis</i> (89%), <i>Myotis ikonnikova</i> (Chiroptera, 91%); <b>D</b> – <i>Verhoeffiella sp.</i> (89%), <i>Stenopsyche</i> (Trichoptera, 92%), <b>E</b> – no significant match, <i>Stenopsyche</i> (Trichoptera, 94%), <b>F</b> – <i>Folsomia</i> (94%), <i>Ophiogomphus</i> (Odonata, 95%), <b>G</b> – <i>Protaphorura</i> (99%), <b>H</b> – <i>Protaphorura</i> (100%), <b>I</b> – <i>Xenylla humicola</i> (90%), <i>Carterocephalus silvicola</i> (Lepidoptera, 91%), <b>J</b> – <i>Bourletiella</i> (89%), <b>K</b> – <i>Lepidocyrtus violaceus</i> (88%), <i>Herona marathus</i> (Lepidoptera, 90%) <b>L</b> – <i>Tullbergia sp.</i> (99%), <b>M</b> – <i>Parisotoma notabilis</i> L3 (92%), <b>N</b> – <i>Folsomina yosii</i> (90%), <b>O</b> – <i>Isotomiella</i> (99%), <b>P</b> – <i>Parisotoma notabilis</i> (100%), <b>Q</b> - <i>Parisotoma notabilis</i> (100%), <b>R</b> – <i>Parisotoma notabilis</i> (100%), <b>S</b> – <i>Xenylla humicola</i> (90%), <i>Finlaya</i> (Culicidae, 91%), <b>T</b> – <i>Verhoeffiella</i> sp. (90%), <b>U</b> – <i>Entomobrya atrocincta</i> (100%), <b>V</b> - <i>Entomobrya atrocincta</i> (99%), <b>W</b> - <i>Entomobrya atrocincta</i> (100%), <b>X</b> – <i>Parisotoma notabilis</i> (94%), <i>Phasus</i> (Lepidoptera, 96%), <b>Y</b> – <i>Isotomurus</i> (92%), <b>Z</b> – <i>Desoria sp.</i> (91%), <i>Bathymunida nebulosa</i> (Decapoda, 95%), <b>AA</b> – Entomobryidae (90%), <i>Polytremis pellucida</i> (Lepidoptera, 93%), <b>AB</b> – <i>Isotoma sp.</i> (91%), <i>Neophylax rickeri</i> (Trichoptera, 92%), <b>AC</b> – <i>Isotomurus</i> (86%), Chordate (90%), <b>AD</b> – <i>Neanura muscorum</i> (100%), <b>AE</b> – <i>Ceratophysella sp.</i> (99%), <b>AF</b> – <i>Ceratophysella sp.</i> (100%). The five sequences with an asterisk are potential numts or pcr error that exceed the final filter threshold. The two sequences with a filled circle are left in as an example of probable numts.</p

    Table_4_The origin and the genetic regulation of the self-compatibility mechanism in clementine (Citrus clementina Hort. ex Tan.).xlsx

    No full text
    Self-incompatibility (SI) is a genetic mechanism common in flowering plants to prevent self-fertilization. Among citrus species, several pummelo, mandarin, and mandarin-like accessions show SI behavior. In these species, SI is coupled with a variable degree of parthenocarpy ensuring the production of seedless fruits, a trait that is highly appreciated by consumers. In Citrus, recent evidences have shown the presence of a gametophytic SI system based on S-ribonucleases (S-RNases) ability to impair self-pollen tube growth in the upper/middle part of the style. In the present study, we combined PCR analysis and next-generation sequencing technologies, to define the presence of S7- and S11-Rnases in the S-genotype of the Citrus clementina (Hort. ex Tan.), the self-incompatible ‘Comune’ clementine and its self-compatible natural mutant ‘Monreal’. The reference genome of ‘Monreal’ clementine is presented for the first time, providing more robust results on the genetic sequence of the newly discovered S7-RNase. SNP discovery analysis coupled with the annotation of the variants detected enabled the identification of 7,781 SNPs effecting 5,661 genes in ‘Monreal’ compared to the reference genome of C. clementina. Transcriptome analysis of unpollinated pistils at the mature stage from both clementine genotypes revealed the lack of expression of S7-RNase in ‘Monreal’ suggesting its involvement in the loss of the SI response. RNA-seq analysis followed by gene ontology studies enabled the identification of 2,680 differentially expressed genes (DEGs), a significant number of those is involved in oxidoreductase and transmembrane transport activity. Merging of DNA sequencing and RNA data led to the identification of 164 DEGs characterized by the presence of at least one SNP predicted to induce mutations with a high effect on their amino acid sequence. Among them, four candidate genes referring to two Agamous-like MADS-box proteins, to MYB111 and to MLO-like protein 12 were validated. Moreover, the transcription factor MYB111 appeared to contain a binding site for the 2.0-kb upstream sequences of the S7- and S11-RNase genes. These results provide useful information about the genetic bases of SI indicating that SNPs present in their sequence could be responsible for the differential expression and the regulation of S7-RNase and consequently of the SI mechanism.</p

    Table_5_The origin and the genetic regulation of the self-compatibility mechanism in clementine (Citrus clementina Hort. ex Tan.).xlsx

    No full text
    Self-incompatibility (SI) is a genetic mechanism common in flowering plants to prevent self-fertilization. Among citrus species, several pummelo, mandarin, and mandarin-like accessions show SI behavior. In these species, SI is coupled with a variable degree of parthenocarpy ensuring the production of seedless fruits, a trait that is highly appreciated by consumers. In Citrus, recent evidences have shown the presence of a gametophytic SI system based on S-ribonucleases (S-RNases) ability to impair self-pollen tube growth in the upper/middle part of the style. In the present study, we combined PCR analysis and next-generation sequencing technologies, to define the presence of S7- and S11-Rnases in the S-genotype of the Citrus clementina (Hort. ex Tan.), the self-incompatible ‘Comune’ clementine and its self-compatible natural mutant ‘Monreal’. The reference genome of ‘Monreal’ clementine is presented for the first time, providing more robust results on the genetic sequence of the newly discovered S7-RNase. SNP discovery analysis coupled with the annotation of the variants detected enabled the identification of 7,781 SNPs effecting 5,661 genes in ‘Monreal’ compared to the reference genome of C. clementina. Transcriptome analysis of unpollinated pistils at the mature stage from both clementine genotypes revealed the lack of expression of S7-RNase in ‘Monreal’ suggesting its involvement in the loss of the SI response. RNA-seq analysis followed by gene ontology studies enabled the identification of 2,680 differentially expressed genes (DEGs), a significant number of those is involved in oxidoreductase and transmembrane transport activity. Merging of DNA sequencing and RNA data led to the identification of 164 DEGs characterized by the presence of at least one SNP predicted to induce mutations with a high effect on their amino acid sequence. Among them, four candidate genes referring to two Agamous-like MADS-box proteins, to MYB111 and to MLO-like protein 12 were validated. Moreover, the transcription factor MYB111 appeared to contain a binding site for the 2.0-kb upstream sequences of the S7- and S11-RNase genes. These results provide useful information about the genetic bases of SI indicating that SNPs present in their sequence could be responsible for the differential expression and the regulation of S7-RNase and consequently of the SI mechanism.</p

    Table_3_The origin and the genetic regulation of the self-compatibility mechanism in clementine (Citrus clementina Hort. ex Tan.).xlsx

    No full text
    Self-incompatibility (SI) is a genetic mechanism common in flowering plants to prevent self-fertilization. Among citrus species, several pummelo, mandarin, and mandarin-like accessions show SI behavior. In these species, SI is coupled with a variable degree of parthenocarpy ensuring the production of seedless fruits, a trait that is highly appreciated by consumers. In Citrus, recent evidences have shown the presence of a gametophytic SI system based on S-ribonucleases (S-RNases) ability to impair self-pollen tube growth in the upper/middle part of the style. In the present study, we combined PCR analysis and next-generation sequencing technologies, to define the presence of S7- and S11-Rnases in the S-genotype of the Citrus clementina (Hort. ex Tan.), the self-incompatible ‘Comune’ clementine and its self-compatible natural mutant ‘Monreal’. The reference genome of ‘Monreal’ clementine is presented for the first time, providing more robust results on the genetic sequence of the newly discovered S7-RNase. SNP discovery analysis coupled with the annotation of the variants detected enabled the identification of 7,781 SNPs effecting 5,661 genes in ‘Monreal’ compared to the reference genome of C. clementina. Transcriptome analysis of unpollinated pistils at the mature stage from both clementine genotypes revealed the lack of expression of S7-RNase in ‘Monreal’ suggesting its involvement in the loss of the SI response. RNA-seq analysis followed by gene ontology studies enabled the identification of 2,680 differentially expressed genes (DEGs), a significant number of those is involved in oxidoreductase and transmembrane transport activity. Merging of DNA sequencing and RNA data led to the identification of 164 DEGs characterized by the presence of at least one SNP predicted to induce mutations with a high effect on their amino acid sequence. Among them, four candidate genes referring to two Agamous-like MADS-box proteins, to MYB111 and to MLO-like protein 12 were validated. Moreover, the transcription factor MYB111 appeared to contain a binding site for the 2.0-kb upstream sequences of the S7- and S11-RNase genes. These results provide useful information about the genetic bases of SI indicating that SNPs present in their sequence could be responsible for the differential expression and the regulation of S7-RNase and consequently of the SI mechanism.</p
    corecore