Specific amino acids in five trichome regulatory genes within the <i>Brassicaceae</i>.

<p>*Selected positions in the aligned consensus amino acid sequence (CAA) were selected from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Figure S1</a> if they distinguished hairy from glabrous germplasm (dark arrows in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Fig. S1</a>) or were unique to <i>B. villosa</i> (*red arrows in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0095877#pone.0095877.s001" target="_blank">Fig. S1</a>). ND, not determined (sequence not available). NIL, missing amino acid. NA, not applicable. Note: Multiple gene copies are only indicated if an amino acid differed between the copies.</p

Phylogenetic relationships for the five major trichome regulatory genes present in <i>Brassica</i> and <i>A. thaliana</i>.

<p>Sequences were analysed by the maximum likelihood method with bootstrap values (%) indicated (100% is implicit in vacant branching positions). Scale indicates amino acid substitutions per site. A consensus sequence based on six <i>B. napus</i> TTG1 copies in NCBI was used for more robust analysis rather than the individual BnTTG1 copies, which each gave very weak associations due to limited overlapping sequence. <i>B. rapa</i> TRY-2 and TRY-3 were also not included since their small size gave spurious weak associations of <50%. Although three copies for <i>TRY</i> exist in <i>B. oleracea</i> and <i>B. villosa</i> (Fig. 2), <i>TRY-3</i> could not be cloned from <i>B. villosa</i> cDNA due to low expression.</p

Transcript levels for individual gene copies of the four trichome positive regulatory genes and four negative regulatory genes in <i>B. villosa</i> compared with <i>B. oleracea</i>.

<p>RNAseq data is expressed as fragments per kilobase of exon per million fragments mapped (FPKM). Within each panel, different letters represent significantly different means (± standard error) for 3 independent RNA extractions (1^st true leaves or cotyledons from up to 10 plants per extraction) at p≤0.05.</p

Database accession numbers for orthologues to the major trichome regulatory genes (<i>GL1</i>, <i>Gl2</i>, <i>EGL3</i>, <i>TTG1</i> and <i>TRY</i>) in <i>B. villosa.</i>

<p>Genes in the same row are closest orthologues to each other. NA = Sequence not available.</p

<i>Ka</i>/<i>Ks</i>^* ratios for trichome regulatory gene comparisons between <i>B. villosa</i> and three other <i>Brassica</i> species and Arabidopsis.

<p>*<i>Ka</i>/<i>K_S</i> (Yang Z, 1997): <i>Ka</i>, non-synonymous nucleotide substitution. <i>Ks</i>, synonymous nucleotide substitution value.</p>+<p><i>B. rapa</i>-2 (BRTRY-2) and <i>B. rapa</i>-3 (BRTRY-3) amino acid sequences were too short to be included. NA, <i>B. napus</i> sequence not available.</p

Theoretical protein size (Mr/Number of amino acid) and isoelectric point (<i>pI</i>) of trichome regulatory coding sequences in the <i>Brassicaceae</i>.

<p>ND, not determined (sequence not available). Closest orthologues between the species are positioned within the same row. Data represents all known orthologues and homologues for each species.</p

MeioCapture: an efficient method for staging and isolation of meiocytes in the prophase I sub-stages of meiosis in wheat

Background Molecular analysis of meiosis has been hindered by difficulties in isolating high purity subpopulations of sporogenous cells representing the succeeding stages of meiosis. Isolation of purified male meiocytes from defined meiotic stages is crucial in discovering meiosis specific genes and associated regulatory networks. Results We describe an optimized method termed MeioCapture for simultaneous isolation of uncontaminated male meiocytes from wheat (Triticum spp.), specifically from the pre-meiotic G2 and the five sub-stages of meiotic prophase I. The MeioCapture protocol builds on the traditional anther squash technique and the capillary collection method, and involves extrusion of intact sporogenous archesporial columns (SACs) containing meiocytes. This improved method exploits the natural meiotic synchrony between anthers of the same floret, the correlation between the length of anthers and meiotic stage, and the occurrence of meiocytes in intact SACs largely free of somatic cells. The main advantage of MeioCapture, compared to previous methods, is that it allows simultaneous collection of meiocytes from different sub-stages of prophase I at a very high level of purity, through correlation of stages with anther sizes. A detailed description is provided for all steps, including the collection of tissue, isolation and size sorting of anthers, extrusion of intact SACs, and staging of meiocytes. Precautions for individual steps throughout the procedure are also provided to facilitate efficient isolation of pure meiocytes. The proof-of-concept was successfully established in wheat, and a light microscopic atlas of meiosis, encompassing all stages from pre-meiosis to telophase II, was developed. Conclusion The MeioCapture method provides an essential technique to study the molecular basis of chromosome pairing and exchange of genetic information in wheat, leading to strategies for manipulating meiotic recombination frequencies. The method also provides a foundation for similar studies in other crop species

De las desigualidades socio-ecológicas a la desigual distribución de vulnerabilidades a desastres

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Additional file 17: Figure S9. of The compact genome of the plant pathogen Plasmodiophora brassicae is adapted to intracellular interactions with host Brassica spp

The terpenoid biosynthesis pathway with enzymes encoded in the P. brassicae genome coloured green. (PNG 823 kb

The coordinated regulation of early meiotic stages is dominated by non-coding RNAs and stage-specific transcription in wheat

Reproductive success hinges on precisely coordinated meiosis, yet our understanding of how structural rearrangements of chromatin and phase transitions during meiosis are transcriptionally regulated is limited. In crop plants, detailed analysis of the meiotic transcriptome could identify regulatory genes and epigenetic regulators that can be targeted to increase recombination rates and broaden genetic variation, as well as provide a resource for comparison among eukaryotes of different taxa to answer outstanding questions about meiosis. We conducted a meiotic stage-specific analysis of messenger RNA (mRNA), small non-coding RNA (sncRNA), and long intervening/intergenic non-coding RNA (lincRNA) in wheat (Triticum aestivum L.) and revealed novel mechanisms of meiotic transcriptional regulation and meiosis-specific transcripts. Amidst general repression of mRNA expression, significant enrichment of ncRNAs was identified during prophase I relative to vegetative cells. The core meiotic transcriptome was comprised of 9309 meiosis-specific transcripts, 48 134 previously unannotated meiotic transcripts, and many known and novel ncRNAs differentially expressed at specific stages. The abundant meiotic sncRNAs controlled the reprogramming of central metabolic pathways by targeting genes involved in photosynthesis, glycolysis, hormone biosynthesis, and cellular homeostasis, and lincRNAs enhanced the expression of nearby genes. Alternative splicing was not evident in this polyploid species, but isoforms were switched at phase transitions. The novel, stage-specific regulatory controls uncovered here challenge the conventional understanding of this crucial biological process and provide a new resource of requisite knowledge for those aiming to directly modulate meiosis to improve crop plants. The wheat meiosis transcriptome dataset can be queried for genes of interest using an eFP browser located at https://bar.utoronto.ca/efp_wheat/cgi-bin/efpWeb.cgi?dataSource=Wheat_Meiosis.</p