New insights into the wheat chromosome 4D structure and virtual gene order, revealed by survey pyrosequencing

AbstractSurvey sequencing of the bread wheat (Triticum aestivum L.) genome (AABBDD) has been approached through different strategies delivering important information. However, the current wheat sequence knowledge is not complete. The aim of our study is to provide different and complementary set of data for chromosome 4D. A survey sequence was obtained by pyrosequencing of flow-sorted 4DS (7.2×) and 4DL (4.1×) arms. Single ends (SE) and long mate pairs (LMP) reads were assembled into contigs (223Mb) and scaffolds (65Mb) that were aligned to Aegilops tauschii draft genome (DD), anchoring 34Mb to chromosome 4. Scaffolds annotation rendered 822 gene models. A virtual gene order comprising 1973 wheat orthologous gene loci and 381 wheat gene models was built. This order was largely consistent with the scaffold order determined based on a published high density map from the Ae. tauschii chromosome 4, using bin-mapped 4D ESTs as a common reference. The virtual order showed a higher collinearity with homeologous 4B compared to 4A. Additionally, a virtual map was constructed and ∼5700 genes (∼2200 on 4DS and ∼3500 on 4DL) predicted. The sequence and virtual order obtained here using the 454 platform were compared with the Illumina one used by the IWGSC, giving complementary information

Volcano plot of all differentially expressed transcripts.

<p>Purple dots denote significantly differentially expressed transcripts with an adjusted p-value lower than 0.001 and at least 4-fold change.</p

Classification of differentially expressed genes.

<p>Classification of differentially expressed genes.</p

Phylogenetic tree of beta-tubulin genes.

<p>The phylogram was obtained by maximum likelihood analysis of beta-tubulin genes across six species: <i>Caenorhabditis elegans</i> (Ce), <i>Haemonchus contortus</i> (Hco), <i>Parascaris equorum</i> (Peq), <i>Ascaris suum</i> (Asu), <i>Trichinella spiralis</i> (Tsp) and <i>Ascaridia galli</i> (Asg). The tree was constructed by model selection based on the BIC criterion using the software prottest3, and maximum likelihood inference using PhyML. The branch support is given as bootstrap sampling proportion (the closer to 100, the more confident). The tree was rooted using the species <i>T</i>. <i>spiralis</i> as outgroup. Beta-tubulin isoforms belonging to the same species are indicated by colour: <i>H</i>. <i>contortus</i> is shown in purple, <i>A</i>. <i>suum</i> in blue, <i>C</i>. <i>elegans</i> in orange, <i>P</i>. <i>equorum</i> in green, <i>T</i>. <i>spiralis</i> in dark green and <i>A</i>. <i>galli</i> candidates in dark red.</p

Number of identified candidate transcripts associated with drug binding and processing.

<p>Number of identified candidate transcripts associated with drug binding and processing.</p

<i>De novo</i> assembly and annotations metrics for the transcriptome of <i>Ascaridia galli</i>.

<p><i>De novo</i> assembly and annotations metrics for the transcriptome of <i>Ascaridia galli</i>.</p

Classification of annotated transcripts.

<p>The 30,959 annotated transcripts were grouped in two classes, LC = low confidence (17,679 transcripts) or HC = high confidence (13,280 transcripts), based on the quality of their annotation. Using a keyword search of their Blast and Pfam description line, the transcripts of each class were further assigned to the following four categories: transposable elements (TE, e.g. transposon, retrotransposon), potential transposons (e.g. zinc finger, ZF), genes with unknown function (U) and genes with an assigned function (G).</p

Hordeum chilense minichromosomes in wheat

Trabajo presentado en el 8th International Triticeae Symposium y la 13th Gatersleben Research Conference, celebrados en Wernigerode/Gatersleben (Alemania) del 12 al 16 de junio de 2017.Cytoplasmic male sterility (CMS) systems are based on the nuclear-cytoplasmic incompatible interaction which are frequently used for hybrid seed production in many crops. Tbe msHl CM ystem results from the incompatibiJity between the nuclear genome of wheat and the cytoplasmic geno me of the wild bar ley species Hordeum chilense (Martín et al. 2008). Chromosomal reorganizations are frequently observed in interspecific bybrids. In a descent obtained from octoploid tritordeum x common wheat, the addition of a modified extra chromosome (acrocentric type) from H chilense with fertility restoring ability in the msHl system was found. Molecular marker and GISH characterization revealed that it was composed by parts from both short arms ofchromosomes lH and 6H (Castillo et al. 2014).In the descent of plants harboring this acrocentric chromosome, smaller modified Chromosomes, also capable of restoring fertility in a single dose, were originated. On of this minichromosomes was characterized by GISH and molecular markers confirming that it was a reorganization of H. chilense chromosome 1H and 6H. It was also isolated and sequenced to identify candidate genes for fertility restoration. Two other lines with minichromosomes derived from the acrocentric were obtained in different events. Preliminary characterizations derived from the acrocentnc with molecular markers show that these minichromosomes are different, being an excellent material to identify putative restoring genes along with their fertility restoration ability.N

Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome

Context: Insulin resistance in skeletal muscle is a major risk factor for the development of type 2diabetes in women with polycystic ovary syndrome (PCOS). Despite this, the mechanisms underlyinginsulin resistance in PCOS are largely unknown.Objective: To investigate the genome-wide DNA methylation and gene expression patterns inskeletal muscle from women with PCOS and controls and relate them to phenotypic variations.Design/Participants: In a case-control study, skeletal muscle biopsies from women with PCOS (n =17) and age-, weight-, and body mass index‒matched controls (n = 14) were analyzed by array-basedDNA methylation and mRNA expression profiling.Results: Eighty-five unique transcripts were differentially expressed in muscle from women with PCOSvs controls, including DYRK1A, SYNPO2, SCP2, and NAMPT. Furthermore, women with PCOS hadreduced expression of genes involved in immune system pathways. Two CpG sites showed differentialDNA methylation after correction for multiple testing. However, an mRNA expression of ;30% of thedifferentially expressed genes correlated with DNA methylation levels of CpG sites in or near the gene.Functional follow-up studies demonstrated that KLF10 is under transcriptional control of insulin,where insulin promotes glycogen accumulation in myotubes of human muscle cells. Testosteronedownregulates the expression levels of COL1A1 and MAP2K6.Conclusion: PCOS is associated with aberrant skeletal muscle gene expression with dysregulatedpathways. Furthermore, we identified specific changes in muscle DNA methylation that may affectgene expression. This study showed that women with PCOS have epigenetic and transcriptionalchanges in skeletal muscle that, in part, can explain the metabolic abnormalities seen inthese women