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  • In this polymorphism assessment our strains were sampled fro

    2018-11-14

    In this polymorphism assessment, our strains were sampled from Dioscorea alata in Guadeloupe, where anthracnose is the main threat [14] and impacted agro-diversity [15]. Comparisons at wider geographical scales might enlighten important population processes: local dispersal [16], up to migration at greater scales [17], as well as genetic differentiation levels.
    Acknowledgements We are grateful to Thibaut Malausa, Nicolas Ris and Sylvie Warot (INRA, Institut Sophia Agrobiotech, France) for technical assistance. This work received the financial support of INRA through the Durayam project (No. P10259). The authors declare having no conflict of interests.
    Data, experimental design, materials and methods Total RNA extracted of five samples of emerging, young, fully expanded, and early and late senescent stages leaves of Ilex paraguariensis breeding line Pg538 were pooled for high throughput sequencing [1]. The attainment of the transcribed 45S rRNA sequence of yerba mate was completed in seven steps: This Transcriptome Shotgun Assembly project has been deposited at DDBJ/EMBL/GenBank [2] under the accession GFHV00000000. The version described in this paper is the first version, GFHV01000000.
    Acknowledgements This study was funded by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT-Argentina), Grant no. UNaM PICT 2014-3328 Préstamo BID Nº AR-L 1181.
    Data Six Caenorhabditis species were used to perform sequence alignments of lin-11 Octreotide acetate cost 3. These are C. briggsae, C. sinica, C. nigoni, C. remanei, C. brenneri, and C. elegans. MussaGL program (http://woldlab.caltech.edu/cgi-bin/mussa) was used at 70% and 80% window thresholds. Multiple alignments were carried out that included C. briggsae and C. nigoni (Fig. 1). In general, conservation decreases as the number of species and alignment threshold are increased. Four-way alignments reveal six distinct conserved blocks at 70% threshold. Some of these blocks are part of larger stretches in 2-way and 3-way alignments. At 80% threshold block 2 lacks conservation when either one of the C. remanei, C. brenneri and C. elegans species are included. Additionally, block 1 is lost in the case of C. elegans. Of the three sequence blocks described in the accompanied article [1], namely, C3-1, C3-2 and C3-3 that are conserved between C. elegans, C. brenneri, C. remanei and C. briggsae, block 3 corresponds to C3-1, block 5 to C3-2, and block 6 to C3-3 (Fig. 1). We used a computational tool CIS-BP (http://cisbp.ccbr.utoronto.ca/TFTools.php) [2] to search for transcription factors (TFs) that may bind to conserved blocks in introns 3 (C3-1) and 7 (C7-1 and C7-2) and potentially lin-11 expression in neurons. A total of 35 TF genes were identified for C3-1, 37 for C7-1, and 46 for C7-2 (Table 1). In addition, we searched for modENCODE dataset (http://www.modencode.org) and found eight TFs that bind to intron 7 sequences Table 1).
    Experimental design, materials and methods The lin-11 intronic sequences from Caenorhabditis species were aligned using MussaGL (multi-species sequence analysis, version 1.1.0 for Mac OS X), an N-way sequence alignment software that was developed by Wold lab (Caltech, USA). The conservation threshold was set at 70% (21 per 30-nucleotide sliding window) and 80% (27 per 30-nucleotide sliding window). To identify the putative TF genes for C. elegans introns 3 and 7, we used the CIS-BP database software. The setting included motif model ‘PWMs-LogOdds’ and Threshold 8. According to the website, this motif model option scores each position in each sequence with all position weight matrices, using a standard log odds scoring method. For more details see the help page on the website (http://cisbp.ccbr.utoronto.ca/help.html).
    Acknowledgments We are grateful to Erich Schwarz, Da Yin, Caitlin Schartner, Edward Ralston, Asher Cutter, Barbara Meyer, and Eric Haag for providing the C. nigoni lin-11 sequence data. This work was supported by the Natural Sciences and Engineering Research Council of Canada Discovery grant to BG.