BSR-Seq.

<p>A. A flowchart of BSR-Seq experimental design. B. The physical position of each SNP marker (x-axis) was plotted versus the probability of each SNP marker being in complete linkage disequilibrium with the causal gene (y-axis). C. <i>gl3</i> mutants (the <i>gl3-ref</i> allele) express a glossy phenotype due to altered accumulation of epicuticular waxes. Water is sprayed on seedlings to distinguish mutant (<i>gl3-ref</i>/<i>gl3-ref</i>) from non-mutant (<i>gl3-ref</i>/+ or +/+). D. Chromosome 4 was scanned by using a window containing 50 SNPs with a step size of 5 SNPs. Within each window, the median linkage probability obtained from a Bayesian BSA analysis across all the 50 SNPs was determined and was plotted against the middle physical position of the window.</p

Gene structure of the <i>gl3</i> gene and lesions of its mutant alleles.

<p>A. RNA-Seq reads shown in the Integrative Genomics Viewer. Blue indicates reads that have a forward orientation relative to the reference genome; red indicates reverse orientation. B. Based on the supporting ESTs and the annotation from the gene models, the <i>gl3</i> gene contains only a single exon. All six lesions associated with <i>gl3</i> mutant alleles are located in the coding region. They include <i>Mu</i> insertion alleles (a: <i>gl3-93-4700-5</i>; b: <i>gl3-93-4700-6</i>; c: <i>gl3-93B111</i>), EMS alleles (1: <i>gl3-AEW-A632-363-EMS</i>, premature stop at position 171 nt in coding region (G->A); 2: <i>gl3-94-1001-326-EMS</i>, premature stop at position 358 nt in coding region (C–T)) and the reference allele (3: <i>gl3-ref</i>, insertion or rearrangement at 430–758 nt of the coding region).</p

High Confidence lncRNAs-Sequence

The transcript sequences of 1,704 High Confidence lncRNAs identified in maiz

pre-lncRNAs-GTF

The GTF file of 18,459 pre-lncRNAs identified in maiz

pre-lncRNAs Sequence

The transcript sequences of 18,459 pre-lncRNAs identified in maiz

LncRNA_Finder - Pipeline Source Code

Source code of the pipeline-LncRNA_Finder THIS SOFTWARE IS PROVIDED BY THE AUTHORS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LIN LI, NATHAN M. SPRINGER, or GARY J. MUEHLBAUER (OR UNIVERSITY OF MINNESOTA) BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. DESCRIPTION: LncRNA_Finder enables the discovery of long noncoding RNAs using native sequence fasta files. This script essentially uses the results from external alignment programs and performs long noncoding RNA filtering via a set of specified parameters. 2, Prerequisite of external softwares Need to install ncbi_blast standalone package, bowtie and cpc in your local environment correctly and set the running path of external programs at the beginning of the pipeline 3, Usage Perl LncRNA_Finder.pl -i -p -k -s -o [-t <# of thread>] [-r ] [-f ] [-m <# of mismatch>] [-e ] Options: -i -p -k -s -o -h help -t number of thread for the computation || default=4 -r minimum lncRNA length || default=200 -f maximum potential ORF length of lncRNAs || default=100 -m number of mismatch in the alignment with smallRNA || default=0 -e E-value of the alignment against protein database || default=1.0e-

all_putative_lncRNAs-Sequence

The transcript sequences of all the 20,163 putative lncRNAs identified in maiz

High Confidence lncRNAs-GTF

The GTF file of 1,704 High Confidence lncRNAs in maiz

The <i>gl13</i> gene encodes a putative ABC transporter G family protein.

<p>The amino acid sequence of the 2 GL13 isoforms (GRMZM2G118243_P01 and GRMZM2G118243_P02) were aligned to 9 homologs downloaded from GenBank (Table S2). Neighbor-joining analysis was used to generate a phylogenetic tree, which was bootstrapped over 1,000 cycles, using MEGA5.0. </p

Phenotypic characterization of the <i>gl13-ref</i> mutant phenotype.

<p>(A) Comparisons of gross morphology and epicuticular wax accumulation and morphology in mutant (upper) and wild-type (lower) seedlings; (B) Comparisons of paraffin sections (10x) of leaves from mutant (left) and wild-type (right) seedlings stained with Fast Green; (C) Detached leaves from mutant (upper) and wild-type (lower) immediately after harvest and after 2 hours at room temperature; (D) Water loss from detached mutant and wild-type seedling leaves at room temperature. Error bars = SE. </p