Additional file 3 of PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

Additional file 3: Figure S1. Replication of the SNP index method and the G-statistic method in Python

Additional file 1 of PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

Additional file 1: Table S1. Verification of potential significant peaks

Additional file 2 of PyBSASeq: a simple and effective algorithm for bulked segregant analysis with whole-genome sequencing data

Additional file 2: Table S2. Chromosomal distribution of SNPs at different sequencing coverage levels

Deletions by Reversed <i>Ac</i> Ends Transposition Generate Chimerical Genes

<div><p>The solid circle indicates the centromere, the short vertical line indicates the target site, and the other symbols have the same meaning as those in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020164#pgen-0020164-g001" target="_blank">Figure 1</a>. (For animated version, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020164#pgen-0020164-sv001" target="_blank">Video S1</a>).</p><p>(A) Ac transposase (blue oval) binds to the 5′ end of <i>Ac</i> and 3′ end of <i>fAc</i>.</p><p>(B) As in ordinary transposition, the <i>Ac</i> 5′ end and the <i>fAc</i> 3′ end are excised by transposase cleavage, and the sequences flanking the <i>Ac/fAc</i> ends join together to form a ~13-kb circle. The X mark at the junction indicates the transposon footprint.</p><p>(C) The excised transposon ends insert into a site in intron 2 of <i>p2</i>. The <i>Ac</i> 5′ end joins to the distal side of the insertion site to form a circle, and the <i>fAc</i> 3′ end joins to the proximal side of the insertion site to generate a chimeric gene containing exon 1 and exon 2 of <i>p2</i> and exon 3 of <i>p1</i>.</p><p>This study reports the isolation of the progenitor (A) and deletion products (C). Note that the hypothetical structures shown in (B) are transient in nature and would not be amenable to physical isolation.</p></div

Phenotypes and Gene Structures of <i>P-oo</i> Alleles

<div><p>(A) The kernel pericarp pigmentation phenotypes specified by the indicated alleles.</p><p>(B) Genomic Southern blot. Genomic DNA from plants homozygous for the indicated alleles was cut with KpnI and HindIII, and hybridized with probes 15 or 8B from the <i>p1</i> gene. Lanes marked <i>P-oo32</i> contain approximately twice as much DNA as lanes marked <i>P1-rr11;</i> this DNA overloading enables the detection of the 7.6-kb band in the KpnI 8B blot, but also results in the intense 6.5-kb band in the HindIII 15 blot.</p><p>(C) Restriction map. The solid and gray boxes are exons 1, 2, and 3 (left to right) of <i>p1</i> and <i>p2,</i> respectively. Red triangles indicate <i>Ac</i> or <i>fAc</i> insertions, and the open and solid arrowheads indicate the 3′ and 5′ ends, respectively, of <i>Ac/fAc</i>. Sequences hybridizing with Southern blot probes are indicated by the solid bars above (probe 8B) and below (probe 15) the map. The short horizontal arrows indicate the orientations and approximate position of PCR primers. Primers are identified by numbers below the arrows. The sequence of the junction of each fusion allele is shown here; the black letters indicate <i>p2</i> sequence, while the red letters indicate <i>fAc</i> sequence. K, KpnI; H, HindIII. Lines below the map indicate the restriction fragments produced by digestion with KpnI or HindIII and hybridizing with the indicated probe; asterisks indicate HindIII restriction sites located within <i>Ac</i> or <i>fAc</i> sequences.</p></div

RT-PCR Analysis of <i>P-oo</i> Transcripts

<p>RNA was extracted from kernel pericarp (20 DAP), reverse transcribed, and PCR-amplified using primers complementary to both <i>p1</i> and <i>p2</i> transcripts. The progenitor allele <i>(P1-rr11)</i> shows amplification of a 605-bp band from <i>p1.</i> The <i>p-ww2</i> and <i>P-oo</i> alleles show amplification of a 522-bp band characteristic of the 5′ region of the <i>p2</i> gene. The <i>p1-ww1112</i> allele has a deletion of <i>p1;</i> the native <i>p2</i> gene is intact in this allele, but is not expressed in kernel pericarp.</p

Catalytic Access to Bridged Sila‑<i>N</i>‑heterocycles from Piperidines via Cascade sp³ and sp² C–Si Bond Formation

Described herein is the development of an unprecedented route to bridged sila-N-heterocycles via B­(C6F5)3-catalyzed cascade silylation of N-aryl piperidines with hydrosilanes. Mechanistic studies indicated that an outer-sphere ionic path is operative to involve three sequential catalytic steps having N-silyl piperidinium borohydride as a resting species: (i) dehydrogenation of the piperidine ring, (ii) β-selective hydrosilylation of a resultant enamine intermediate, and (iii) intramolecular dehydrogenative sp2 C–H silylation

Synthesis of Cyclohexane-Fused Isocoumarins via Cationic Palladium(II)-Catalyzed Cascade Cyclization Reaction of Alkyne-Tethered Carbonyl Compounds Initiated by Intramolecular Oxypalladation of Ester-Substituted Aryl Alkynes

A cationic Pd­(II)-catalyzed cascade cyclization reaction of alkyne-tethered carbonyl compounds was developed. This reaction is initiated by intramolecular oxypalladation of alkynes with an ester group followed by 1,2-addition of the formed C–Pd­(II) bond to the carbonyl group, providing a highly efficient method for the synthesis of cyclohexane-fused isocoumarins

PCR analysis of the twinned alleles with primers 1+2+Ac5.

<p>Lane 1: DNA ladder; lanes 2 and 5: water (negative control); lanes 3 and 4: <i>P1-ovov454</i>, <i>P1-rr-T1</i>; lanes 6 and 7: <i>P1-ovov454</i>, <i>P1-rr-T481</i>. Note that primers 1 and 2 are specific for each allele.</p