Draft pan-genome sequence of american B73 and european F2 maize lines

The archive file contains the draft sequence of the american B73 and the european F2 maize lines pan-genome (fast format), the gene prediction for F2-specific regions (gtf format) and the location of F2- and B73-specific regions (gff format). More details are available from README files included in the archive

LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-1

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>sponding to a LTR divergence of 0.01 (0.385 My). For complete copies, ("2 LTRs") this divergence corresponds to the divergence between the two LTRs. For truncated copies (Internal Region [IR], LTR, and LTR-Internal region [LTR-IR]), the divergence is derived from the "2 LTRs" copies (see Materials and Methods and Figure 1)

LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss-0

<p><b>Copyright information:</b></p><p>Taken from "LTR retrotransposons in rice (, L.): recent burst amplifications followed by rapid DNA loss"</p><p>http://www.biomedcentral.com/1471-2164/8/218</p><p>BMC Genomics 2007;8():218-218.</p><p>Published online 6 Jul 2007</p><p>PMCID:PMC1940013.</p><p></p>proximately at the same time. Upon insertion, all the new copies are identical in sequence as well as the two LTRs of each copy, leading to a null divergence between copies (Div = 0) and between the two LTRs of each copy (Div= 0). Over time, all sequences evolve at the same rate, so both the divergence between two copies and the divergence between the two LTRs of one copy are equal at a given time. Hence, if the nucleotide divergence between a truncated copy and a copy with two LTRs ("2 LTRs" copy) is equal to the nucleotide divergence between the two LTRs of the "2 LTRs" copy, the two copies originated from the same burst of amplification and the insertion date estimated for the "2 LTRs" copy can be used as an approximation of the insertion date of the truncated one

Number of genes exhibiting patterns consistent with Differential Selection (DS_candidates) in each pairwise comparison.

<p>Number of genes exhibiting patterns consistent with Differential Selection (DS_candidates) in each pairwise comparison.</p

Historical splits and admixtures between populations as inferred by TreeMix using a model with 3 admixture events.

<p>The TreeMix model explains 99.75% of the variation. Admixtures are colored according to their weight. The model indicates an admixed origin of Corn Belts Dents (arrow weight = 0.44), the European Flints (arrow weight = 0.47), and the Italian material (arrow weight = 0.35).</p

Genome-wide patterns of nucleotide diversity of American and European samples.

<p>A: Box-plots of non-genic per-bp nucleotide diversity (<i>π</i>) estimated on 4,799 non-overlapping segments of 10kb along the genome. B: Folded Site Frequency Spectra of the European sample and the American sample projected down to 29 samples. SFS were built on a common set of 2,941,528 non-genic SNPs. SFS expectation for American landraces from a model incorporating a domestication bottleneck, population expansion and gene flow (parameters from [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006666#pgen.1006666.ref028" target="_blank">28</a>]) is shown by a red line. C: Variation of <i>π</i>/bp along chromosome 1 computed from 50kb sliding windows.</p

Patterns of differential selection at <i>SU1</i> gene and the nearby <i>TGA1</i> domestication gene.

<p>(A) Nei’s genetic diversity (H) averaged on overlapping sliding windows of 1,000 SNPs (1 SNP step) along chromosome 4 with positions indicated in kb (CBDs in dark blue, NFs in green). (B) Status of biallelic SNPs per line within each genetic group as inferred from Structure is shown (with most frequent allele in dark grey) as well as pairwise LD computed from r² from positions 41,000,000 to 45,001,000 bp. Gene positions <i>SU1</i>, <i>GRMZM2G138198</i> are indicated with boxes in red (candidate genes) and <i>TGA1</i> in black. (C) Zoom within the region with XP-CLR (dots) and <i>D</i> values (lines with the same color code as in A) presented along with the genome-wide 5% quantile (dark blue and green dotted line for <i>D</i> within CBDs and NFs respectively, and black dotted line for XP-CLR between CBDs and NFs). <i>GRMZM2G138198</i> and <i>SU1</i> positions are indicated by red boxes.</p

The effectiveness of sophisticated capital budgeting practices: Empirical evidence from the Netherlands

This study examines the effectiveness of sophisticated capital budgeting practices. The theoretical applications of sophisticated capital budgeting practices (defined as the use of real option reasoning and/or game theory decision rules) have been well documented; however, empirical evidence on the effectiveness of these sophisticated capital budgeting practices is scarce. The empirical results from a survey of Dutch organizations suggest that the use of sophisticated capital budgeting practices is not necessarily associated with higher performance. However, the results also indicate that particular industries may benefit from sophisticated capital budgeting practices. Additional research may identify the specific characteristics that affect the effectiveness of sophisticated capital budgeting practices for individual companies

ZeaMaysF2 draft assembly

Zea mays F2 assembly draft release 1.0 02/2014 Aude Darracq, Johann Joets Contact: [email protected] UMR GGE, 91190 Gif-sur-Yvette, France Assembly was conducted from a set of several illumina sequencing libraries paired-end and mate-pair as well as w mseq library for a total depth of 90X. Reads have been cleaned and error corrected before beeing assembled with ABySS software (K=81). Contigs were further assembled into scaffolds using SSPACE and gap were filled using Gapfiller. # scaffolds (>200 bp) 590,011 largest scaffold 130 kb scaffold N50 14 kb assembly length 1.6 Gb % of covered genome 6

Additional file 2: Figure S1. of Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants

Quality analysis of F2 WGA in a gene-rich region. A. A MUMmer alignment showing that more than 44% of a 112.2 kb F2 BAC sequence from the Bronze locus is covered by 3 scaffolds from the F2 WGA. B. Nearly all genes of this region are assembled into one single scaffold while the two other scaffolds cover mostly non-genic DNA and TE. Gaps indicated by a star (A) or an orange box (B) delineate contigs of each scaffold. All contigs are correctly ordered and oriented even in non-genic regions. (PDF 464 kb