Single sketches of hyperspectral dynamics of plant diseases for visible-near infrared (VNIR) wavelengths.

<p>Each sketch consists of parts encoding major states during pathogenesis of the plant disease with similar weights. Thus, the shorter a part, the higher the impact of the corresponding period. (Best viewed in color)</p

Characteristic phenotypes of healthy and diseased barley leaves.

<p>(<b>A</b>) Healthy barley leaf, (<b>B</b>) net blotch caused by <i>Pyrenophora teres</i>, (<b>C</b>) brown rust caused by <i>Puccinia hordei</i>, and (<b>C</b>) powdery mildew caused by <i>Blumeria graminis hordei</i>.</p

Collective disease progression via Metro Maps of hyperspectral dynamics of diseased plants for visible-near infrared (VNIR) (top) and short-wave infrared (SWIR) wavelengths (bottom).

<p>Each disease track from hyperspectral images exhibits a specific route in the metro map, the direction and the dynamic steps are in correspondence to biophysical and biochemical processes during disease development. The beginning of all routes is at the same time point/train station (day of inoculation, gray circle). (Best viewed in color)</p

Interpolated mean signatures and archetypal signatures for visible-near infrared (VNIR) and shortwave infrared (SWIR) wavelengths (measured 4–14 dai).

<p>In the left column mean signatures of diseased barley plants before selecting disease archetypal signatures and in the right column mean archetypal signatures for <i>η</i> = 1 are illustrated. Archetypal signatures allow a better differentiation between different developing stages of the diseases. Moreover, they are in accordance to visually and manually extracted reflectance signatures during disease development. (Best viewed in color)</p

Disease archetypal selections.

<p>An example image showing diseased barley plants (RGB, first column) with powdery mildew (first row), net blotch (second row) and rust (third row) 14 dai. False color images present automatically determined diseased plant pixels based on disease archetypal signatures for VNIR and SWIR data (middle and right columns). The yellower/redder the color, the greather the difference of the pixel to a healthy plant. (Best viewed in color)</p

Structures of the indole-diterpene biosynthesis loci (<i>IDT/LTM</i>) in sequenced genomes.

<p><i>IDT/LTM</i> genes are indicated by single letters, whereby <i>Q = idtQ</i> or <i>ltmQ</i> (in <i>E. festucae</i>), and so forth. Tracks from top to bottom of each map represent the following: genes, repeats, MITEs, and graphs of AT (red) and GC (blue) contents. Each gene is represented by a filled arrow indicating its direction of transcription. Closed circles indicate telomeres, and distances from the telomere on the <i>E. festucae</i> map are indicated in kilobasepairs (kb). Cyan bars representing repeat sequences are labeled with names or numbers to indicate relationships between repeats in the different species. Vertical bars beneath the repeat maps indicate MITEs. Genes for the first fully cyclized intermediate, paspaline, are indicated in blue, those for subsequent chemical decorations are shown in red, and <i>idt/ltmS</i>, with undetermined function, is in purple. Identifiable genes flanking the clusters are indicated in gray, and unfilled arrows indicate pseudogenes. The major pathway end-product for each strain is listed at the right of its map, abbreviated as indicated in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g003" target="_blank">Figure 3</a>, and in bold for those confirmed in this study.</p

Phylogenies of <i>rpbA</i> from sequenced isolates and other Clavicipitaceae.

<p>The phylogenetic tree is based on nucleotide alignment for a portion of the RNA polymerase II largest subunit gene, <i>rpbA</i>. This tree is rooted with <i>Fusarium graminearum</i> as the outgroup. Epichloae are indicated in green, <i>Claviceps</i> species are indicated in blue, <i>Periglandula</i> species are indicated in red, and <i>Aciculosporium take</i> is in black. Species for which genomes were sequenced in this study are shown in bold type, and asterisks indicate plant-associated fungi. Alkaloids listed are the major pathway end-products predicted from the genome sequences, abbreviated as shown in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g002" target="_blank">Figure 2</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g003" target="_blank">Figure 3</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g004" target="_blank">Figure 4</a>. Other abbreviations: (−) = some genes or remnants present, but not predicted to make alkaloids of this class, – = no genes present for this alkaloid class, EA = ergot alkaloids may be produced; IDT = indole-diterpenes may be produced, (ΔR*) = deletion of terminal reductase domain of <i>perA</i>.</p

Structures of the ergot alkaloid biosynthesis loci (<i>EAS</i>) in sequenced genomes.

<p>Tracks from top to bottom of each map represent the following: genes, repeats, MITEs, and graphs of AT (red) and GC (blue) contents. Each gene is represented by one or more boxes representing the coding sequences in exons, and an arrow indicating the direction of transcription. Double-slash marks (//) indicate sequence gaps within scaffolds of the assembled <i>E. festucae</i> genome sequences. Closed circles indicate telomeres, and distances from the telomere on the <i>E. festucae</i> map are indicated in kilobasepairs (kb). Cyan bars beneath each map represent repeat sequences, and are labeled with names or numbers to indicate relationships between repeats in the different species. Vertical bars beneath the repeat maps indicate MITEs. Gene names are abbreviated <i>A</i> through <i>P</i> for <i>easA</i> through <i>easP</i>, <i>W</i> for <i>dmaW</i>, and <i>clo</i> for <i>cloA</i>. Genes for synthesis of the ergoline ring system (skeleton) are shown in dark blue for the steps to chanoclavine-I (<i>W</i>, <i>F</i>, <i>E</i>, and <i>C</i>), and in light blue (<i>D</i>, <i>A</i>, and <i>G</i>) for steps to agroclavine. Genes for subsequent chemical decorations are shown in red (<i>clo</i>, <i>H</i>, <i>O</i>, <i>P</i>, <i>lpsA</i>, <i>lpsB</i>, and <i>lpsC</i>). Identifiable genes flanking the clusters are indicated in gray, and unfilled arrows indicate pseudogenes. The major pathway end-products for each strain are listed below each species name, abbreviated as indicated in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003323#pgen-1003323-g002" target="_blank">Figure 2</a>, and in bold for those confirmed in this study. Note that LAH is a reported product of <i>C. paspali</i>, but the sequenced strain is predicted not to synthesize it due to a defective <i>easE</i> gene.</p

Alkaloid profiles of sequenced isolates.^a

a<p>Strains are abbreviated as follow: <i>Cpu</i> = <i>Claviceps purpurea</i> 20.1, <i>Cfu</i> = <i>C. fusiformis</i> PRL 1980, Cpa = <i>C. paspali</i> RRC-1481, <i>Eam</i> = <i>Epichloë amarillans</i> E57, <i>Ebe</i> = <i>E. brachyelytri</i> E4804, <i>Eel</i> = <i>E. elymi</i> E56, <i>Ef</i>1 = <i>E. festucae</i> Fl1, <i>Ef</i>2 = <i>E. festucae</i> E2368, <i>Egl</i> = <i>E. glyceriae</i> E2772, <i>Et</i>8 = <i>E. typhina</i> E8, <i>Et</i>5 = <i>E. typhina</i> E5819, <i>Nga</i> = <i>N. gansuense</i> E7080, <i>Ngi</i> = <i>N. gansuense</i> var. <i>inebrians</i> E818, <i>Nun</i> = <i>N. uncinatum</i> E167, <i>Pip</i> = <i>P. ipomoeae</i> IasaF13. Symbols: + = present, (+) = intermediate inferred to be synthesized because downstream product is present, − = not predicted and not detected, (−) = predicted but not detected, nt = predicted but not tested, ERA = ergotamine, ERB = ergobalansine, ERC = ergocryptine, ERV = ergovaline. Blank cells indicate compounds not predicted from genotype, and not tested.</p>b<p>Identification of IDT-436 and terpendoles E, I, J, K, M, M, and A are tentative because authentic standards are unavailable.</p

Summary of loline alkaloid-biosynthesis pathway.

<p>Arrows indicate one or more steps catalyzed by products of the genes indicated. Arrows and genes in blue indicate steps in synthesis of the first fully cyclized intermediate (NANL). Arrows and genes in red indicate steps in modification of NANL to give the variety of lolines found in the epichloae. Asterisks indicate <i>LOL</i> genes that were newly discovered in the genome sequence of <i>E. festucae</i> E2368.</p