R and Structure scripts

R and Structure script

original Structure results

7-zip archive containing the results from the structure runs for the original data; to use copy to /R/structure/result

Morphological divergence of <i>Rheum nobile</i>.

<p>(A) An individual of <i>R. nobile</i>. (B) Bract. (C) Normal leaf. Bars 1 cm.</p

KEGG biochemical mappings for <i>Rheum nobile</i>.

<p>KEGG biochemical mappings for <i>Rheum nobile</i>.</p

Genome-Scale Transcriptome Analysis of the Alpine “Glasshouse” Plant <i>Rheum nobile</i> (Polygonaceae) with Special Translucent Bracts

<div><p>Background</p><p><i>Rheum nobile</i> is an alpine plant with translucent bracts concealing the inflorescence which produce a “glasshouse” effect promoting the development of fertile pollen grains in such conditions. The current understanding of the adaptation of such bracts to alpine environments mainly focuses on the phenotypic and physiological changes while the genetic basis is very limited. By sequencing the upper bract and the lower rosulate leaf from the same <i>R. nobile</i> stem, we identified candidate genes that may be involved in alpine adaption of the translucent bract in “glasshouse” plants and illustrated the changes in gene expression underlying the adaptive and complex evolution of the bracts phenotype.</p><p>Results</p><p>A total of 174.2 million paired-end reads from each transcriptome were assembled into 25,249 unigenes. By comparing the gene expression profiles, we identified 1,063 and 786 genes up-regulated respectively in the upper bract and the lower leaf. Functional enrichment analyses of these genes recovered a number of differential important pathways, including flavonoid biosynthesis, mismatch repair and photosynthesis related pathways. These pathways are mainly involved in three types of functions: 9 genes in the UV protective process, 9 mismatch repair related genes and 88 genes associated with photosynthesis.</p><p>Conclusions</p><p>This study provides the first comprehensive dataset characterizing <i>Rheum nobile</i> gene expression at the transcriptomic scale, and provides novel insights into the gene expression profiles associated with the adaptation of the “glasshouse” plant bracts. The dataset will be served as a public genetic resources for further functional and evolutionary studies of “glasshouse” plants.</p></div

Summary of transcriptome assembly for <i>Rheum nobile</i>.

<p>Summary of transcriptome assembly for <i>Rheum nobile</i>.</p

Schematic of the flavonoid biosynthetic pathway.

<p>ANR, anthocyanidin reductase; ANS, anthocyanidin synthase; CHR, chalcone reductase; CHS, chalcone synthase; CHI, chalcone isomerase; DFR, dihydroflavonol 4-reductase; DMID, 7, 2′-dihydroxy, 4′-methoxyisoflavanol dehydratase; FLS, flavonol synthase; F3H, flavanone 3-hydroxylase; F3′H, flavonoid 3′ hydroxylase; F3′5′H, flavonoid 3′5′ hydroxylase; FS1/FS2, flavone synthase; I2′H, isoflavone 2′-hydroxylase; IFR, isoflavone reductase; IFS, isoflavone synthase; IOMT, isoflavone O-methyltransferase; LAR, leucoanthocyanidin reductase; LDOX, leucoanthocyanidin dioxygenase; OMT, O-methyltransferase; RT, rhamnosyl transferase; UFGT, UDPG flavonoid glucosyl transferase; VR, vestitone reductase. The names of the major classes of flavonoid endproducts are boxed. Some of the known functions of the compounds in each class are indicated in italics. Genes annotated in significantly enriched KEGG pathway in differentially expressed genes are highlighted in blue. Individual T0 (left) and T1 (right) are indicated in 2-box strings. Heat maps were drawn using ratio of RPKM (upper bract/lower leaf) values. Red indicates high RPKM value, green indicates low RPKM value. Adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0110712#pone.0110712-WinkelShirley2" target="_blank">[64]</a>.</p

The mismatch repair pathway.

<p>Genes up-regulated significantly (P-value ≤0.05) enriched in mismatch repair pathway are highlighted in blue.</p

COG function classification of the <i>Rheum nobile</i> transcriptome.

<p>In total, 4,560 sequences out of 25,249 unigenes were grouped into 24 COG classifications.</p

The coding and scoring for the characters in this study.

<p>^a). The five states are [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141821#pone.0141821.ref046" target="_blank">46</a>]:</p><p><b>Lanceolate</b>: Lance-shaped; 4–5 times longer than wide; widest point between base and middle.</p><p><b>Broad triangle</b>: Triangle-shaped; <1 times longer than wide; widest point at base.</p><p><b>Narrow triangle</b>: Triangle-shaped; 1–2 times longer than wide; widest point at base.</p><p><b>Linear</b>: long and narrow; >5 times longer than wide; with more or less parallel sides.</p><p><b>Oblong</b>: oval with parallel sides for much of its length; 2–4 times longer than broad.</p><p><b>Ovate</b>: Egg-shaped in outline, 1–2 times longer than wide, widest point between base and middle.</p><p>^b). <b>Semi triplinerved</b> means three-nerved, with the one lateral nerves arising from the mid-nerve above the base [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0141821#pone.0141821.ref047" target="_blank">47</a>].</p><p>The coding and scoring for the characters in this study.</p