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

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

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

Additional file 1: of Association of APEX1 and OGG1 gene polymorphisms with breast cancer risk among Han women in the Gansu Province of China

A questionnaire survey of breast health. Questionnaire included participant's eating habits, living environment, lifestyle, smoking, physiological state, reproductive condition, past medical history and family history of cancer. (PDF 415 kb

Measuring H₂¹⁸O Tracer Incorporation on a QQQ-MS Platform Provides a Rapid, Transferable Screening Tool for Relative Protein Synthesis

Intracellular proteins are in a state of flux, continually being degraded into amino acids and resynthesized into new proteins. The rate of this biochemical recycling process varies across proteins and is emerging as an important consideration in drug discovery and development. Here, we developed a triple-stage quadrupole mass spectrometry assay based on product ion measurements at unit resolution and H₂¹⁸O stable tracer incorporation to measure relative protein synthesis rates. As proof of concept, we selected to measure the relative in vivo synthesis rate of ApoB100, an apolipoprotein where elevated levels are associated with an increased risk of coronary heart disease, in plasma-isolated very low density lipoprotein (VLDL) and low density lipoprotein (LDL) in a mouse in vivo model. In addition, serial time points were acquired to measure the relative in vivo synthesis rate of mouse LDL ApoB100 in response to vehicle, microsomal triacylglycerol transfer protein (MTP) inhibitor, and site-1 protease inhibitor, two potential therapeutic targets to reduce plasma ApoB100 levels at 2 and 6 h post-tracer-injection. The combination of H₂¹⁸O tracer with the triple quadrupole mass spectrometry platform creates an assay that is relatively quick and inexpensive to transfer across different biological model systems, serving as an ideal rapid screening tool for relative protein synthesis in response to treatment

Measuring H₂¹⁸O Tracer Incorporation on a QQQ-MS Platform Provides a Rapid, Transferable Screening Tool for Relative Protein Synthesis

Intracellular proteins are in a state of flux, continually being degraded into amino acids and resynthesized into new proteins. The rate of this biochemical recycling process varies across proteins and is emerging as an important consideration in drug discovery and development. Here, we developed a triple-stage quadrupole mass spectrometry assay based on product ion measurements at unit resolution and H₂¹⁸O stable tracer incorporation to measure relative protein synthesis rates. As proof of concept, we selected to measure the relative in vivo synthesis rate of ApoB100, an apolipoprotein where elevated levels are associated with an increased risk of coronary heart disease, in plasma-isolated very low density lipoprotein (VLDL) and low density lipoprotein (LDL) in a mouse in vivo model. In addition, serial time points were acquired to measure the relative in vivo synthesis rate of mouse LDL ApoB100 in response to vehicle, microsomal triacylglycerol transfer protein (MTP) inhibitor, and site-1 protease inhibitor, two potential therapeutic targets to reduce plasma ApoB100 levels at 2 and 6 h post-tracer-injection. The combination of H₂¹⁸O tracer with the triple quadrupole mass spectrometry platform creates an assay that is relatively quick and inexpensive to transfer across different biological model systems, serving as an ideal rapid screening tool for relative protein synthesis in response to treatment