La Petite presse : journal quotidien... / [rédacteur en chef : Balathier Bragelonne]

02 mai 18731873/05/02 (N2551)

Additional file 1: Table S1. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Collection of sequence data. (DOCX 14 kb

Additional file 18: Table S16. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Functional enrichment analysis of 6302 reference genes involved in the formation of non-reference sequences through exon/intron shuffling. The hmm accession for all the 6302 reference genes was extracted, and the number of genes with a specific hmm accession involved in the formation of non-reference sequences through exon/intron shuffling were compared with the whole genome level to find enriched accessions. In total, 3581 of these 6302 genes and 33,581 genes of the whole genome were annotated by Pfam. (DOC 40 kb

Additional file 12: of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Supplementary methods. (PDF 356 kb

Additional file 16: Table S14. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Sheet 1 shows contigs of the indica dispensable genome that were composed by reads mainly from a subgroup. Sheet 2 shows contigs of the japonica dispensable genome that were composed by reads mainly from a subgroup. Columns 2–4 show the percentage of reads mapped to the contig that belong to each subgroup. (XLS 1556 kb

Additional file 7: Table S6. of Exploring the rice dispensable genome using a metagenome-like assembly strategy

Blastn alignment result of the full-length cDNA sequences of 12 O. rufipogon genes to the contigs of the dispensable genome. (DOC 35 kb

OsNRAMP3 Is a Vascular Bundles-Specific Manganese Transporter That Is Responsible for Manganese Distribution in Rice

<div><p>Manganese (Mn) is an essential trace element for plants. Recently, the genes responsible for uptake of Mn in plants were identified in <i>Arabidopsis</i> and rice. However, the mechanism of Mn distribution in plants has not been clarified. In the present study we identified a natural resistance-associated macrophage protein (NRAMP) family gene in rice, <i>OsNRAMP3</i>, involved in Mn distribution. <i>OsNRAMP3</i> encodes a plasma membrane-localized protein and was specifically expressed in vascular bundles, especially in phloem cells. Yeast complementation assay showed that OsNRAMP3 is a functional Mn-influx transporter. When <i>OsNRAMP3</i> was absent, rice plants showed high sensitivity to Mn deficiency. Serious necrosis appeared on young leaves and root tips of the <i>OsNRAMP3</i> knockout line cultivated under low Mn conditions, and high Mn supplies could rescue this phenotype. However, the necrotic young leaves of the knockout line possessed similar levels of Mn to the wild type, suggesting that the necrotic appearance was caused by disturbed distribution of Mn but not a general Mn shortage. Additionally, compared with wild type, leaf Mn content in <i>osnramp3</i> plants was mostly in older leaves. We conclude that OsNRAMP3 is a vascular bundle-localized Mn-influx transporter involved in Mn distribution and contributes to remobilization of Mn from old to young leaves.</p></div

Expression of genes in wild-type transgenic plants under normal Pi condition.

<p>Expression of central transporters affecting Pi absorption and homeostasis in WT and transgenic plants. Error bars indicate ±SD (n = 3). (**<i>p</i><0.01 and *<i>P</i><0.05, one-way ANOVA).</p

Characterization of wild-type and transgenic plants.

<p>A: Expression of OsPT4 in transgenic plants. Seven-day-old seedlings were transferred to nutrient solution for 2 weeks. RNA was extracted from the shoots of the seedling. Oe1, Oe2, Ri1, and Ri2 represented independent <i>OsPT4</i>-overexpressing and RNA interference lines. Relative expression levels are shown as percentages compared with wild-type shown as 100% expression. B, C, and D: Growth of wild-type and transgenic plants. Plants were grown in nutrient solutions to which 0 mM Pi (LP), 1.5 mM Pi (HP), and 0.3 mM Pi (CK) were added for 21 days. E–H: Phenotypic analysis of OsPT4 transgenic plants. Height, root length, number of main roots, and tiller numbers were obtained from the 21-day-old wild-type and transgenic plants grown in nutrient solutions with different Pi concentrations. Five plants per line were measured. I and J: The Pi concentration of shoots and roots in wild-type and transgenic plants. Data are means ± SD of five biological replicates. Values are significantly different from those of wild-type: *P<0.05 and **P<0.01. (one-way ANOVA).</p

Function expression of <i>OsPT4</i> in yeast.

<p>The yeast cells were grown in solution that had been stained for acidification. The pH indicator, bromocresol purple, did not change from blue to yellow until the yeast cells had significant growth in culture. The medium contained 0 μM and 75 μM Pi, respectively. A: Color shifts in wild-type (WT), yeast strain <i>pho84</i> (control), and <i>pho84+OsPT4</i>, which express <i>OsPT4</i> in <i>pho84</i> grown on synthetic defined (SD) Ura mediums. B: Growth conditions of wild-type, <i>pho84</i>, and <i>pho84</i> transformed with pYES2-<i>OsPT4</i> generated in a 24-hour liquid culture under 0μM and 75μM Pi conditions. Statistically significant differences are indicated: **<i>p</i><0.01, Student’s one-way ANOVA analysis.</p