Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

Gene duplication occurs by either DNA- or RNA-based processes; the latter duplicates single genes via retroposition of messenger RNA. The expression of a retroposed gene copy (retrocopy) is expected to be uncorrelated with its source gene because upstream promoter regions are usually not part of the retroposition process. In contrast, DNA-based duplication often encompasses both the coding and the intergenic (promoter) regions; hence, expression is often correlated, at least initially, between DNA-based duplicates. In this study, we identified 150 retrocopies in rice (Oryza sativa L. ssp japonica), most of which represent ancient retroposition events. We measured their expression from high-throughput RNA sequencing (RNAseq) data generated from seven tissues. At least 66% of the retrocopies were expressed but at lower levels than their source genes. However, the tissue specificity of retrogenes was similar to their source genes, and expression between retrocopies and source genes was correlated across tissues. The level of correlation was similar between RNA- and DNA-based duplicates, and they decreased over time at statistically indistinguishable rates. We extended these observations to previously identified retrocopies in Arabidopsis thaliana, suggesting they may be general features of the process of retention of plant retrogenes

Expression of Flavone Synthase II and Flavonoid 3′-Hydroxylase is Associated with Color Variation in Tan-colored Injured Leaves of Sorghum

Sorghum (Sorghum bicolor L. Moench) exhibits various color changes in injured leaves in response to cutting stress. Here, we aimed to identify key genes for the light brown and dark brown color variations in tan-colored injured leaves of sorghum. For this purpose, sorghum M36001 (light brown injured leaves), Nakei-MS3B (purple), and a progeny, #7 (dark brown), from Nakei-MS3B × M36001, were used. Accumulated pigments were detected by using high-performance liquid chromatography: M36001 accumulated only apigenin in its light brown leaves; #7 accumulated both luteolin and a small amount of apigenin in its dark brown leaves, and Nakei-MS3B accumulated 3-deoxyanthocyanidins (apigeninidin and luteolinidin) in its purple leaves. Apigenin or luteolin glucoside derivatives were also accumulated, in different proportions. Differentially expressed genes before and after cutting stress were identified by using RNA-seq. Integration of our metabolic and RNA-seq analyses suggested that expression of only flavone synthase II (FNSII) led to the synthesis of apigenin in M36001, expression of both FNSII and flavonoid 3′-hydroxylase (F3′H) led to the synthesis of apigenin and luteolin in #7, and expression of both flavanone 4-reductase and F3’H led to the synthesis of 3-deoxyanthocyanidins in Nakei-MS3B. These results suggest that expression of FNSII is related to the synthesis of flavones (apigenin and luteolin) and the expression level of F3′H is related to the balance of apigenin and luteolin. Expression of FNSII and F3′H is thus associated with dark or light brown coloration in tan-colored injured leaves of sorghum

Simultaneous transcriptome analysis of Sorghum and Bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly.

The recent development of RNA sequencing (RNA-seq) technology has enabled us to analyze the transcriptomes of plants and their pathogens simultaneously. However, RNA-seq often relies on aligning reads to a reference genome and is thus unsuitable for analyzing most plant pathogens, as their genomes have not been fully sequenced. Here, we analyzed the transcriptomes of Sorghum bicolor (L.) Moench and its pathogen Bipolaris sorghicola simultaneously by using RNA-seq in combination with de novo transcriptome assembly. We sequenced the mixed transcriptome of the disease-resistant sorghum cultivar SIL-05 and B. sorghicola in infected leaves in the early stages of infection (12 and 24 h post-inoculation) by using Illumina mRNA-Seq technology. Sorghum gene expression was quantified by aligning reads to the sorghum reference genome. For B. sorghicola, reads that could not be aligned to the sorghum reference genome were subjected to de novo transcriptome assembly. We identified genes of B. sorghicola for growth of this fungus in sorghum, as well as genes in sorghum for the defense response. The genes of B. sorghicola included those encoding Woronin body major protein, LysM domain-containing intracellular hyphae protein, transcriptional factors CpcA and HacA, and plant cell-wall degrading enzymes. The sorghum genes included those encoding two receptors of the simple eLRR domain protein family, transcription factors that are putative orthologs of OsWRKY45 and OsWRKY28 in rice, and a class III peroxidase that is a homolog involved in disease resistance in the Poaceae. These defense-related genes were particularly strongly induced among paralogs annotated in the sorghum genome. Thus, in the absence of genome sequences for the pathogen, simultaneous transcriptome analysis of plant and pathogen by using de novo assembly was useful for identifying putative key genes in the plant-pathogen interaction

Le Peuple : organe quotidien du syndicalisme

01 juin 19381938/06/01 (A20,N6339)-1938/06/01

Additional file 2: Table S1. of Root lodging is a physical stress that changes gene expression from sucrose accumulation to degradation in sorghum

Comparison of expression levels of sorghum genes in intact and lodged stems. Columns show the following, from the left: gene name (gene_id), chromosomal position (locus), average FPKM (fragments per kilobase of exon per million mapped sequence reads) of three intact sorghum plants (fpkm_intact), average FPKM of three lodged sorghum plants (fpkm_lodged), log2 value of fold change from lodged sorghum to intact sorghum (log2_ratio), P-value (p_value), q-value (q_value), and statistical significance (yes/no). (XLSX 2174 kb

MOESM1 of The sorghum SWEET gene family: stem sucrose accumulation as revealed through transcriptome profiling

Additional file 1: Fig. S1. Amino acid alignment of SWEET proteins. (A) Alignment of SWEET4-1, SWEET4-2, and SWEET4-3 of SIL-05 and BTx623. Red arrows indicate amino acids that differ between SIL-05 and BTx623: V172L of SWEET4-1 and D229E of SWEET4-3. (B) Alignment of putative orthologs of SWEET4-1 among plants. The aspartic acid at 229 of SWEET4-1 (corresponding to position 229 of sorghum SWEET4-3; red arrow) is conserved among putative SWEET orthologs in Brachypodium distachyon, Oryza sativa, Setaria italica, and Zea mays

Additional file 1: Figure S1. of Root lodging is a physical stress that changes gene expression from sucrose accumulation to degradation in sorghum

Comparison of sizes and weights in intact and lodged sorghum. Average plant height, stem diameter, raw stem weight, and raw panicle weight of 36 intact plants and 12 lodged plants are shown. (PDF 27 kb

Molecular and Functional Characterization of PEBP Genes in Barley Reveal the Diversification of Their Roles in Flowering1[W][OA]

Five barley (Hordeum vulgare) PEBP (for phosphatidylethanolamine-binding protein) genes were analyzed to clarify their functional roles in flowering using transgenic, expression, and quantitative trait locus analyses. Introduction of HvTFL1 and HvMFT1 into rice (Oryza sativa) plants did not result in any changes in flowering, suggesting that these two genes have functions distinct from flowering. Overexpression of HvFT1, HvFT2, and HvFT3 in rice resulted in early heading, indicating that these FT-like genes can act as promoters of the floral transition. HvFT1 transgenic plants showed the most robust flowering initiation. In barley, HvFT1 was expressed at the time of shoot meristem phase transition. These results suggest that HvFT1 is the key gene responsible for flowering in the barley FT-like gene family. HvFT2 transgenic plants also showed robust flowering initiation, but HvFT2 was expressed only under short-day (SD) conditions during the phase transition, suggesting that its role is limited to specific photoperiodic conditions in barley. Flowering activity in HvFT3 transgenic rice was not as strong and was modulated by the photoperiod. These results suggest that HvFT3 functions in flowering promotion but that its effect is indirect. HvFT3 expression was observed in Morex, a barley cultivar carrying a dominant allele of Ppd-H2, a major quantitative trait locus for flowering under SD conditions, although no expression was detected in Steptoe, a cultivar carrying ppd-H2. HvFT3 was expressed in Morex under both long-day and SD conditions, although its expression was increased under SD conditions. HvFT3 was mapped to chromosome 1HL, the same chromosome that carries Ppd-H2. Genomic sequence analyses revealed that Morex possesses an intact HvFT3 gene, whereas most of this gene has been lost in Steptoe. These data strongly suggest that HvFT3 may be identical to Ppd-H2