Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

<p>Abstract</p> <p>Background</p> <p>Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs) are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out.</p> <p>Results</p> <p>Sixty complete LTR-RT elements were classified into 35 families within four <it>Copia </it>and three <it>Gypsy </it>lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of <it>Gyps</it>y/heterochromatin, <it>Copia</it>/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of <it>Ale1</it>, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements.</p> <p>Conclusions</p> <p>Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.</p

Mutator system derivatives isolated from sugarcane genome sequence

Mutator-like transposase is the most represented transposon transcript in the sugarcane transcriptome. Phylogenetic reconstructions derived from sequenced transcripts provided evidence that at least four distinct classes exist (I- IV) and that diversification among these classes occurred early in Angiosperms, prior to the divergence of Monocots/ Eudicots. The four previously described classes served as probes to select and further sequence six BAC clones from a genomic library of cultivar R570. A total of 579,352 sugarcane base pairs were produced from these "Mutator system" BAC containing regions for further characterization. The analyzed genomic regions confirmed that the predicted structure and organization of the Mutator system in sugarcane is composed of two true transposon lineages, each containing a specific terminal inverted repeat and two transposase lineages considered to be domesticated. Each Mutator transposase class displayed a particular molecular structure supporting lineage specific evolution. MUSTANG, previously described domesticated genes, are located in syntenic regions across Sacharineae and, as expected for a host functional gene, posses the same gene structure as in other Poaceae. Two sequenced BACs correspond to hom(eo)logous locus with specific retrotransposon insertions that discriminate sugarcane haplotypes. The comparative studies presented, add information to the Mutator systems previously identified in the maize and rice genomes by describing lineage specific molecular structure and genomic distribution pattern in the sugarcane genome. (Résumé d'auteur

In silico analysis of cytochrome p450 genes involved in the metabolism of diterpenes in Coffea.

Brazil is the largest world producer and exporter of coffee, being also the second largest consumer market. Among the main goals of coffee breeders, studies aiming the improvement of cup quality and plant tolerance to biotic and abiotic stresses have extreme importance. Beverage nutraceutical properties and plant defense mechanisms are directly linked to diterpenes present in the lipid fraction of coffee beans, such as cafestol (Caf ) and caveol (Cav). Many members of P 450 gene family are involved in plant secondary metabolism, including diterpenes synthesis. In order to depict biochemical and genetic aspects of diterpenes byosinthesis, we did an in silico characterization of p450 gene family in Coffea spp., and we also quantified Caf and Cav in coffee fruit tissues for further gene expression studies involving diterpens metabolism. Using keyword and Blast search, 1396 ESTs related to Cyt p450 were selected from the Brazilian Coffee Genome Project (http://www.lge.ibi. unicamp.br/cafe). After assembling, we observed 157 putative unigenes, distributed in 92 contigs and 65 singlets. The contigs were analyzed using BLAST X versus public sequences databases (GenBank and Harvest Coffea), confirming their identity to 91 Cyt P450 genes. Expression profiles were inferred by electronic Northern blot of all contigs, allowing the selection of 7 candidate genes for transcriptional analysis based in fruit cDNA library expression. Caf and Cav were measured using HPLC in two different fruit developmental stages: 90 DAF (Days After Flowering) vs 120 DAF and in fruits (120 DAF) treated with 2?M methyl Jasmonate (MJ). Fruits at 120 DAF had an increase of 42% in Cav and 19% in Caf levels in relation to 90DAF fruits. MJ treatment resulted in samples with an average increase of 18% of Cav and 35% of Caf. RNAs were extracted from these samples for future transcriptional analyses. This study establish a platform for expression analysis of cyt P450 candidate genes in RNA samples from tissues with contrasting accumulation of Cav and Caf. (Texte intégral

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily. The mapping population parents (‘IAC66-6’ and ‘TUC71-7’) contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization. Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease13CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESPnão temnão tem2010/51708-

Decreased production of TNF-alpha by lymph node cells indicates experimental autoimmune encephalomyelitis remission in Lewis rats

Experimental autoimmune encephalomyelitis (EAE) is mediated by CD4+ Th1 cells that mainly secrete IFN-&#947; and TNF-&#945;, important cytokines in the pathophysiology of the disease. Spontaneous remission is, in part, attributed to the down regulation of IFN-&#947; and TNF-&#945; by TGF-&#946;. In the current paper, we compared weight, histopathology and immunological parameters during the acute and recovery phases of EAE to establish the best biomarker for clinical remission. Female Lewis rats were immunised with myelin basic protein (MBP) emulsified with complete Freund's adjuvant. Animals were evaluated daily for clinical score and weight prior to euthanisation. All immunised animals developed the expected characteristics of EAE during the acute phase, including significant weight loss and high clinical scores. Disease remission was associated with a significant reduction in clinical scores, although immunised rats did not regain their initial weight values. Brain inflammatory infiltrates were higher during the acute phase. During the remission phase, anti-myelin antibody levels increased, whereas TNF-&#945; and IFN-&#947; production by lymph node cells cultured with MBP or concanavalin A, respectively, decreased. The most significant difference observed between the acute and recovery phases was in the induction of TNF-&#945; levels in MBP-stimulated cultures. Therefore, the in vitro production of this cytokine could be used as a biomarker for EAE remission