Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. One of the sucrose pathway genes, sucrose-6-phosphate phosphohydrolase, is duplicated in sugarcane and sorghum, but not in rice and maize. A diversity analysis of the s6pp duplication region revealed haplotype-structured sequence composition. Examination of hom(e)ologous loci indicate both sequence structural and sRNA landscape variation. A synteny analysis shows that the sugarcane genome has expanded relative to the sorghum genome, largely due to the presence of transposable elements and uncharacterized intergenic and intronic sequences.Conclusion: This release of sugarcane genomic sequences will advance our understanding of sugarcane genetics and contribute to the development of molecular tools for breeding purposes and gene discovery. © 2014 de Setta et al.; licensee BioMed Central Ltd.151European Commission: Agriculture and Rural Development: Sugar http://ec.europa.eu/agriculture/sugar/index_en.htmKellogg, E.A., Evolutionary history of the grasses (2001) Plant Physiol, 125, pp. 1198-1205Grivet, L., Arruda, P., Sugarcane genomics: depicting the complex genome of an important tropical crop (2001) Curr Opin Plant Biol, 5, pp. 122-127Piperidis, G., Piperidis, N., D'Hont, A., Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane (2010) Mol Genet Genomics, 284, pp. 65-73D'Hont, A., 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Ferric Iron Uptake Genes Are Differentially Expressed In The Presence Of Copper Sulfides In Acidithiobacillus Ferrooxidans Strain Lr

Acidithiobacillus ferrooxidans is one of the most widely used microorganisms in bioleaching operations to recover copper from low-grade copper sulfide ores. This work aimed to investigate the relative expression of genes related to the iron uptake system when A. ferrooxidans LR was maintained in contact with chalcopyrite or bornite as the sole energy source. Real-time quantitative PCR analysis revealed that the presence of bornite had no effect on the expression of seven genes related to the siderophore-mediated Fe(III) uptake system, while in the presence of chalcopyrite the expression of the genes was up-regulated. Bioinformatic analysis of the genomic region where these genes were found revealed the existence of three new putative DNA-binding sequences for the ferric iron uptake transcriptional regulator (Fur). Electrophoretic mobility shift assays demonstrated that a purified A. ferrooxidans His-tagged Fur protein was able to bind in vitro to each of these putative Fur boxes, suggesting that Fur regulated the expression of these genes. The expression of fur and two known Fur-regulated genes, mntH and dsrK, was also investigated in the presence of chalcopyrite. While the expression of fur and mntH was up-regulated, the expression of dsrK was down-regulated. The low amount of ferrous iron in the medium was probably responsible for the up-regulation of fur and the genes related to the siderophore-mediated Fe(III) uptake system when A. ferrooxidans LR was kept in the presence of chalcopyrite. A homology model of the A. ferrooxidans Fur was constructed and revealed that the putative DNA-binding surface presents conserved positively charged residues, supporting a previously suggested mode of interaction with DNA. 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De Novo Assembly And Transcriptome Analysis Of Contrasting Sugarcane Varieties.

Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species.9

De Novo Assembly And Transcriptome Analysis Of Contrasting Sugarcane Varieties

Sugarcane is an important crop and a major source of sugar and alcohol. In this study, we performed de novo assembly and transcriptome annotation for six sugarcane genotypes involved in bi-parental crosses. The de novo assembly of the sugarcane transcriptome was performed using short reads generated using the Illumina RNA-Seq platform. We produced more than 400 million reads, which were assembled into 72,269 unigenes. Based on a similarity search, the unigenes showed significant similarity to more than 28,788 sorghum proteins, including a set of 5,272 unigenes that are not present in the public sugarcane EST databases; many of these unigenes are likely putative undescribed sugarcane genes. From this collection of unigenes, a large number of molecular markers were identified, including 5,106 simple sequence repeats (SSRs) and 708,125 single-nucleotide polymorphisms (SNPs). This new dataset will be a useful resource for future genetic and genomic studies in this species. © 2014 Cardoso-Silva et al

De Novo Assembly And Transcriptome Analysis Of The Rubber Tree (hevea Brasiliensis) And Snp Markers Development For Rubber Biosynthesis Pathways

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection. © 2014 Mantello et al.97Sakdapipanich, J.T., Structural characterization of natural rubber based on recent evidence from selective enzymatic treatments (2007) J Biosci Bioeng, 103, pp. 287-292. , doi:10.1263/jbb.103.287Cornish, K., Similarities and differences in rubber biochemistry among plant species (2001) Phytochemistry, 57, pp. 1123-1134Gronover, C.S., Wahler, D., Prüfer, D., (2005) Natural Rubber Biosynthesis and Physic- Chemical Studies on Plant Derived LatexSaha, T., Priyadarshan, P.M., (2012) Genomics of Tree Crops, , Schnell RJ, Priyadarshan PM, editors New York, NY: Springer New York. doi:10.1007/978-1-4614-0920-5Priyadarshan, P.M., Goncalves, P.D.S., (2003) Hevea Gene Pool for Breeding, pp. 101-114Leitch, A.R., Lim, K.Y., Leitch, I.J., Neill, M.O., Molecular cytogenetic studies in rubber (1998) Hevea, pp. 464-467Pires, J.M., Secco, R., Gomes, J.I., (2002) Taxonomia e Filogeografia Das Seringueiras (Hevea Spp) Belem: Embrapa Amazonia Oriental, p. 103Pushparajah, E., Natural rubber (2001) Tree Crop Ecosystems, , Last, F.T. (ed) Amsterdam, The Netherlands: Elsevier ScienceRaj, S., Das, G., Pothen, J., Dey, S.K., Relationship between latex yield of Hevea brasiliensis and antecedent environmental parameters (2005) International Journal of Biometeorology, 49 (3), pp. 189-196. , DOI 10.1007/s00484-004-0222-6Le Guen, V., Garcia, D., Doaré, F., Mattos, C.R.R., Condina, V., A rubber tree's durable resistance to Microcyclus ulei is conferred by a qualitative gene and a major quantitative resistance factor (2011) Tree Genet Genomes, 7, pp. 877-889. , doi:10.1007/s11295-011-0381-7Mantello, C.C., Suzuki, F.I., Souza, L.M., Gonçalves, P.S., Souza, A.P., Microsatellite marker development for the rubber tree (Hevea brasiliensis): Characterization and cross-amplification in wild Hevea species (2012) BMC Res Notes, 5, p. 329. , doi:10.1186/1756-0500-5-329Feng, S.P., Li, W.G., Huang, H.S., Wang, J.Y., Wu, Y.T., Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis) (2008) Mol Breed, 23, pp. 85-97. , doi:10.1007/s11032-008-9216-0Triwitayakorn, K., Chatkulkawin, P., Kanjanawattanawong, S., Sraphet, S., Yoocha, T., Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map (2011) DNA Res, 18, pp. 471-482. , doi:10.1093/dnares/dsr034Li, D., Deng, Z., Qin, B., Liu, X., Men, Z., De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.) 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Vagal reflexes following an exercise stress test: A simple clinical tool for gene-specific risk stratification in the long QT syndrome.

Objectives The study assessed whether heart rate (HR) reduction following an exercise stress test (ExStrT), an easily quantifiable marker of vagal reflexes, might identify high-and low-risk long QT syndrome (LQTS) type 1 (LQT1) patients. Background Identification of LQTS patients more likely to be symptomatic remains elusive. We have previously shown that depressed baroreflex sensitivity, an established marker of reduced vagal reflexes, predicts low probability of symptoms among LQT1. Methods We studied 169 LQTS genotype-positive patients < 50 years of age who performed an ExStrT with the same protocol, on and off beta-blockers including 47 South African LQT1 patients all harboring the KCNQ1-A341V mutation and 122 Italian LQTS patients with impaired (I-Ks-, 66 LQT1) or normal (I-Ks +/-, 50 LQT2 and 6 LQT3) I-Ks current. Results Despite similar maximal HR and workload, by the first minute after cessation of exercise the symptomatic patients in both IKs-groups had a greater HR reduction compared with the asymptomatic (19 +/- 7 beats/min vs. 13 +/- 5 beats/min and 27 +/- 10 beats/min vs. 20 +/- 8 beats/min, both p = 0.009). By contrast, there was no difference between the I-Ks +/- symptomatic and asymptomatic patients (23 +/- 9 beats/min vs. 26 +/- 9 beats/min, p = 0.47). LQT1 patients in the upper tertile for HR reduction had a higher risk of being symptomatic (odds ratio: 3.28, 95% confidence interval: 1.3 to 8.3, p = 0.012). Conclusions HR reduction following exercise identifies LQT1 patients at high or low arrhythmic risk, independently of beta-blocker therapy, and contributes to risk stratification. Intense exercise training, which potentiates vagal reflexes, should probably be avoided by LQT1 patients

Uso de cera na conservação pós-colheita do caqui cv. Giombo Use of wax in 'Giombo' persimmon cold stored

Este trabalho teve como objetivo avaliar a eficiência da cera de carnaúba na conservação pós-colheita do caqui cv. Giombo. Os tratamentos consistiram do tratamento- controle e rápida imersão nas soluções contendo 12,5; 25 e 50 % do produto comercial Meghwax ECF 100®, que é uma emulsão de cera de carnaúba não-iônica a 30 %. Após a secagem, os frutos foram armazenados a 4ºC ± 1ºC e 80 % de umidade relativa. As avaliações foram realizadas em intervalos de 15 dias de conservação em câmara fria, seguidos de 4 dias à temperatura de 20 ± 1ºC, simulando o período de comercialização. As variáveis analisadas foram: firmeza de polpa; sólidos solúveis; acidez titulável; pH; teor de ácido ascórbico, fenóis e perda de massa fresca. O uso de cera de carnaúba, independentemente da concentração utilizada, diminuiu a perda de massa dos frutos em até 7,8 % em armazenagem por 60 dias em câmara fria, seguido de quatro dias em temperatura ambiente. A imersão dos frutos em solução com 12,5% de cera foi eficiente na manutenção do teor de ácido ascórbico e da firmeza, prolongando o tempo de armazenamento por 6 dias. Com o decorrer do armazenamento, houve decréscimo da acidez e aumento do pH.<br>This research had the objective of evaluating the efficiency of the "carnaúba" wax in post-harvest of persimmon fruits (Diospyros kaki), cv. Giombo. The treatments were the rapid immersion of fruits into solutions containing 12.5, 25 and 50 % of the commercial product Meghwax ECF 100®, being a 30 % non ionic emulsion of carnaúba wax. After drying, fruits were stored at 4 ºC and 80 % RH. Chemical and physical characteristics of the fruits were measured throughout sixty days, at fifteen day intervals, followed by a 4-day period at 20 ºC simulating commercialization periods. The pulp firmness, pH, soluble solids, titratable acidity, water loss, tannins and ascorbic acid contents were evaluated. The use of carnaúba wax, regardless of the concentration, diminished the loss of fresh mass of the fruits at up to 7.8 % during storage periods of 60 days under cold chamber conditions, followed by a 4-day period at 20 ºC. The immersion of the fruits into 12.5 % of wax solutions was efficient to reduce losses of ascorbic acid and pulp firmness, extending therefore the storage period in 6 days. Throughout the time and ripening of the fruits, reductions of the acidity and increases of pH were also observed in the current study