Function of MYST3 / MOZ: a histone acetyltransferase and chromatin regulator implicated in haematopoietic stem cell development and leukaemia

MOZ (also known as KAT6A and MYST3) is a histone acetyltransferase that is implicated in the development of hematopoietic, heart and craniofacial tissues. Reciprocal translocations generating MOZ fusion proteins are associated with acute myeloid leukaemia (AML), a heterogeneous hematopoietic stem cell disorder where the myeloid cells do not enter into differentiation process, resulting in accumulation of blast cells and absence of a fully functional granulocyte lineage. Also, mutations that truncate the C-terminus of MOZ are associated with global developmental delay. Mechanistically, it is known that MOZ acts as a cofactor for certain transcription factors, particularly those with haematopoietic or neuronal specificity, such as acute myeloid leukaemia/Runt-related transcription factor 1 (AML1/RUNX1) and PU.1. However, at the outset of this project, it was relatively unknown which genes that are regulated by MOZ in leukaemia. Thus, this work investigates MOZ target genes in a leukemic cell line to fully understand its importance in cell function and disease conditions. Firstly, we performed siRNA silencing in K562 cell line, coupled with transcription profiling by RNA sequencing. We identified 406 deregulated genes under MOZ knockdown, of which 76 were downregulated. Many of the MOZ-target genes identified are implicated in haematopoietic development and cell proliferation. Secondly, we generated MOZ/KAT6A knockout K562 cells using CRISPR CAS9n nickase technology. It allowed further analysis of the function of MOZ in leukaemia. Our results confirmed the role of MOZ in maintaining levels of H3K14ac and H3K9ac and an apparent inverse relationship with the levels of H3K14 crotonylation. Furthermore, the results indicated that MOZ is important for leukemic cell proliferation and the gene dosage influences on the cell proliferation rate. Finally, we found that genes requiring MOZ for their expression are sensitive to a novel class of bromodomain inhibitors called iBETs. Furthermore, we found evidence for the existence of MOZ in complex with BRD4 protein. This provides a hitherto unknown link between MOZ, MLL and BRD2-4 complexes and insight into how these epigenetic regulators cooperate to control gene expression

Long-term effects of chronic cocaine exposure throughout adolescence on anxiety and stress responsivity in a wistar rat model

Adolescents display increased vulnerability to engage in drug experimentation. This is often considered a risk factor for later drug abuse. In this scenario, the permanent effects of cocaine exposure during adolescence on anxiety levels and stress responsivity, which may result in behavioral phenotypes prone to addiction, are now starting to be unveiled. Thus, the purpose of the present study was to evaluate the long-lasting effects of chronic cocaine administration during adolescence, on anxiety-like behavior and on stress response. Adolescent male Wistar rats were daily administered 45-mg cocaine/kg of body weight in three equal intraperitoneal doses with 1-h interval, from postnatal day (PND) 35 to 50. The effects of cocaine administration on anxiety levels, assessed in the Elevated Plus Maze (EPM), and on social stress response, assessed in the resident-intruder paradigm (R/I), were evaluated 10 days after withdrawal, when rats were reaching the adulthood. The underlying dopaminergic activity, and the corticosterone and testosterone levels were determined. Our results showed that cocaine induced long-lasting alterations in the hypothalamus-pituitary-adrenals (HPA) axis function and in testosterone levels. Such alterations resulted in significant and enduring changes in behavioral responses to environmental challenges, such as the EPM and R/I, including the evaluation of potential threats that may lead to high-risk behavior and low-benefit choices. This was further supported by an altered dopaminergic function in the amygdala and hippocampus. The present findings provide new insights into how the use of cocaine during adolescent development may modulate emotional behavior later in life. Compromised ability to recognize and deal with potential threats is an important risk factor to perpetuate compulsive drug seeking and relapse susceptibility.info:eu-repo/semantics/publishedVersio

Being deaf in mainstream schools: the effect of a hearing loss in children’s playground behaviors

Pathways through Adolescenc

Growth and Mechanical and Tribological Characterization of Multi-Layer Hard Carbon Films

Vacuum-arc deposition is used to deposit multilayer C films by modulating the sample bias during deposition. Effect of varying the sublayer thickness in multilayer films consisting of alternating layers of ``hard`` (68.4 GPa, -100 V bias) and ``soft`` (27.5 GPa, - 200 V bias) was investigated. Films consisting of equal thickness layers of hard and soft material and an individual layer thickness varying from 10 to 35 nm were deposited. Mechanical property measurements were obtained by finite element modeling of nanoindentation load-displacement curves. The film hardness values were about 20% below the average of the component layers and relatively independent of the layer thickness. TEM revealed deterioration of the multilayer structure when the sublayer thickness was below 15 nm due to implantation damage of the hard layers caused by the energetic C{sup +} ions of the soft layers (-2000 V bias) deposited over them. Pin-on-disk wear tests show that the wear rate drops when sublayer thickness is decreased below 20 nm and remains constant with further decreases in the layer thickness

Growth and mechanical and tribological characterization of multi-layer hard carbon films

Vacuum-arc deposition is used to deposit multilayer C films by modulating the sample bias during deposition. Effect of varying the sublayer thickness in multilayer films consisting of alternating layers of ``hard`` (68.4 GPa, -100 V bias) and ``soft`` (27.5 GPa, - 200 V bias) was investigated. Films consisting of equal thickness layers of hard and soft material and an individual layer thickness varying from 10 to 35 nm were deposited. Mechanical property measurements were obtained by finite element modeling of nanoindentation load-displacement curves. The film hardness values were about 20% below the average of the component layers and relatively independent of the layer thickness. TEM revealed deterioration of the multilayer structure when the sublayer thickness was below 15 nm due to implantation damage of the hard layers caused by the energetic C{sup +} ions of the soft layers (-2000 V bias) deposited over them. Pin-on-disk wear tests show that the wear rate drops when sublayer thickness is decreased below 20 nm and remains constant with further decreases in the layer thickness

A feasibility cachaca type recognition using computer vision and pattern recognition

Brazilian rum (also known as cachaça) is the third most commonly consumed distilled alcoholic drink in the world, with approximately 2.5 billion liters produced each year. It is a traditional drink with refined features and a delicate aroma that is produced mainly in Brazil but consumed in many countries. It can be aged in various types of wood for 1-3 years, which adds aroma and a distinctive flavor with different characteristics that affect the price. A research challenge is to develop a cheap automatic recognition system that inspects the finished product for the wood type and the aging time of its production. Some classical methods use chemical analysis, but this approach requires relatively expensive laboratory equipment. By contrast, the system proposed in this paper captures image signals from samples and uses an intelligent classification technique to recognize the wood type and the aging time. The classification system uses an ensemble of classifiers obtained from different wavelet decompositions. Each classifier is obtained with different wavelet transform settings. We compared the proposed approach with classical methods based on chemical features. We analyzed 105 samples that had been aged for 3 years and we showed that the proposed solution could automatically recognize wood types and the aging time with an accuracy up to 100.00% and 85.71% respectively, and our method is also cheaper.info:eu-repo/semantics/publishedVersio

Targeted PEG-poly(glutamic acid) complexes for inhalation protein delivery to the lung

Pulmonary delivery is increasingly seen as an attractive, non-invasive route for the delivery of forthcoming protein therapeutics. In this context, here we describe protein complexes with a new ‘complexing excipient’ - vitamin B12-targeted poly(ethylene glycol)-block-poly(glutamic acid) copolymers. These form complexes in sub-200 nm size with a model protein, suitable for cellular targeting and intracellular delivery. Initially we confirmed expression of vitamin B12-internalization receptor (CD320) by Calu-3 cells of the in vitro lung epithelial model used, and demonstrated enhanced B12 receptor-mediated cellular internalization of B12-targeted complexes, relative to non-targeted counterparts or protein alone. To develop an inhalation formulation, the protein complexes were spray dried adopting a standard protocol into powders with aerodynamic diameter within the suitable range for lower airway deposition. The cellular internalization of targeted complexes from dry powders applied directly to Calu-3 model was found to be 2–3 fold higher compared to non-targeted complexes. The copolymer complexes show no complement activation, and in vivo lung tolerance studies demonstrated that repeated administration of formulated dry powders over a 3 week period in healthy BALB/c mice induced no significant toxicity or indications of lung inflammation, as assessed by cell population count and quantification of IL-1β, IL-6, and TNF-α pro-inflammatory markers. Importantly, the in vivo data appear to suggest that B12-targeted polymer complexes administered as dry powder enhance lung retention of their protein payload, relative to protein alone and non-targeted counterparts. Taken together, our data illustrate the potential developability of novel B12-targeted poly(ethylene glycol)-poly(glutamic acid) copolymers as excipients suitable to be formulated into a dry powder product for the inhalation delivery of proteins, with no significant lung toxicity, and with enhanced protein retention at their in vivo target tissue

The edge-on protoplanetary disk HH 48 NE: II. Modeling ices and silicates

Stars and planetary system

Growth and mortality of coccolithophores during spring in a temperate Shelf Sea (Celtic Sea, April 2015)

Coccolithophores are key components of phytoplankton communities, exerting a critical impact on the global carbon cycle and the Earth’s climate through the production of coccoliths made of calcium carbonate (calcite) and bioactive gases. Microzooplankton grazing is an important mortality factor in coccolithophore blooms, however little is currently known regarding the mortality (or growth) rates within non-bloom populations. Measurements of coccolithophore calcite production (CP) and dilution experiments to determine microzooplankton (≤63 µm) grazing rates were made during a spring cruise (April 2015) at the Central Celtic Sea (CCS), shelf edge (CS2), and within an adjacent April bloom of the coccolithophore Emiliania huxleyi at station J2. CP at CCS ranged from 10.4 to 40.4 µmol C m−3 d−1 and peaked at the height of the spring phytoplankton bloom (peak chlorophyll-a concentrations ∼6 mg m−3). Cell normalised calcification rates declined from ∼1.7 to ∼0.2 pmol C cell−1 d−1, accompanied by a shift from a mixed coccolithophore species community to one dominated by the more lightly calcified species E. huxleyi and Calciopappus caudatus. At the CCS, coccolithophore abundance increased from 6 to 94 cells mL−1, with net growth rates ranging from 0.06 to 0.21 d−1 from the 4th to the 28th April. Estimates of intrinsic growth and grazing rates from dilution experiments, at the CCS ranged from 0.01 to 0.86 d−1 and from 0.01 to 1.32 d−1, respectively, which resulted in variable net growth rates during April. Microzooplankton grazers consumed 59 to >100% of daily calcite production at the CCS. Within the E. huxleyi bloom a maximum density of 1986 cells mL−1 was recorded, along with CP rates of 6000 µmol C m−3 d−1 and an intrinsic growth rate of 0.29 d−1, with ∼80% of daily calcite production being consumed. Our results show that microzooplankton can exert strong top-down control on both bloom and non-bloom coccolithophore populations, grazing over 60% of daily growth (and calcite production). The fate of consumed calcite is unclear, but may be lost either through dissolution in acidic food vacuoles, and subsequent release as CO2, or export to the seabed after incorporation into small faecal pellets. With such high microzooplankton-mediated mortality losses, the fate of grazed calcite is clearly a high priority research direction

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., Unraveling the genome structure of polyploids using FISH and GISHexamples of sugarcane and banana (2005) Cytogenet Genome Res, 109, pp. 27-33D'Hont, A., Glaszmann, J.C., Sugarcane genome analysis with molecular markers: a first decade of research (2001) Int Soc Sugar Cane Technol Proc XXIV Congr, pp. 556-559Tomkins, J., Yu, Y., Miller-Smith, H., Frisch, D., Woo, S., Wing, R., A bacterial artificial chromosome library for sugarcane (1999) Theor Appl Genet, 99, pp. 419-424Vettore, L., Silva, F.R., Kemper, E.L., Souza, G.M., Silva, A.M., Ferro, M., Henrique-Silva, F., Monteiro-Vitorello, C.B., Analysis and functional annotation of an expressed sequence tag collection for tropical crop sugarcane (2003) Genome Res, 13, pp. 2725-2735Repbase http://www.girinst.org/repbase/Domingues, D.S., Cruz, G.M.Q., Metcalfe, C.J., Nogueira, F.T.S., Vicentini, R., Alves, C.S., Van Sluys, M.-A., Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns (2012) BMC Genomics, 13, p. 137National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/Meyer, F., Paarmann, D., D'Souza, M., Olson, R., Glass, E.M., Kubal, M., Paczian, T., Edwards, R.A., The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes (2008) BMC Bioinformatics, 9, p. 386Keeling, P.L., Myers, A.M., Biochemistry and genetics of starch synthesis (2010) Annu Rev Food Sci Technol, 1, pp. 271-303Phytozome v9.1: Home http://www.phytozome.net/Dias, E.S., Carareto, C.M.A., Ancestral polymorphism and recent invasion of transposable elements in Drosophila species (2012) BMC Evol Biol, 12, p. 119Posada, D., Crandall, K., Intraspecific gene genealogies: trees grafting into networks (2001) Trends Ecol Evol, 16, pp. 37-45Swaminathan, K., Alabady, M.S., Varala, K., De Paoli, E., Ho, I., Rokhsar, D.S., Arumuganathan, A.K., Hudson, M.E., Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses (2010) Genome Biol, 11, pp. R12Zanca, A.S., Vicentini, R., Ortiz-Morea, F.A., Del Bem, L.E., da Silva, M.J., Vincentz, M., Nogueira, F.T., Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane (2010) BMC Plant Biol, 10, p. 260Piriyapongsa, J., Jordan, I.K., A family of human microRNA genes from miniature inverted-repeat transposable elements (2007) PLoS ONE, 2, pp. e203Barrera-Figueroa, B.E., Gao, L., Wu, Z., Zhou, X., Zhu, J., Jin, H., Liu, R., Zhu, J.-K., High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice (2012) BMC Plant Biol, 12, p. 132Nagaki, K., Tsujimoto, H., Sasakuma, T., A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions (1998) Chromosom Res, 6, pp. 295-302Nagaki, K., Neumann, P., Zhang, D., Ouyang, S., Buell, C.R., Cheng, Z., Jiang, J., Structure, divergence, and distribution of the CRR centromeric retrotransposon family in rice (2005) Mol Biol Evol, 22, pp. 845-855Vicentini, R., Del Bem, L.E., Van Sluys, M.-A., Nogueira, F., Vincentz, M., Gene content analysis of sugarcane public ESTs reveals thousands of missing coding-genes and an unexpected pool of grasses conserved ncRNAs (2012) Trop Plant Biol, 5, pp. 199-205Kim, C., Lee, T.-H., Compton, R.O., Robertson, J.S., Pierce, G.J., Paterson, A.H., A genome-wide BAC end-sequence survey of sugarcane elucidates genome composition, and identifies BACs covering much of the euchromatin (2013) Plant Mol Biol, 81, pp. 139-147Paterson, A.H., Bowers, J.E., Bruggmann, R., Dubchak, I., Grimwood, J., Gundlach, H., Haberer, G., Carpita, N.C., The Sorghum bicolor genome and the diversification of grasses (2009) Nature, 457, pp. 551-556Chang, Y., Gong, L., Yuan, W., Li, X., Chen, G., Li, X., Zhang, Q., Wu, C., Replication protein A (RPA1a) is required for meiotic and somatic DNA repair but is dispensable for DNA replication and homologous recombination in rice (2009) Plant Physiol, 151, pp. 2162-2173Feschotte, C., Transposable elements and the evolution of regulatory networks (2008) Nat Rev Genet, 9, pp. 397-405Wang, J., Roe, B., Macmil, S., Yu, Q., Murray, J.E., Tang, H., Chen, C., Ming, R., Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes (2010) BMC Genomics, 11, p. 261Garsmeur, O., Charron, C., Bocs, S., Jouffe, V., Samain, S., Couloux, A., Droc, G., D'Hont, A., High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane (2011) New Phytol, 189, pp. 629-642Jannoo, N., Grivet, L., Chantret, N., Garsmeur, O., Glaszmann, J.C., Arruda, P., D'Hont, A., Orthologous comparison in a gene-rich region among grasses reveals stability in the sugarcane polyploid genome (2007) Plant J, 50, pp. 574-585Figueira, T.R.E.S., Okura, V., da Silva, F.R., da Silva, M.J., Kudrna, D., Ammiraju, J.S.S., Talag, J., Arruda, P., A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome (2012) BMC Res Notes, 5, p. 185Schnable, P.S., Ware, D., Fulton, R.S., Stein, J.C., Wei, F., Pasternak, S., Liang, C., Gillam, B., The B73 maize genome: complexity, diversity, and dynamics (2009) Science, 326, pp. 1112-1115Tenaillon, M.I., Hufford, M.B., Gaut, B.S., Ross-Ibarra, J., Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians (2011) Genome Biol Evol, 3, pp. 219-229Zhang, J., Yu, C., Krishnaswamy, L., Peterson, T., Transposable Elements as Catalysts for Chromosome Rearrangements (2011) Methods Mol Biol, pp. 315-326. , Totowa, NJ: Humana Press, Birchler JAMa, J., Wing, R.A., Bennetzen, J.L., Jackson, S.A., Plant centromere organization: a dynamic structure with conserved functions (2007) Trends Genet, 23, pp. 134-139D'Hont, A., Grivet, L., Feldmann, P., Rao, S., Berding, N., Glaszmann, J.C., Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics (1996) Mol Gen Genet, 250, pp. 405-413Bao, Y., Wendel, J.F., Ge, S., Multiple patterns of rDNA evolution following polyploidy in Oryza (2010) Mol Phylogenet Evol, 55, pp. 136-142Lynch, M., (2007) The Origins of Genome Architecture, , Sunderland, Massachussetts, USA: Sinauer Associates IncThe map-based sequence of the rice genome (2005) Nature, 436, pp. 793-800. , International Rice Genome Sequencing ProjectLiu, B., Xu, C., Zhao, N., Qi, B., Kimatu, J.N., Pang, J., Han, F., Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement (2009) J Genet Genomics, 36, pp. 519-528Lisch, D., How important are transposons for plant evolution? (2012) Nat Rev Genet, 14, pp. 49-61Udall, J.A., Wendel, J.F., Polyploidy and crop improvement (2006) Crop Sci, 46, pp. S3-S14Varshney, R.K., Graner, A., Sorrells, M.E., Genomics-assisted breeding for crop improvement (2005) Trends Plant Sci, 10, pp. 621-630Menossi, M., Silva-Filho, M.C., Vincentz, M., Van-Sluys, M.-A., Souza, G.M., Sugarcane functional genomics: gene discovery for agronomic trait development (2008) Int J Plant Genomics, 2008, p. 458732. , doi:10.1155/2008/458732Palhares, A.C., Rodrigues-Morais, T.B., Van Sluys, M.-A., Domingues, D.S., Maccheroni, W., Jordão, H., Souza, A.P., Vieira, M.L.C., A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers (2012) BMC Genet, 13, p. 51Andersen, J.R., Lübberstedt, T., Functional markers in plants (2003) Trends Plant Sci, 8, pp. 554-560Kalendar, R., Flavell, A.J., Ellis, T.H.N., Sjakste, T., Moisy, C., Schulman, A., Analysis of plant diversity with retrotransposon-based molecular markers (2011) Heredity (Edinb), 106, pp. 520-530PGML BACMan On The Web: Grasses http://www.plantgenome.uga.edu/bacman/BACManwww.phpRice Genome Annotation Project http://rice.plantbiology.msu.edu/Bowers, J.E., Arias, M.A., Asher, R., Avise, J.A., Ball, R.T., Brewer, G.A., Buss, R.W., Soderlund, C.A., Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses (2005) Proc Natl Acad Sci U S A, 102, pp. 13206-13211Adam-Blondon, A.-F., Bernole, A., Faes, G., Lamoureux, D., Pateyron, S., Grando, M.S., Caboche, M., Chalhoub, B., Construction and characterization of BAC libraries from major grapevine cultivars (2005) Theor Appl Genet, 110, pp. 1363-1371Manetti, M.E., Rossi, M., Cruz, G.M.Q., Saccaro, N.L., Nakabashi, M., Altebarmakian, V., Rodier-Goud, M., Van Sluys, M.A., Mutator system derivatives isolated from sugarcane genome sequence (2012) Trop Plant Biol, 5, pp. 233-243Phrap http://www.phrap.org/RepeatMasker http://www.repeatmasker.org/Jurka, J., Kapitonov, V.V., Pavlicek, A., Klonowski, P., Kohany, O., Repbase update, a database of eukaryotic repetitive elements (2005) Cytogenet Genome Res, 110, pp. 462-467Han, Y., Wessler, S.R., MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences (2010) Nucleic Acids Res, 38 (22), pp. e199. , doi: 10.1093/nar/gkq862. Epub 2010 Sep 29Frickey, T., Lupas, A., CLANS: a Java application for visualizing protein families based on pairwise similarity (2004) Bioinformatics, 20, pp. 3702-3704Han, Y., Qin, S., Wessler, S.R., Comparison of class 2 transposable elements at superfamily resolution reveals conserved and distinct features in cereal grass genomes (2013) BMC Genomics, 14, p. 71Keller, O., Kollmar, M., Stanke, M., Waack, S., A novel hybrid gene prediction method employing protein multiple sequence alignments (2011) Bioinformatics, 27, pp. 757-763Majoros, W.H., Pertea, M., Salzberg, S.L., TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders (2004) Bioinformatics, 20, pp. 2878-2879Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith, R.K., Hannick, L.I., Maiti, R., White, O., Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies (2003) Nucleic Acids Res, 31, pp. 5654-5666Haas, B.J., Salzberg, S.L., Zhu, W., Pertea, M., Allen, J.E., Orvis, J., White, O., Wortman, J.R., Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to assemble spliced alignments (2008) Genome Biol, 9, pp. R7Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., SignalP 4.0: discriminating signal peptides from transmembrane regions (2011) Nat Methods, 8, pp. 785-786TMHMM Server v. 2.0 http://www.cbs.dtu.dk/services/TMHMM-2.0/Rutherford, K., Parkhill, J., Crook, J., Horsnell, T., Rice, P., Rajandream, M.A., Barrell, B., Artemis: sequence visualization and annotation (2000) Bioinformatics, 16, pp. 944-945UniProt http://www.uniprot.org/InterPro: Protein sequence analysis and classification http://www.ebi.ac.uk/interpro/Conesa, A., Götz, S., Blast2GO: a comprehensive suite for functional analysis in plant genomics (2008) Int J Plant Genomics, 2008, pp. 1-12SUCEST-FUN Project http://sucest-fun.org/MG-RAST: metagenomics analysis server http://metagenomics.anl.gov/KAAS - KEGG automatic annotation server http://www.genome.jp/kegg/kaas/Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., Kumar, S., MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods (2011) Mol Biol Evol, 28, pp. 2731-2739Lyons, E., Freeling, M., How to usefully compare homologous plant genes and chromosomes as DNA sequences (2008) Plant J, 53, pp. 661-673Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT (1999) Nucleic Acids Symp Ser, 41, pp. 95-98Geneious - Homepage http://www.geneious.com/Heslop-Harrison, P., Schwarzacher, T., (2000) Practical In Situ Hybridization, , Oxford, UK: BIOS Scientific Publishers LtdAljanabi, S., Forget, L., Dookun, A., An improved and rapid protocol for the isolation of polysaccharide-and polyphenol-free sugarcane DNA (1999) Plant Mol Biol Report, 17, pp. 1-8Maq: Mapping and assembly with qualities http://maq.sourceforge.net/SeqMonk http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/Gasic, K., Hernandez, A., Korban, S.S., RNA extraction from different apple tissues rich in polyphenols and polysaccharides for cDNA (2004) Plant Mol Biol Report, 22 (DECEMBER), pp. 437a-437gLi, H., Durbin, R., Fast and accurate short read alignment with Burrows-Wheeler transform (2009) Bioinformatics, 25, pp. 1754-1760Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Durbin, R., The sequence Alignment/Map format and SAMtools (2009) Bioinformatics, 25, pp. 2078-2079Thompson, J.D., Higgins, D.G., Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice (1994) Nucleic Acids Res, 22, pp. 4673-4680Bandelt, H.J., Forster, P., Röhl, A., Median-joining networks for inferring intraspecific phylogenies (1999) Mol Biol Evol, 16, pp. 37-48Paterson, A.H., Freeling, M., Tang, H., Wang, X., Insights from the comparison of plant genome sequences (2010) Annu Rev Plant Biol, 61, pp. 349-37