Pulses of enhanced North Pacific Intermediate Water ventilation from the Okhotsk Sea and Bering Sea during the last deglaciation

Under modern conditions only North Pacific Intermediate Water is formed in the Northwest Pacific Ocean. This situation might have changed in the past. Recent studies with General Circulation Models indicate a switch to deep-water formation in the Northwest Pacific during Heinrich Stadial 1 (17.5–15.0 kyr) of the last glacial termination. Reconstructions of past ventilation changes based on paleoceanographic proxy records are still insufficient to test whether a deglacial mode of deep-water formation in the North Pacific Ocean existed. Here we present deglacial ventilation records based on radiocarbon-derived ventilation ages in combination with epibenthic stable carbon isotopes from the Northwest Pacific including the Okhotsk Sea and Bering Sea, the two potential source regions for past North Pacific ventilation changes. Evidence for most rigorous ventilation of the mid-depth North Pacific occurred during Heinrich Stadial 1 and the Younger Dryas, simultaneous to significant reductions in Atlantic Meridional Overturning Circulation. Concurrent changes in δ13C and ventilation ages point to the Okhotsk Sea as driver of millennial-scale changes in North Pacific Intermediate Water ventilation during the last deglaciation. Our records additionally indicate that changes in the δ13C intermediate water (700–1750 m water depth) signature and radiocarbon-derived ventilation ages are in antiphase to those of the deep North Pacific Ocean (>2100 m water depth) during the last glacial termination. Thus, intermediate and deep-water masses of the Northwest Pacific have a differing ventilation history during the last deglaciation

Modelling of recalescence effect on austenite decomposition

A model for recalescence has been established by integrating a model for the decomposition of austenite and one dealing with heat transfer with latent heat release taken into account. The effects of recalescence on each individual austenite transformation product have been studied. It was found that Widmanstätten ferrite and pearlite reactions are most affected. The calculated cooling curve, as affected by the recalescence, has also been verified with a commercial steel subjected to two different environment conditions

Modelling of transition from upper to lower bainite in multi-component system

A model for estimating the upper to lower bainite transition has been developed for the iron–carbon–manganese–chromium–silicon alloy system by comparing the time required to decarburise a supersaturated bainitic ferrite platelet and that needed for the start of cementite precipitation in the ferrite. The problem is treated as a competition between the decarburisation time and the kinetics of cementite precipitation. Lower bainite is induced when the latter process is faster. The time for forming a volume fraction of 0.01 of the equilibrium amount of cementite is taken as the precipitation start time. The model was calibrated using experimental data from the iron–carbon system, and verified with the iron–carbon–manganese–molybdenum system and an experimental steel currently being developed for high-strength applications.Swiss SteelThis is the author accepted manuscript. The final version is available from Taylor & Francis via https://doi.org/10.1080/02670836.2016.122149

Variations in export production, lithogenic sediment transport and iron fertilization in the Pacific sector of the Drake Passage over the past 400 kyr

Changes in Southern Ocean export production have broad biogeochemical and climatic implications. Specifically, iron fertilization likely increased subantarctic nutrient utilization and enhanced the efficiency of the biological pump during glacials. However, past export production in the subantarctic southeastern Pacific is poorly documented, and its connection to Fe fertilization, potentially related to Patagonian Ice Sheet dynamics, is unknown. We report biological productivity changes over the past 400 kyr, based on a combination of 230Thxs-normalized and stratigraphy-based mass accumulation rates of biogenic barium, organic carbon, biogenic opal and calcium carbonate as indicators of paleo-export production in a sediment core upstream of the Drake Passage (57.5∘ S, 70.3∘ W). In addition, we use fluxes of iron and lithogenic material as proxies for terrigenous input, and thus potential micronutrient supply. Stratigraphy-based mass accumulation rates are strongly influenced by bottom-current dynamics, which result in variable sediment focussing or winnowing at our site. Carbonate is virtually absent in the core, except during peak interglacial intervals of the Holocene, and Marine Isotope Stages (MIS) 5 and 11, likely caused by transient decreases in carbonate dissolution. All other proxies suggest that export production increased during most glacial periods, coinciding with high iron fluxes. Such augmented glacial iron fluxes at the core site were most likely derived from glaciogenic input from the Patagonian Ice Sheet promoting the growth of phytoplankton. Additionally, glacial export production peaks are also consistent with northward shifts of the Subantarctic and Polar Fronts, which positioned our site south of the Subantarctic Front and closer to silicic acid-rich waters of the Polar Frontal Zone. However, glacial export production near the Drake Passage was lower than in the Atlantic and Indian sectors of the Southern Ocean, which may relate to complete consumption of silicic acid in the study area. Our results underline the importance of micro-nutrient fertilization through lateral terrigenous input from South America rather than eolian transport and exemplify the role of frontal shifts and nutrient limitation for past productivity changes in the Pacific entrance to the Drake Passage

Performance of the FOS and GHRS Pt/(Cr)-Ne Hollow-cathode Lamps after their Return from Space and Comparison with Archival Data

The Space Telescope European Coordinating Facility (ST-ECF) and National Institute of Standards and Technology (NIST) are collaborating to study hollow cathode calibration lamps as used onboard the Hubble Space Telescope (HST). As part of the STIS Calibration Enhancement (STIS-CE) Project we are trying to improve our understanding of the performance of hollow cathode lamps and the physical processes involved in their long term operation. The original flight lamps from the Faint Object Spectrograph (FOS) and the Goddard High Resolution Spectrograph (GHRS) are the only lamps that have ever been returned to Earth after extended operation in space. We have taken spectra of all four lamps using NIST s 10.7-m normal-incidence spectrograph and Fourier transform spectrometer (FTS) optimized for use in the ultraviolet (UV). These spectra, together with spectra archived from six years of on-orbit operations and pre-launch spectra, provide a unique data set - covering a period of about 20 years - for studying aging effects in these lamps. Our findings represent important lessons for the choice and design of calibration sources and their operation in future UV and optical spectrographs in space

Санитарно-эпидемиологическая экспертиза импортной пищевой продукции и продовольственного сырья как составляющая профилактического направления транспортной медицины

Санітарно епідеміологічна експертиза імпортної харчової продукції й продовольчої сировини (далі експертиза) є одним з пріоритетних напрямів діяльності транспортних підрозділів санепідслужби. Здійснюючи функцію по контролю, виявленню та попередженню впливу небезпечних факторів, пов’язаних з перевезенням вантажів, вона є однією зі складових частин профілактичного напряму транспортної медицини. Експертиза імпортованої продукції харчового призначення нерозривно пов’язана та базується на загальних принципах всієї державної політики у сфері безпеки харчової продукції та продовольчої сировини. Основою для проведення усього комплексу робіт санітарно епідеміологічного направлення є нормативна база, яка була сформована в нашій країні кілька десятиліть назад. Механізм визначення безпеки продукції та ті критерії оцінки, які були закладені в її основі, вимагають перегляду у відповідності з вимогами сьогодення та враховуючи розвиток міжнародних відносин. Зроблені деякі кроки у цьому напрямку. Наприклад, визначення експертизи у законі «Про внесення змін до закону України «Про якість та безпеку харчових продуктів та продовольчої сировини» поряд зі встановленням відповідності продукції нормативним вимогам передбачає оцінку ризику дії шкідливих факторів у процесі обігу харчових продуктів, що відповідає сучас ним вимогам до вирішення задач профілактичного напрямку, запобігання шкідливого впливу факторів, керування санітарно-епідеміологічною ситуацією взагалі та на етапі транспортування харчових грузів зокрема. Такий підхід потрібно враховувати при подальшому необхідному перегляді та формуванні нової нормативної бази.Sanіtarу epidemiological examination of imported foodstuffs and edible raw materials (then «examination») is one of the priority directions of transport sanіtarу epidemiological servise. Examination controls, discovers and prevents an influence of dangerous factors while in transportation of loads. So it’s one of the component of the transport medicine preventive activity. Examination of import foodstuffs and edible raw materials inseparably linked with and based on general principles of the food safety state policy. The foundation of the sanitary service work is the normative base, that was formed in our country about twenty years ago. It is necessary to review the mechanism of the food safety determination and its criteria in accordance with requirements of present day time and with account of the development of the international relations. One of taken steps in this direction is a characteristic of examination in law «About contributing the modification to law of the Ukraine «About quality and safety of foodstuffs and foodraw materials» where along with determination of the products correspondence to the normative requirements is provided forrisk assessment of the harmful factors in process of the turn of the food stuffs. Such approach corresponds with modern requests to decision of the prophylactic problems, prevention bad influence dangerous factors, management sanіtarу epidemiological situation in general and in step of transportation food cargo in particular. And it should be taken into account during the further necessary process of revision and forming the new normative base

Multi-year observations of Breiðamerkurjökull, a marine-terminating glacier in southeastern Iceland, using terrestrial radar interferometry

Terrestrial radar interferometry (TRI) is a new technique for studying ice motion and volume change of glaciers. TRI is especially useful for temporally and spatially dense measurements of highly dynamic glacial termini. We conducted a TRI survey of Breiðamerkurjökull, a marine-terminating glacier in Iceland, imaging its terminus near the end of the melt season in 2011, 2012 and 2013. The ice velocities were as high as 5 m d−1, with the fastest velocities near the calving front. Retreat of the glacier over the 3 year observation period was accompanied by strong embayment formation. Iceberg tracking with the radar shows high current velocities near the embayment, probably indicating strong meltwater outflow and mixing with relatively warm lagoon water

Upper-ocean temperature characteristics in the subantarctic southeastern Pacific based on biomarker reconstructions

As remnants of living organisms, alkenones and isoprenoid glycerol dialkyl glycerol tetraether lipids (isoGDGTs) are widely used biomarkers for determining ocean water temperatures from the past. The organisms that these proxy carriers stem from are influenced by a number of environmental parameters, such as water depth, nutrient availability, light conditions, or seasonality, which all may significantly bias the calibration to ambient water temperatures. Reliable temperature determinations thus remain challenging, especially in higher latitudes and for undersampled regions. We analyzed 33 sediment surface samples from the southern Chilean continental margin and the Drake Passage for alkenones and isoGDGTs and compared the results with gridded instrumental reference data from the World Ocean Atlas 2005 (WOA05) and previously published data from an extended study area covering the central and western South Pacific towards the Aotearoa / New Zealand continental margin. We show that for alkenone-derived sea surface temperatures (SSTs), the widely used global core-top calibration of Müller et al. (1998) yields the smallest deviation of the WOA05-based SSTs. On the contrary, the calibration of Sikes et al. (1997), determined for higher latitudes and summer SSTs, overestimates modern WOA05-based SSTs in both the annual mean and summer. Our alkenone SSTs show a slight seasonal shift of ∼ 1 ∘C at the southern Chilean margin and up to ∼ 2 ∘C in the Drake Passage towards austral summer SSTs. Samples in the central South Pacific, on the other hand, reflect an annual mean signal. We show that for isoGDGT-based temperatures, the subsurface calibration of Kim et al. (2012a) best reflects temperatures from the WOA05 in areas north of the Subantarctic Front (SAF). Temperatures south of the SAF are, in contrast, significantly overestimated by up to 14 ∘C, irrespective of the applied calibration. In addition, we used the GDGT [2]/[3] ratios, which give an indication of the production depth of the isoGDGTs and/or potential influences from land. Our samples reflect a subsurface (0–200 m water depth) rather than a surface (0–50 m water depth) signal in the entire study area and show a correlation with the monthly dust distribution in the South Pacific, indicating terrigenous influences. The overestimation of isoGDGT surface and subsurface temperatures south of the SAF highlights the need for a reassessment of existing calibrations in the polar Southern Ocean. Therefore, we suggest a modified Southern Ocean tetraether index (TEX86)-based calibration for surface and subsurface temperatures, which shows a lower temperature sensitivity and yields principally lower absolute temperatures, which align more closely with WOA05-derived values and also OH–isoGDGT-derived temperatures.</p

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