Effects of in vitro digestion and in vitro colonic fermentation on stability and functional properties of yerba mate (Ilex paraguariensis A. St. Hil.) beverages

Yerba mate (Ilex paraguariensis) is a plant that grows naturally in South America. From its leaves and thin stems different kinds of beverages are prepared (chimarrão, tererê and tea mate), all of them rich in bioactive substances. The aim of this study was to evaluate the influence of in vitro gastrointestinal digestion and colonic fermentation on the stability of the polyphenols and on the antioxidant, antimicrobial and antitumoral activities of the yerba mate beverages. The phenolic chromatographic profile revealed that both the in vitro digestion and the colonic fermentation caused a pronounced decrease in 3,5-O-dicaffeoylquinic acid and 5-O-caffeoylquinic acid in the preparations. However, 3-O-caffeoylquinic acid, 4-O-caffeoylquinic acid and salvianolic acid I were only barely affected in all preparations. Despite the decrease in the phytochemicals content, yerba mate beverages maintain their functional properties such as antioxidant, antibacterial and antitumoral activities.The authors thank the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq, Proc. 3079/2015-8) and Fundação Araucária (Proc.24/2012) for funding this study. Authors V.G. Correa and G.A. Gonçalves thanks Coordenação de Aperfeiçoamento do Pessoal do Ensino Superior (CAPES) for the financial support provided for their post-graduate studies in Universidade Estadual de Maringá. A. Bracht, and R.M. Peralta research grant recipients of CNPq. The authors are also thankful to the Foundation for Science and Technology (FCT, Portugal) and FEDER under Program PT2020 for financial support to CIMO (UID/AGR/00690/2013), L. Barros (SFRH/BPD/107855/2015) and M.I. Dias (SFRH/BD/84485/2012) grant. To POCI-01-0145-FEDER-006984 (LA LSRE-LCM), funded by ERDF, through POCI-COMPETE2020 and FCT.info:eu-repo/semantics/publishedVersio

Dark energy, non-minimal couplings and the origin of cosmic magnetic fields

In this work we consider the most general electromagnetic theory in curved space-time leading to linear second order differential equations, including non-minimal couplings to the space-time curvature. We assume the presence of a temporal electromagnetic background whose energy density plays the role of dark energy, as has been recently suggested. Imposing the consistency of the theory in the weak-field limit, we show that it reduces to standard electromagnetism in the presence of an effective electromagnetic current which is generated by the momentum density of the matter/energy distribution, even for neutral sources. This implies that in the presence of dark energy, the motion of large-scale structures generates magnetic fields. Estimates of the present amplitude of the generated seed fields for typical spiral galaxies could reach $10^{-9}$ G without any amplification. In the case of compact rotating objects, the theory predicts their magnetic moments to be related to their angular momenta in the way suggested by the so called Schuster-Blackett conjecture.Comment: 5 pages, no figure

Fusarium wilt incidence and common bean yield according to the preceding crop and the soil tillage system

The objective of this work was to evaluate the effects of preceding crops and tillage systems on the incidence of Fusarium wilt (Fusarium oxysporum f. sp. phaseoli) and common bean (Phaseolus vulgaris) yield. The cultivar BRS Valente was cultivated under center‑pivot irrigation in the winter seasons of 2003, 2004 and 2005, after several preceding crops established in the summer seasons. Preceding crops included the legumes Cajanus cajan (pigeon pea), Stylosanthes guianensis, and Crotalaria spectabilis; the grasses Pennisetum glaucum (millet), Sorghum bicolor (forage sorghum), Panicum maximum, and Urochloa brizantha; and a consortium of maize (Zea mays) and U. brizantha (Santa Fé system). Experiments followed a strip‑plot design, with four replicates. Fusarium wilt incidence was higher in the no‑tillage system. Higher disease incidences corresponded to lower bean yields in 2003 and 2004. Previous summer cropping with U. brizantha, U. brizantha + maize consortium, and millet showed the lowest disease incidence. Therefore, the choice of preceding crops must be taken into account for managing Fusarium wilt on irrigated common bean crops in the Brazilian Cerrado

Perception of COVID-19 pandemic restrictions on dental researchers

Background/objectives: Historical evidence shows a gender-based disproportionate effect of pandemics across different populations. In 2020, the coronavirus disease 2019 (COVID-19) pandemic began spreading its devastating effects worldwide. The goal of the present study was to investigate the effect of the COVID-19 pandemic on research productivity, work-life arrangements, and mental health of dental professionals worldwide with focus on gender differences. Methods: A 38-item survey, concerning demographics, career stage, employer support, family structure, mental health, and relationships, was distributed to 7692 active members of the International Association for Dental Research. Bivariate associations between independent variables and the primary outcome variable were tested using Spearman's correlation test. A logistic regression model was used to assess the simultaneous, independent associations between each variable and researcher productivity. Results: A total of 722 responses were obtained, indicating a 9.4% response rate. Higher productivity was reported by male respondents (p = 0.021), and by those in senior career stages (p = 0.001). Institutional support was associated with higher productivity (p < 0.0001). Lower productivity was reported by younger researchers (p = 0.003). Remote work negatively affected productivity (p < 0.0001) and female respondents reported working more hours, regardless of work location (p = 0.004). Poor mental health was associated with low productivity (p < 0.0001). Conclusions: Our results showed that the COVID-19 pandemic significantly affected dental professionals’ perceived productivity and mental health around the globe. Younger individuals and women were disproportionally affected, and institutional support had a significant influence to mitigate effects of the pandemic for dental researchers

Activated Random Walkers: Facts, Conjectures and Challenges

We study a particle system with hopping (random walk) dynamics on the integer lattice $\mathbb Z^d$. The particles can exist in two states, active or inactive (sleeping); only the former can hop. The dynamics conserves the number of particles; there is no limit on the number of particles at a given site. Isolated active particles fall asleep at rate $\lambda > 0$, and then remain asleep until joined by another particle at the same site. The state in which all particles are inactive is absorbing. Whether activity continues at long times depends on the relation between the particle density $\zeta$ and the sleeping rate $\lambda$. We discuss the general case, and then, for the one-dimensional totally asymmetric case, study the phase transition between an active phase (for sufficiently large particle densities and/or small $\lambda$) and an absorbing one. We also present arguments regarding the asymptotic mean hopping velocity in the active phase, the rate of fixation in the absorbing phase, and survival of the infinite system at criticality. Using mean-field theory and Monte Carlo simulation, we locate the phase boundary. The phase transition appears to be continuous in both the symmetric and asymmetric versions of the process, but the critical behavior is very different. The former case is characterized by simple integer or rational values for critical exponents ($\beta = 1$, for example), and the phase diagram is in accord with the prediction of mean-field theory. We present evidence that the symmetric version belongs to the universality class of conserved stochastic sandpiles, also known as conserved directed percolation. Simulations also reveal an interesting transient phenomenon of damped oscillations in the activity density

PAK2 is an effector of TSC1/2 signaling independent of mTOR and a potential therapeutic target for Tuberous Sclerosis Complex

Tuberous sclerosis complex (TSC) is caused by inactivating mutations in either TSC1 or TSC2 and is characterized by uncontrolled mTORC1 activation. Drugs that reduce mTOR activity are only partially successful in the treatment of TSC, suggesting that mTOR-independent pathways play a role in disease development. Here, kinome profiles of wild-type and Tsc2-/- mouse embryonic fibroblasts (MEFs) were generated, revealing a prominent role for PAK2 in signal transduction downstream of TSC1/2. Further investigation showed that the effect of the TSC1/2 complex on PAK2 is mediated through RHEB, but is independent of mTOR and p21RAC. We also demonstrated that PAK2 over-activation is likely responsible for the migratory and cell cycle abnormalities observed in Tsc2-/- MEFs. Finally, we detected high levels of PAK2 activation in giant cells in the brains of TSC patients. These results show that PAK2 is a direct effector of TSC1-TSC2-RHEB signaling and a new target for rational drug therapy in TSC

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