7 results on '"van der Vossen, E."'
Search Results
2. Abstracts of presentations on selected topics at the XIVth international plant protection congress (IPPC) July 25-30, 1999
- Author
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Hull, R., Kuiper, H., Noordam, Maryvon, Hoy, Marjorie, Cory, Jenny, Fereres, A., Gonzalez, P., Meins, F., Elkind, Y., Charrier, Benedicte, Meyer, P., Metzlaff, M., Schuch, W., Ikin, R., Parnell, T., Frison, E., Spiegel, S., Diekmann, Marlene, Ausher, R., Hollingworth, R., Holm, Robert, Ragsdale, N., Federici, B., Vlak, J., Chejanovsky, N., Bianchi, F., Joosten, Nina, Gutierrez, Serafin, van der Wert, W., Regev, A., Inceoglu, B., Reske, G., Gershburg, E., Rivkin, H., Zilberberg, N., Froy, O., Gurevitz, M., Hammock, B., Llobell, A., Monte, E., González-Candelas, L., Dealessi, Laura, Camponogara, Andrea, Ramón-Vidal, D., Migheli, Q., Chernin, L., Zhou, L., Ovadis, M., Ismailov, Z., Chet, I., Teng, P., Mohankumar, S., Renganayaki, K., Nagarajan, P., Balasaraswathi, R., Shanmugasundaram, P., Reddy, Avutu, Sadasivam, S., Thottappilly, G., Ng, S., Winter, S., Shvidchenko, V., Manadilova, A., Sadvakasova, G., Sozinova, L., Levy, D., Loebenstein, G., Khadi, B., Kulkarni, V., Patil, S., Freyssinet, G., Kaufmann, J., Owen, M., Dolgov, S., Rotteveel, A., Gressel, J., Tzotzos, G., Ammann, K., Jacot, Yolande, Raybould, A., Gray, A., Maskell, L., Cooper, J., Edwards, M., Pallet, D., Williams, D., Smith, M., Aldwinckle, H., Norelli, J., Bolar, J., Harman, G., Martini, N., Porsch, Petra, Mahn, A., Bulow, L., Brinkmann, O., Giet't'ers, W., During, K., Dahan, Aviva, Fahima, T., Nevo, E., Dickman, M., Gonsalves, D., Cheng, Z., Wu, M., He, X., Chen, C., Zhang, J., Gafni, Y., Daly, J., Fitt, G., Olsen, K., Mares, C., Moran, R., Garcia, R., Mena, J., Zaldua, Zurima, Garcia, Melba, Lopez, Alina, Somonte, Danalay, Alvarez, Irene, de la Riva, G., Selman, G., Shomer-Ilan, Adiva, Walsh, J., Jenner, Carol, Rusholme, Rachel, Hughes, Sara, Sanchez, Flora, Ponz, F., Lydiate, D., Röder, Marion, Peng, Jun-Hua, Grama, Adriana, Korol, A., Paran, I., Zamir, D., van der Voort, J., van Eck, H., van Koert, P., van Os, H., Buntjer, J., Visser, R., Stiekema, W., Bakker, J., Lankhorst, R., van der Vossen, E., Kanyuka, K., Bendahmane, A., Monk, Kathy, Tomerlin, J., Petersen, B., Leonard, P., Smith, I., Shaner, D., Delbridge, T., Levy, Edna, Kovanci, O., Kovanci, B., Salpiggidis, G., Navrozidis, E., Zartaloudis, Z., El-Shemy, Hamied, Di Primo, P., Cartia, G., Rahman, Mohamed, Lopez-Martinez, Nuria, De Prado, R., El-Nahhal, Y., Safi, J., Polubesova, Tamara, Levi, Avishag, Margulies, L., Rubin, B., and Undabeytia, T.
- Published
- 2018
3. Abstracts of presentations on plant protection issues at the fifth international Mango Symposium Abstracts of presentations on plant protection issues at the Xth international congress of Virology: September 1-6, 1996 Dan Panorama Hotel, Tel Aviv, Israel August 11-16, 1996 Binyanei haoma, Jerusalem, Israel
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Peña, J., Wysoki, M., Singh, Gajendra, Boscán de M., Nancy, Godoy, Freddy, Obligado, A., Rossetto, C., Ribeiro, I., Gallo, P., Soares, N., Sabino, J., Martins, A., Bortoletto, N., Ploetz, R., Benscher, D., Vázquez, Aimé, Colls, A., Nagel, Julianne, Schaffer, B., Pinkas, Y., Maymon, M., Freeman, S., Bostros Bastawros, Mikhail, Gosbee, M., Johnson, G., Joyce, D., Irwin, J., Saaiman, W., Prusky, D., Falik, E., Kobiler, I., Fuchs, Y., Zauberman, G., Pesis, E., Ackerman, M., Roth, I., Weksler, A., Yekutiely, O., Waisblum, A., Keinan, A., Ofek, G., Reved, R., Barak, R., Bel, P., Artes, L., Visarathanonth, N., Xu, Z., Ponce de León, L., Muñoz, C., Pérez, L., Diaz de León, F., Kerbel, C., Esparza, S., Bósquez, E., Trinidad, M., Coates, L., Cooke, A., Dean, J., Lucia Duarte, Ana, Alberto Otto, Paulo, Malavasi, Aldo, Lizado, M., Bautista, M., Bacalangco, N., Farungsang, U., Farungsang, N., Waskar, D., Masalkar, S., Gaikwad, R., Damame, S., Bally, Ian, O'Hare, Tim, Holmes, Rowland, Atabekov, J., Fauquet, Claude, Tomori, O., Nuss, D., Ahlquist, P., Díez, J., Ishikawa, M., Janda, M., Price, B., Restrepo-Hartwig, M., Bol, J., van Rossum, C., Garcia, M., van der Vossen, E., Reusken, Chantal, Canto, T., Gal-On, A., Palukaitis, P., Roossinck, M., Flasinski, S., Restrepo-Hartwig, Maria, Ahlquist, Paul, Smirnyagina, Ekaterina, Lin, Na-Sheng, Nagy, Peter, Figlerowicz, Marek, Bujarski, Jozef, Proll, D., Guyatt, K., Davidson, A., Kim, Kook-Hyung, Miller, Eric, Hemenway, Cynthia, Havelda, Z., Dalmay, T., Burgyán, J., Kearney, C., Thomson, M., Roland, K., Dawson, W., Bao, Y., Carter, S., Nelson, R., Derrick, P., Shun Ding, Xin, Eskarous, J., Sarkar, S., El-Shamy, M., Chen, J., Sako, N., Yuichiro, W., Ohshima, K., Okada, Y., Felden, Brice, Kuznetsov, Yuri, Malkin, Alexander, Greenwood, Aaron, McPherson, Alexander, Ivanov, K., Dorokhov, Y., Kim, C., Sálanki, Katalin, Carrére, Isabelle, Jacquemond, Mireille, Tepfer, Mark, Balazs, Ervin, Sanz, A., Serra, M., García-Luque, I., Revers, F., Candresse, T., LeGall, O., Souche, S., Lot, H., Dunez, J., Cecchini, E., Milner, J., Al-Kaff, N., Covey, S., Gong, Z., Geri, C., Richert-Pöggeler, K., Shepherd, R., Casper, R., Meiri, Eti, Raccah, B., Gera, A., Singer, S., Allam, E., El Afifi, Soheir, Abo El Nasr, M., Abd El Ghaffar, M., Elisabeth Johansen, I., Keller, K., Hampton, R., SÕrensen, Karina, Bishnoi, S., Rishi, Narayan, Gumedzoe, M., Atissime, K., Yedibahoma, S., Wellink, Joan, Verver, Jan, Bertens, Peter, van Lent, Jan, Goldbach, Rob, van Kammen, Ab, Lekkerkerker, Annemarie, Taylor, K., Spall, V., Lomonossoff, G., Yu. Morozov, S., Solovyev, A., Zelenina, D., Savenkov, E., Grdzelishvili, V., Morozov, S., Jansen, K., Wolfs, C., Lohuis, H., Verduin, B., Stein-Margolina, V., Hsu, Y., Chang, B., Lin, N., Pilartz, Marcel, Jeske, Holger, Verchot, Jeanmarie, Baulcombe, David, English, David, Müller, E., Baulcombe, D., Malcuit, Isabelle, Kavanagh, Tony, Valkonen, J., Puurand, Ü., Merits, A., Rabinstein, F., Sorri, O., Saarma, M., Liao, Y., Vaquero-Martin, C., Monecke, M., Rohde, W., Prüfer, D., Fischer, R., Antignus, Y., Lachman, O., Pearlsman, M., Cohen, S., Qiu, W., Moyer, J., Feldhoff, A., Kikkert, M., Kormelink, R., Krczal, G., Peters, D., Szittya, György, Burgyán, József, Wvpijewski, K., Paduch-Cichal, E., Rezler, A., Skrzeczkowska, S., Augustyniak, J., Nemchinov, L., Maiss, E., Hadidi, A., Wittner, Anita, Palkovics, László, Balázs, Ervin, Crescenzi, A., Piazzolla, P., Kheyr-Pour, A., Dafalla, G., Lecoq, H., Gronenborn, B., Bauer, U., Laux, I., Hajimorad, M., Ding, X., Flasinski, Stanislaw, Cassidy, Pour, Dugdale, B., Beetham, P., Harding, R., Dale, J., Qiu, G., Shaw, J., Molnár, A., Más, P., Balsalobre, J., Sánchez-Pina, M., Pallás, V., Rahontei, J., López, L., Lázara, J., Barón, M., Owens, R., Steger, G., Hu, Y., Fels, A., Hammond, R., Riesner, D., Schröder, A., Góra, A., Pawlowicz, J., Kierzek, A., Zagorski, W., Baumstark, T., Schiebel, W., Schiebel, R., Axmann, A., Haas, B., Sänger, H., Xicai, Yang, Yin, Yie, Feng, Zhu, Yule, Liu, Liangyi, Kang, Po, Tien, Poliyka, H., Staub, U., Wagner, M., Gross, H., Sano, Teruo, Ishiguro, Akiro, Fayos, J., Garro, R., Bellés, J., Conejero, V., Bonfiglioli, R., Webb, D., Symons, R., El-Dougdoug, K., Abo-Zeid, A., Ambrós, S., Hernandez, C., Desvignes, J., Flores, R., d'Aquilio, M., Lisa, V., Boccardo, G., Vera, A., Daròs, J., Henkel, J., Spieker, R., Higgins, C., Turley, R., Chamberlain, D., Bateson, M., d'Aquino, L., Ragozzino, A., Henderson, J., Chaleeprom, W., Gibbs, A., Graichen, K., Rabenstein, F., Schliephake, E., Smith, H., Stevens, M., Sadowy, E., Hulanicka, D., Wegener, B., Martin, M., Wetzel, T., Cook, G., Kasdorf, G., Pietersen, G., Braithwaite, Kathryn, Gambley, Cherie, Smith, Grant, Druka, Arnis, Villegas, Lucille, Dahal, Ganesh, Hull, Roger, Senchugova, N., Büchen-Osmond, C., Dallwitz, M., Blaine, L., Naik, P., Sonone, A., Kolaskar, A., Sgro, J., Palmenberg, A., Leclerc, Denis, Hohn, Thomas, Moriones, E., Batlle, A., Luis, M., Alvarez, J., Bernal, J., Alonso, J., Spak, J., Kubelkova, D., Kuo, T., Gachechiladze, K., Adamia, R., Balardshishvili, N., Chanishvili, T., Krüger, D., Nagy, Tibor, Élö, Péter, Papp, Péter, Orosz, László, Licis, N., Berzins, V., Sariol-Carbelo, Carlos, RodrCarlos, C., Janzen, D., Ward, Colin, Scott, S., Shiel, P., Berger, P., Aleman, M., Beachy, R., Fauquet, C., Salm, S., Rybicki, E., Rey, M., Briddon, R., Harper, G., Druka, A., Phillips, S., Brunt, A., Hull, R., Hay, Jo, Dasgupta, Indranil, Zaifeng, Fan, Meehan, Brian, Todd, Daniel, Bunk, Hans-Jörk, Grieco, F., Martelli, G., Saldarelli, P., Minafra, A., Morag, A., Mumcuoglu, M., Baybikov, T., Schlesinger, M., Zakay-Rones, Z., Shohat, B., Shohat, M., Miller, M., Shaklay, M., Kalvatchev, Z., Walder, R., Garzaro, D., Barrios, M., Karagöz, Ali, Kuru, Avni, Karim, M., Johnson, A., Takida, S., Thompson, M., Omer, H., Omer, O., Biyiti, L., Amvam, R., Lamaty, G., Bouchet, P., Xu, J., Hefferon, K., Abou Haidar, M., and Meng, A.
- Published
- 2018
4. Shifting the limits in wheat research and breeding using a fully annotated reference genome
- Author
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Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., Pozniak, C.J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Sharpe, A.G., Ben-Zvi, G., Josselin, A-A, Himmelbach, A., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Koh, C., Muehlbauer, G., Pasam, R.K., Paux, E., Rigault, P., Tibbits, J., Tiwari, V., Spannagl, M., Lang, D., Gundlach, H., Haberer, G., Mayer, K.F.X., Ormanbekova, D., Prade, V., Šimková, H., Wicker, T., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Kaithakottil, G., Keilwagen, J., Leroy, P., Lux, T., Twardziok, S., Venturini, L., Juhász, A., Abrouk, M., Fischer, I., Uauy, C., Borrill, P., Ramirez-Gonzalez, R.H., Arnaud, D., Chalabi, S., Chalhoub, B., Cory, A., Datla, R., Davey, M.W., Jacobs, J., Robinson, S.J., Steuernagel, B., van Ex, F., Wulff, B.B.H., Benhamed, M., Bendahmane, A., Concia, L., Latrasse, D., Alaux, M., Bartoš, J., Bellec, A., Berges, H., Doležel, J., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O-A, Singh, K., Valárik, M., van der Vossen, E., Vautrin, S., Weining, S., Fahima, T., Glikson, V., Raats, D., Číhalíková, J., Toegelová, H., Vrána, J., Sourdille, P., Darrier, B., Barabaschi, D., Cattivelli, L., Hernandez, P., Galvez, S., Budak, H., Jones, J.D.G., Witek, K., Yu, G., Small, I., Melonek, J., Zhou, R., Belova, T., Kanyuka, K., King, R., Nilsen, K., Walkowiak, S., Cuthbert, R., Knox, R., Wiebe, K., Xiang, D., Rohde, A., Gold, T., Čížková, J., Akpinar, B.A., Biyiklioglu, S., Gao, L., N’Daiye, A., Kubaláková, M., Šafář, J., Alfama, F., Adam-Blondon, A-F, Flores, R., Guerche, C., Loaec, M., Quesneville, H., Condie, J., Ens, J., Koh, C.S., Maclachlan, R., Tan, Y., Alberti, A., Aury, J-M, Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., Kaur, G., Luo, M., Sehgal, S., Chhuneja, P., Gupta, O.P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., Singh, N.K., Khurana, J.P., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R.S., Holušová, K., Plíhal, O., Clark, M.D., Heavens, D., Kettleborough, G., Wright, J., Balcárková, B., Hu, Y., Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., Cattonaro, F., Jiumeng, M., Kugler, K.G., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., Batley, J., Bayer, P.E., Edwards, D., Hayashi, S., Tulpová, Z., Visendi, P., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., Wang, L., Appels, R., Eversole, K., Feuillet, C., Keller, B., Rogers, J., Stein, N., Pozniak, C.J., Choulet, F., Distelfeld, A., Poland, J., Ronen, G., Barad, O., Baruch, K., Keeble-Gagnère, G., Mascher, M., Sharpe, A.G., Ben-Zvi, G., Josselin, A-A, Himmelbach, A., Balfourier, F., Gutierrez-Gonzalez, J., Hayden, M., Koh, C., Muehlbauer, G., Pasam, R.K., Paux, E., Rigault, P., Tibbits, J., Tiwari, V., Spannagl, M., Lang, D., Gundlach, H., Haberer, G., Mayer, K.F.X., Ormanbekova, D., Prade, V., Šimková, H., Wicker, T., Swarbreck, D., Rimbert, H., Felder, M., Guilhot, N., Kaithakottil, G., Keilwagen, J., Leroy, P., Lux, T., Twardziok, S., Venturini, L., Juhász, A., Abrouk, M., Fischer, I., Uauy, C., Borrill, P., Ramirez-Gonzalez, R.H., Arnaud, D., Chalabi, S., Chalhoub, B., Cory, A., Datla, R., Davey, M.W., Jacobs, J., Robinson, S.J., Steuernagel, B., van Ex, F., Wulff, B.B.H., Benhamed, M., Bendahmane, A., Concia, L., Latrasse, D., Alaux, M., Bartoš, J., Bellec, A., Berges, H., Doležel, J., Frenkel, Z., Gill, B., Korol, A., Letellier, T., Olsen, O-A, Singh, K., Valárik, M., van der Vossen, E., Vautrin, S., Weining, S., Fahima, T., Glikson, V., Raats, D., Číhalíková, J., Toegelová, H., Vrána, J., Sourdille, P., Darrier, B., Barabaschi, D., Cattivelli, L., Hernandez, P., Galvez, S., Budak, H., Jones, J.D.G., Witek, K., Yu, G., Small, I., Melonek, J., Zhou, R., Belova, T., Kanyuka, K., King, R., Nilsen, K., Walkowiak, S., Cuthbert, R., Knox, R., Wiebe, K., Xiang, D., Rohde, A., Gold, T., Čížková, J., Akpinar, B.A., Biyiklioglu, S., Gao, L., N’Daiye, A., Kubaláková, M., Šafář, J., Alfama, F., Adam-Blondon, A-F, Flores, R., Guerche, C., Loaec, M., Quesneville, H., Condie, J., Ens, J., Koh, C.S., Maclachlan, R., Tan, Y., Alberti, A., Aury, J-M, Barbe, V., Couloux, A., Cruaud, C., Labadie, K., Mangenot, S., Wincker, P., Kaur, G., Luo, M., Sehgal, S., Chhuneja, P., Gupta, O.P., Jindal, S., Kaur, P., Malik, P., Sharma, P., Yadav, B., Singh, N.K., Khurana, J.P., Chaudhary, C., Khurana, P., Kumar, V., Mahato, A., Mathur, S., Sevanthi, A., Sharma, N., Tomar, R.S., Holušová, K., Plíhal, O., Clark, M.D., Heavens, D., Kettleborough, G., Wright, J., Balcárková, B., Hu, Y., Salina, E., Ravin, N., Skryabin, K., Beletsky, A., Kadnikov, V., Mardanov, A., Nesterov, M., Rakitin, A., Sergeeva, E., Handa, H., Kanamori, H., Katagiri, S., Kobayashi, F., Nasuda, S., Tanaka, T., Wu, J., Cattonaro, F., Jiumeng, M., Kugler, K.G., Pfeifer, M., Sandve, S., Xun, X., Zhan, B., Batley, J., Bayer, P.E., Edwards, D., Hayashi, S., Tulpová, Z., Visendi, P., Cui, L., Du, X., Feng, K., Nie, X., Tong, W., and Wang, L.
- Abstract
Wheat is one of the major sources of food for much of the world. However, because bread wheat's genome is a large hybrid mix of three separate subgenomes, it has been difficult to produce a high-quality reference sequence. Using recent advances in sequencing, the International Wheat Genome Sequencing Consortium presents an annotated reference genome with a detailed analysis of gene content among subgenomes and the structural organization for all the chromosomes. Examples of quantitative trait mapping and CRISPR-based genome modification show the potential for using this genome in agricultural research and breeding. Ramírez-González et al. exploited the fruits of this endeavor to identify tissue-specific biased gene expression and coexpression networks during development and exposure to stress. These resources will accelerate our understanding of the genetic basis of bread wheat.
- Published
- 2018
5. Development of a Sequence-Based Reference Physical Map of Pea ( Pisum sativum L.).
- Author
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Gali KK, Tar'an B, Madoui MA, van der Vossen E, van Oeveren J, Labadie K, Berges H, Bendahmane A, Lachagari RVB, Burstin J, and Warkentin T
- Abstract
Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (∼4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N
50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.- Published
- 2019
- Full Text
- View/download PDF
6. A mosaic monoploid reference sequence for the highly complex genome of sugarcane.
- Author
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Garsmeur O, Droc G, Antonise R, Grimwood J, Potier B, Aitken K, Jenkins J, Martin G, Charron C, Hervouet C, Costet L, Yahiaoui N, Healey A, Sims D, Cherukuri Y, Sreedasyam A, Kilian A, Chan A, Van Sluys MA, Swaminathan K, Town C, Bergès H, Simmons B, Glaszmann JC, van der Vossen E, Henry R, Schmutz J, and D'Hont A
- Subjects
- Base Sequence, Chromosomes, Artificial, Bacterial genetics, Chromosomes, Plant genetics, DNA Transposable Elements genetics, Gene Amplification, Genomic Structural Variation, Models, Genetic, Polymorphism, Single Nucleotide genetics, Sequence Analysis, DNA, Sorghum genetics, Genome, Plant genetics, Mosaicism, Ploidies, Saccharum genetics
- Abstract
Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich part of the sorghum genome was selected based on whole-genome profiling, sequenced, and assembled in a 382-Mb single tiling path of a high-quality sequence. A total of 25,316 protein-coding gene models are predicted, 17% of which display no colinearity with their sorghum orthologs. We show that the two species, S. officinarum and S. spontaneum, involved in modern cultivars differ by their transposable elements and by a few large chromosomal rearrangements, explaining their distinct genome size and distinct basic chromosome numbers while also suggesting that polyploidization arose in both lineages after their divergence.
- Published
- 2018
- Full Text
- View/download PDF
7. MaGuS: a tool for quality assessment and scaffolding of genome assemblies with Whole Genome Profiling™ Data.
- Author
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Madoui MA, Dossat C, d'Agata L, van Oeveren J, van der Vossen E, and Aury JM
- Subjects
- Chromosomes, Artificial, Bacterial, Contig Mapping, Repetitive Sequences, Nucleic Acid, Sequence Alignment, Arabidopsis genetics, Chromosomes, Plant genetics, Genome, Plant, High-Throughput Nucleotide Sequencing methods, Physical Chromosome Mapping, Sequence Analysis, DNA methods
- Abstract
Background: Scaffolding is an essential step in the genome assembly process. Current methods based on large fragment paired-end reads or long reads allow an increase in contiguity but often lack consistency in repetitive regions, resulting in fragmented assemblies. Here, we describe a novel tool to link assemblies to a genome map to aid complex genome reconstruction by detecting assembly errors and allowing scaffold ordering and anchoring., Results: We present MaGuS (map-guided scaffolding), a modular tool that uses a draft genome assembly, a Whole Genome Profiling™ (WGP) map, and high-throughput paired-end sequencing data to estimate the quality and to enhance the contiguity of an assembly. We generated several assemblies of the Arabidopsis genome using different scaffolding programs and applied MaGuS to select the best assembly using quality metrics. Then, we used MaGuS to perform map-guided scaffolding to increase contiguity by creating new scaffold links in low-covered and highly repetitive regions where other commonly used scaffolding methods lack consistency., Conclusions: MaGuS is a powerful reference-free evaluator of assembly quality and a WGP map-guided scaffolder that is freely available at https://github.com/institut-de-genomique/MaGuS. Its use can be extended to other high-throughput sequencing data (e.g., long-read data) and also to other map data (e.g., genetic maps) to improve the quality and the contiguity of large and complex genome assemblies.
- Published
- 2016
- Full Text
- View/download PDF
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