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1. Phylogenomics and the rise of the angiosperms

Author

Zuntini, Alexandre R., Carruthers, Tom, Maurin, Olivier, Bailey, Paul C., Leempoel, Kevin, Brewer, Grace E., Epitawalage, Niroshini, Françoso, Elaine, Gallego-Paramo, Berta, McGinnie, Catherine, Negrão, Raquel, Roy, Shyamali R., Simpson, Lalita, Toledo Romero, Eduardo, Barber, Vanessa M. A., Botigué, Laura, Clarkson, James J., Cowan, Robyn S., Dodsworth, Steven, Johnson, Matthew G., Kim, Jan T., Pokorny, Lisa, Wickett, Norman J., Antar, Guilherme M., DeBolt, Lucinda, Gutierrez, Karime, Hendriks, Kasper P., Hoewener, Alina, Hu, Ai-Qun, Joyce, Elizabeth M., Kikuchi, Izai A. B. S., Larridon, Isabel, Larson, Drew A., de Lírio, Elton John, Liu, Jing-Xia, Malakasi, Panagiota, Przelomska, Natalia A. S., Shah, Toral, Viruel, Juan, Allnutt, Theodore R., Ameka, Gabriel K., Andrew, Rose L., Appelhans, Marc S., Arista, Montserrat, Ariza, María Jesús, Arroyo, Juan, Arthan, Watchara, Bachelier, Julien B., Bailey, C. Donovan, Barnes, Helen F., Barrett, Matthew D., Barrett, Russell L., Bayer, Randall J., Bayly, Michael J., Biffin, Ed, Biggs, Nicky, Birch, Joanne L., Bogarín, Diego, Borosova, Renata, Bowles, Alexander M. C., Boyce, Peter C., Bramley, Gemma L. C., Briggs, Marie, Broadhurst, Linda, Brown, Gillian K., Bruhl, Jeremy J., Bruneau, Anne, Buerki, Sven, Burns, Edie, Byrne, Margaret, Cable, Stuart, Calladine, Ainsley, Callmander, Martin W., Cano, Ángela, Cantrill, David J., Cardinal-McTeague, Warren M., Carlsen, Mónica M., Carruthers, Abigail J. A., de Castro Mateo, Alejandra, Chase, Mark W., Chatrou, Lars W., Cheek, Martin, Chen, Shilin, Christenhusz, Maarten J. M., Christin, Pascal-Antoine, Clements, Mark A., Coffey, Skye C., Conran, John G., Cornejo, Xavier, Couvreur, Thomas L. P., Cowie, Ian D., Csiba, Laszlo, Darbyshire, Iain, Davidse, Gerrit, Davies, Nina M. J., Davis, Aaron P., van Dijk, Kor-jent, Downie, Stephen R., Duretto, Marco F., Duvall, Melvin R., Edwards, Sara L., Eggli, Urs, Erkens, Roy H. J., Escudero, Marcial, de la Estrella, Manuel, Fabriani, Federico, Fay, Michael F., Ferreira, Paola de L., Ficinski, Sarah Z., Fowler, Rachael M., Frisby, Sue, Fu, Lin, Fulcher, Tim, Galbany-Casals, Mercè, Gardner, Elliot M., German, Dmitry A., Giaretta, Augusto, Gibernau, Marc, Gillespie, Lynn J., González, Cynthia C., Goyder, David J., Graham, Sean W., Grall, Aurélie, Green, Laura, Gunn, Bee F., Gutiérrez, Diego G., Hackel, Jan, Haevermans, Thomas, Haigh, Anna, Hall, Jocelyn C., Hall, Tony, Harrison, Melissa J., Hatt, Sebastian A., Hidalgo, Oriane, Hodkinson, Trevor R., Holmes, Gareth D., Hopkins, Helen C. F., Jackson, Christopher J., James, Shelley A., Jobson, Richard W., Kadereit, Gudrun, Kahandawala, Imalka M., Kainulainen, Kent, Kato, Masahiro, Kellogg, Elizabeth A., King, Graham J., Klejevskaja, Beata, Klitgaard, Bente B., Klopper, Ronell R., Knapp, Sandra, Koch, Marcus A., Leebens-Mack, James H., Lens, Frederic, Leon, Christine J., Léveillé-Bourret, Étienne, Lewis, Gwilym P., Li, De-Zhu, Li, Lan, Liede-Schumann, Sigrid, Livshultz, Tatyana, Lorence, David, Lu, Meng, Lu-Irving, Patricia, Luber, Jaquelini, Lucas, Eve J., Luján, Manuel, Lum, Mabel, Macfarlane, Terry D., Magdalena, Carlos, Mansano, Vidal F., Masters, Lizo E., Mayo, Simon J., McColl, Kristina, McDonnell, Angela J., McDougall, Andrew E., McLay, Todd G. B., McPherson, Hannah, Meneses, Rosa I., Merckx, Vincent S. F. T., Michelangeli, Fabián A., Mitchell, John D., Monro, Alexandre K., Moore, Michael J., Mueller, Taryn L., Mummenhoff, Klaus, Munzinger, Jérôme, Muriel, Priscilla, Murphy, Daniel J., Nargar, Katharina, Nauheimer, Lars, Nge, Francis J., Nyffeler, Reto, Orejuela, Andrés, Ortiz, Edgardo M., Palazzesi, Luis, Peixoto, Ariane Luna, Pell, Susan K., Pellicer, Jaume, Penneys, Darin S., Perez-Escobar, Oscar A., Persson, Claes, Pignal, Marc, Pillon, Yohan, Pirani, José R., Plunkett, Gregory M., Powell, Robyn F., Prance, Ghillean T., Puglisi, Carmen, Qin, Ming, Rabeler, Richard K., Rees, Paul E. J., Renner, Matthew, Roalson, Eric H., Rodda, Michele, Rogers, Zachary S., Rokni, Saba, Rutishauser, Rolf, de Salas, Miguel F., Schaefer, Hanno, Schley, Rowan J., Schmidt-Lebuhn, Alexander, Shapcott, Alison, Al-Shehbaz, Ihsan, Shepherd, Kelly A., Simmons, Mark P., Simões, André O., Simões, Ana Rita G., Siros, Michelle, Smidt, Eric C., Smith, James F., Snow, Neil, Soltis, Douglas E., Soltis, Pamela S., Soreng, Robert J., Sothers, Cynthia A., Starr, Julian R., Stevens, Peter F., Straub, Shannon C. K., Struwe, Lena, Taylor, Jennifer M., Telford, Ian R. H., Thornhill, Andrew H., Tooth, Ifeanna, Trias-Blasi, Anna, Udovicic, Frank, Utteridge, Timothy M. A., Del Valle, Jose C., Verboom, G. Anthony, Vonow, Helen P., Vorontsova, Maria S., de Vos, Jurriaan M., Al-Wattar, Noor, Waycott, Michelle, Welker, Cassiano A. D., White, Adam J., Wieringa, Jan J., Williamson, Luis T., Wilson, Trevor C., Wong, Sin Yeng, Woods, Lisa A., Woods, Roseina, Worboys, Stuart, Xanthos, Martin, Yang, Ya, Zhang, Yu-Xiao, Zhou, Meng-Yuan, Zmarzty, Sue, Zuloaga, Fernando O., Antonelli, Alexandre, Bellot, Sidonie, Crayn, Darren M., Grace, Olwen M., Kersey, Paul J., Leitch, Ilia J., Sauquet, Hervé, Smith, Stephen A., Eiserhardt, Wolf L., Forest, Félix, and Baker, William J.

Published
2024
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2. Comparative evolutionary analyses of eight whitefly Bemisia tabaci sensu lato genomes: cryptic species, agricultural pests and plant-virus vectors

Author

Campbell, Lahcen I., Nwezeobi, Joachim, van Brunschot, Sharon L., Kaweesi, Tadeo, Seal, Susan E., Swamy, Rekha A. R., Namuddu, Annet, Maslen, Gareth L., Mugerwa, Habibu, Armean, Irina M., Haggerty, Leanne, Martin, Fergal J., Malka, Osnat, Santos-Garcia, Diego, Juravel, Ksenia, Morin, Shai, Stephens, Michael E., Muhindira, Paul Visendi, Kersey, Paul J., Maruthi, M. N., Omongo, Christopher A., Navas-Castillo, Jesús, Fiallo-Olivé, Elvira, Mohammed, Ibrahim Umar, Wang, Hua-Ling, Onyeka, Joseph, Alicai, Titus, and Colvin, John

Published
2023
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3. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara KN, Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M, Baker, William J, Belov, Katherine, Blaxter, Mark L, Bonet, Tomas Marques, Childers, Anna K, Coddington, Jonathan A, Crandall, Keith A, Crawford, Andrew J, Davey, Robert P, Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J, Howe, Kerstin, Jarvis, Erich D, Johnson, Warren E, Johnson, Rebecca N, Kersey, Paul J, Liu, Xin, Lopez, Jose Victor, Myers, Eugene W, Pettersson, Olga Vinnere, Phillippy, Adam M, Poelchau, Monica F, Pruitt, Kim D, Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A, Soltis, Pamela S, Swarbreck, David, Thibaud-Nissen, Françoise, Wang, Sibo, Wegrzyn, Jill L, Zhang, Guojie, Zhang, He, Lewin, Harris A, and Richards, Stephen

Subjects
Human Genome, Genetics, Animals, Base Sequence, Biodiversity, Eukaryota, Genomics, Humans, Reference Standards, Reference Values, Sequence Analysis, DNA, Earth BioGenome Project, genomics, ethics, genome assembly
Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

4. Enabling reusability of plant phenomic datasets with MIAPPE 1.1

Author

Papoutsoglou, Evangelia A., Faria, Daniel, Arend, Daniel, Arnaud, Elizabeth, Athanasiadis, Ioannis N., Chaves, Inês, Coppens, Frederik, Cornut, Guillaume, Costa, Bruno V., Ćwiek-Kupczyńska, Hanna, Droesbeke, Bert, Finkers, Richard, Gruden, Kristina, Junker, Astrid, King, Graham J., Krajewski, Paweł, Lange, Matthias, Laporte, Marie-Angélique, Michotey, Célia, Oppermann, Markus, Ostler, Richard, Poorter, Hendrik, Ramırez-Gonzalez, Ricardo, Ramšak, Živa, Reif, Jochen C., Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Scholz, Uwe, Tardieu, François, Uauy, Cristobal, Usadel, Björn, Visser, Richard G. F., Weise, Stephan, Kersey, Paul J., Miguel, Célia M., Adam-Blondon, Anne-Françoise, and Pommier, Cyril

Published
2020

5. An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations

Author

Clavijo, Bernardo J, Venturini, Luca, Schudoma, Christian, Accinelli, Gonzalo Garcia, Kaithakottil, Gemy, Wright, Jonathan, Borrill, Philippa, Kettleborough, George, Heavens, Darren, Chapman, Helen, Lipscombe, James, Barker, Tom, Lu, Fu-Hao, McKenzie, Neil, Raats, Dina, Ramirez-Gonzalez, Ricardo H, Coince, Aurore, Peel, Ned, Percival-Alwyn, Lawrence, Duncan, Owen, Trösch, Josua, Yu, Guotai, Bolser, Dan M, Namaati, Guy, Kerhornou, Arnaud, Spannagl, Manuel, Gundlach, Heidrun, Haberer, Georg, Davey, Robert P, Fosker, Christine, Di Palma, Federica, Phillips, Andrew L, Millar, A Harvey, Kersey, Paul J, Uauy, Cristobal, Krasileva, Ksenia V, Swarbreck, David, Bevan, Michael W, and Clark, Matthew D

Subjects
Genetics, Biotechnology, Human Genome, Algorithms, Contig Mapping, Genome, Plant, Molecular Sequence Annotation, Plant Proteins, Polymorphism, Genetic, Polyploidy, Translocation, Genetic, Triticum, Biological Sciences, Medical and Health Sciences, Bioinformatics
Abstract

Advances in genome sequencing and assembly technologies are generating many high-quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop.

Published
2017

6. RNAcentral: a comprehensive database of non-coding RNA sequences

Author

Petrov, Anton I, Kay, Simon JE, Kalvari, Ioanna, Howe, Kevin L, Gray, Kristian A, Bruford, Elspeth A, Kersey, Paul J, Cochrane, Guy, Finn, Robert D, Bateman, Alex, Kozomara, Ana, Griffiths-Jones, Sam, Frankish, Adam, Zwieb, Christian W, Lau, Britney Y, Williams, Kelly P, Chan, Patricia P, Lowe, Todd M, Cannone, Jamie J, Gutell, Robin, Machnicka, Magdalena A, Bujnicki, Janusz M, Yoshihama, Maki, Kenmochi, Naoya, Chai, Benli, Cole, James R, Szymanski, Maciej, Karlowski, Wojciech M, Wood, Valerie, Huala, Eva, Berardini, Tanya Z, Zhao, Yi, Chen, Runsheng, Zhu, Weimin, Paraskevopoulou, Maria D, Vlachos, Ioannis S, Hatzigeorgiou, Artemis G, Ma, Lina, Zhang, Zhang, Puetz, Joern, Stadler, Peter F, McDonald, Daniel, Basu, Siddhartha, Fey, Petra, Engel, Stacia R, Cherry, J Michael, Volders, Pieter-Jan, Mestdagh, Pieter, Wower, Jacek, Clark, Michael B, Quek, Xiu Cheng, and Dinger, Marcel E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Generic health relevance, Animals, Databases, Nucleic Acid, Genomics, Humans, Nucleotides, RNA, Untranslated, Sequence Analysis, RNA, Species Specificity, The RNAcentral Consortium, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

RNAcentral is a database of non-coding RNA (ncRNA) sequences that aggregates data from specialised ncRNA resources and provides a single entry point for accessing ncRNA sequences of all ncRNA types from all organisms. Since its launch in 2014, RNAcentral has integrated twelve new resources, taking the total number of collaborating database to 22, and began importing new types of data, such as modified nucleotides from MODOMICS and PDB. We created new species-specific identifiers that refer to unique RNA sequences within a context of single species. The website has been subject to continuous improvements focusing on text and sequence similarity searches as well as genome browsing functionality. All RNAcentral data is provided for free and is available for browsing, bulk downloads, and programmatic access at http://rnacentral.org/.

Published
2017

7. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, Keith R., Fass, Joseph N., Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, İnanç, Boisvert, Sébastien, Chapman, Jarrod A., Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T. Roderick, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A., Ganapathy, Ganeshkumar, Gibbs, Richard A., Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B., Ho, Isaac Y., Howard, Jason, Hunt, Martin, Jackman, Shaun D., Jaffe, David B, Jarvis, Erich, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J., Kitzman, Jacob O., Knight, James R., Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Vieira, Bruno Miguel, Naquin, Delphine, Ning, Zemin, Otto, Thomas D., Paten, Benedict, Paulo, Octávio S., Phillippy, Adam M., Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S., Ruby, J. Graham, Scalabrin, Simone, Schatz, Michael C., Schwartz, David C., Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I., Shendure, Jay, Shi, Yujian, Simpson, Jared T., Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Wang, Jun, Worley, Kim C., Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F.

Subjects
Quantitative Biology - Genomics
Abstract

Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another., Comment: Additional files available at http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional_files/ Major changes 1. Accessions for the 3 read data sets have now been included 2. New file: spreadsheet containing details of all Study, Sample, Run, & Experiment identifiers 3. Made miscellaneous changes to address reviewers comments. DOIs added to GigaDB datasets

Published
2013
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8. Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Author

Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton, Baranay, Paul, Bechner, Michael, Birol, Inanç, Boisvert, Sébastien, Chapman, Jarrod A, Chapuis, Guillaume, Chikhi, Rayan, Chitsaz, Hamidreza, Chou, Wen-Chi, Corbeil, Jacques, Del Fabbro, Cristian, Docking, T, Durbin, Richard, Earl, Dent, Emrich, Scott, Fedotov, Pavel, Fonseca, Nuno A, Ganapathy, Ganeshkumar, Gibbs, Richard A, Gnerre, Sante, Godzaridis, Élénie, Goldstein, Steve, Haimel, Matthias, Hall, Giles, Haussler, David, Hiatt, Joseph B, Ho, Isaac Y, Howard, Jason, Hunt, Martin, Jackman, Shaun D, Jaffe, David B, Jarvis, Erich D, Jiang, Huaiyang, Kazakov, Sergey, Kersey, Paul J, Kitzman, Jacob O, Knight, James R, Koren, Sergey, Lam, Tak-Wah, Lavenier, Dominique, Laviolette, François, Li, Yingrui, Li, Zhenyu, Liu, Binghang, Liu, Yue, Luo, Ruibang, MacCallum, Iain, MacManes, Matthew D, Maillet, Nicolas, Melnikov, Sergey, Naquin, Delphine, Ning, Zemin, Otto, Thomas D, Paten, Benedict, Paulo, Octávio S, Phillippy, Adam M, Pina-Martins, Francisco, Place, Michael, Przybylski, Dariusz, Qin, Xiang, Qu, Carson, Ribeiro, Filipe J, Richards, Stephen, Rokhsar, Daniel S, Ruby, J, Scalabrin, Simone, Schatz, Michael C, Schwartz, David C, Sergushichev, Alexey, Sharpe, Ted, Shaw, Timothy I, Shendure, Jay, Shi, Yujian, Simpson, Jared T, Song, Henry, Tsarev, Fedor, Vezzi, Francesco, Vicedomini, Riccardo, Vieira, Bruno M, Wang, Jun, Worley, Kim C, Yin, Shuangye, Yiu, Siu-Ming, Yuan, Jianying, Zhang, Guojie, Zhang, Hao, Zhou, Shiguo, and Korf, Ian F

Abstract

Abstract Background The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Published
2013

10. Data management challenges for artificial intelligence in plant and agricultural research

Author

Williamson, Hugh F., primary, Brettschneider, Julia, additional, Caccamo, Mario, additional, Davey, Robert P., additional, Goble, Carole, additional, Kersey, Paul J., additional, May, Sean, additional, Morris, Richard J., additional, Ostler, Richard, additional, Pridmore, Tony, additional, Rawlings, Chris, additional, Studholme, David, additional, Tsaftaris, Sotirios A., additional, and Leonelli, Sabina, additional

Published
2023
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11. Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

Author

Beier, Sebastian, primary, Fiebig, Anne, additional, Pommier, Cyril, additional, Liyanage, Isuru, additional, Lange, Matthias, additional, Kersey, Paul J., additional, Weise, Stephan, additional, Finkers, Richard, additional, Koylass, Baron, additional, Cezard, Timothee, additional, Courtot, Mélanie, additional, Contreras-Moreira, Bruno, additional, Naamati, Guy, additional, Dyer, Sarah, additional, and Scholz, Uwe, additional

Published
2022
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12. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez, Allende, Miguel L., Archibald, John M., Bálint, Miklós M., Barker, Katharine M., Baumgartnerk, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark, Cai, Jing, Caperello, Nicolette, Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu-Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., Di Palma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott, Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Marshall Graves, Jennifer A., Greely, Henry, Grigoriev, Igor, Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J.M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin-Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K.N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sofhie, Mazet, Jonna, Mazzoni, Camila J., Myers, Eugene W., O'Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene, Roquet, Cristina, Ryder, Oliver, Sabir, Jamal S.M., Shaffer, Howard Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela, Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne, and Zhang, Guojie

Published
2022

13. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K.N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J, Belov, Katherine, Blaxter, Mark, Marques-Bonet, Tomas, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina, Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca, Kersey, Paul J., Liu, Xin, Lopez, Jose V., Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica, Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela, Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill, Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

14. Standards recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark L., Bonet, Tomas Marques, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, Lopez, Jose Victor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, Kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Sahu, Sunil Kumar, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022
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15. Standards recommendations for the Earth BioGenome Project

Author

National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, National Library of Medicine (US), National Institutes of Health (US), Swedish Research Council, National Museum of Natural History Smithsonian Institution, Howard Hughes Medical Institute, Wellcome, European Molecular Biology Laboratory, National Science Foundation (US), Department of Agriculture (US), Agricultural Research Service (US), Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Abstract

A global international initiative, such as the Earth BioGenome Project (EBP), requires both agreement and coordination on standards to ensure that the collective effort generates rapid progress toward its goals. To this end, the EBP initiated five technical standards committees comprising volunteer members from the global genomics scientific community: Sample Collection and Processing, Sequencing and Assembly, Annotation, Analysis, and IT and Informatics. The current versions of the resulting standards documents are available on the EBP website, with the recognition that opportunities, technologies, and challenges may improve or change in the future, requiring flexibility for the EBP to meet its goals. Here, we describe some highlights from the proposed standards, and areas where additional challenges will need to be met.

Published
2022

16. Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR

Author

Beier, Sebastian, Fiebig, Anne, Pommier, Cyril, Liyanage, Isuru, Lange, Matthias, Kersey, Paul J., Weise, Stephan, Finkers, Richard, Koylass, Baron, Cezard, Timothee, Courtot, Mélanie, Contreras-Moreira, Bruno, Naamati, Guy, Dyer, Sarah, Scholz, Uwe, Beier, Sebastian, Fiebig, Anne, Pommier, Cyril, Liyanage, Isuru, Lange, Matthias, Kersey, Paul J., Weise, Stephan, Finkers, Richard, Koylass, Baron, Cezard, Timothee, Courtot, Mélanie, Contreras-Moreira, Bruno, Naamati, Guy, Dyer, Sarah, and Scholz, Uwe

Abstract

In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of metadata in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. They form a basis for the proposed VCF extensions here. We have learned from the existing application of VCF that the definition of relevant metadata using controlled standards, vocabulary and the consistent use of cross-references via resolvable identifiers (machine-readable) are particularly necessary and propose their encoding. VCF is an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant data (for example, the HapMap and the gVCF formats), but none currently have the reach of VCF. For the sake of simplicity, we will only discuss VCF and our recommendations for its use, but these recommendations could also be applied to gVCF. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.

Published
2022

17. The Earth BioGenome Project 2020:Starting the clock

Author

Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., Zhang, Guojie, Lewin, Harris A., Richards, Stephen, Aiden, Erez Lieberman, Allende, Miguel L., Archibald, John M., Bálint, Miklós, Barker, Katharine B., Baumgartner, Bridget, Belov, Katherine, Bertorelle, Giorgio, Blaxter, Mark L., Cai, Jing, Caperello, Nicolette D., Carlson, Keith, Castilla-Rubio, Juan Carlos, Chaw, Shu Miaw, Chen, Lei, Childers, Anna K., Coddington, Jonathan A., Conde, Dalia A., Corominas, Montserrat, Crandall, Keith A., Crawford, Andrew J., DiPalma, Federica, Durbin, Richard, Ebenezer, ThankGod E., Edwards, Scott V., Fedrigo, Olivier, Flicek, Paul, Formenti, Giulio, Gibbs, Richard A., Gilbert, M. Thomas P., Goldstein, Melissa M., Graves, Jennifer Marshall, Greely, Henry T., Grigoriev, Igor V., Hackett, Kevin J., Hall, Neil, Haussler, David, Helgen, Kristofer M., Hogg, Carolyn J., Isobe, Sachiko, Jakobsen, Kjetill Sigurd, Janke, Axel, Jarvis, Erich D., Johnson, Warren E., Jones, Steven J. M., Karlsson, Elinor K., Kersey, Paul J., Kim, Jin Hyoung, Kress, W. John, Kuraku, Shigehiro, Lawniczak, Mara K. N., Leebens-Mack, James H., Li, Xueyan, Lindblad-Toh, Kerstin, Liu, Xin, Lopez, Jose V., Marques-Bonet, Tomas, Mazard, Sophie, Mazet, Jonna A. K., Mazzoni, Camila J., Myers, Eugene W., O’Neill, Rachel J., Paez, Sadye, Park, Hyun, Robinson, Gene E., Roquet, Cristina, Ryder, Oliver A., Sabir, Jamal S. M., Shaffer, H. Bradley, Shank, Timothy M., Sherkow, Jacob S., Soltis, Pamela S., Tang, Boping, Tedersoo, Leho, Uliano-Silva, Marcela, Wang, Kun, Wei, Xiaofeng, Wetzer, Regina, Wilson, Julia L., Xu, Xun, Yang, Huanming, Yoder, Anne D., and Zhang, Guojie

Published
2022

18. Uses and benefits of digital sequence information from plant genetic resources:Lessons learnt from botanical collections

Author

Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, Kersey, Paul J., Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, and Kersey, Paul J.

Abstract

Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as “Digital Sequence Information” (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary: Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possib

Published
2022

20. The Earth BioGenome Project 2020: Starting the clock

Author

Lewin, Harris A., primary, Richards, Stephen, additional, Lieberman Aiden, Erez, additional, Allende, Miguel L., additional, Archibald, John M., additional, Bálint, Miklós, additional, Barker, Katharine B., additional, Baumgartner, Bridget, additional, Belov, Katherine, additional, Bertorelle, Giorgio, additional, Blaxter, Mark L., additional, Cai, Jing, additional, Caperello, Nicolette D., additional, Carlson, Keith, additional, Castilla-Rubio, Juan Carlos, additional, Chaw, Shu-Miaw, additional, Chen, Lei, additional, Childers, Anna K., additional, Coddington, Jonathan A., additional, Conde, Dalia A., additional, Corominas, Montserrat, additional, Crandall, Keith A., additional, Crawford, Andrew J., additional, DiPalma, Federica, additional, Durbin, Richard, additional, Ebenezer, ThankGod E., additional, Edwards, Scott V., additional, Fedrigo, Olivier, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Gibbs, Richard A., additional, Gilbert, M. Thomas P., additional, Goldstein, Melissa M., additional, Graves, Jennifer Marshall, additional, Greely, Henry T., additional, Grigoriev, Igor V., additional, Hackett, Kevin J., additional, Hall, Neil, additional, Haussler, David, additional, Helgen, Kristofer M., additional, Hogg, Carolyn J., additional, Isobe, Sachiko, additional, Jakobsen, Kjetill Sigurd, additional, Janke, Axel, additional, Jarvis, Erich D., additional, Johnson, Warren E., additional, Jones, Steven J. M., additional, Karlsson, Elinor K., additional, Kersey, Paul J., additional, Kim, Jin-Hyoung, additional, Kress, W. John, additional, Kuraku, Shigehiro, additional, Lawniczak, Mara K. N., additional, Leebens-Mack, James H., additional, Li, Xueyan, additional, Lindblad-Toh, Kerstin, additional, Liu, Xin, additional, Lopez, Jose V., additional, Marques-Bonet, Tomas, additional, Mazard, Sophie, additional, Mazet, Jonna A. K., additional, Mazzoni, Camila J., additional, Myers, Eugene W., additional, O’Neill, Rachel J., additional, Paez, Sadye, additional, Park, Hyun, additional, Robinson, Gene E., additional, Roquet, Cristina, additional, Ryder, Oliver A., additional, Sabir, Jamal S. M., additional, Shaffer, H. Bradley, additional, Shank, Timothy M., additional, Sherkow, Jacob S., additional, Soltis, Pamela S., additional, Tang, Boping, additional, Tedersoo, Leho, additional, Uliano-Silva, Marcela, additional, Wang, Kun, additional, Wei, Xiaofeng, additional, Wetzer, Regina, additional, Wilson, Julia L., additional, Xu, Xun, additional, Yang, Huanming, additional, Yoder, Anne D., additional, and Zhang, Guojie, additional

Published
2022
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21. Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections

Author

Cowell, Carly, primary, Paton, Alan, additional, Borrell, James S., additional, Williams, China, additional, Wilkin, Paul, additional, Antonelli, Alexandre, additional, Baker, William J., additional, Buggs, Richard, additional, Fay, Michael F., additional, Gargiulo, Roberta, additional, Grace, Olwen M., additional, Kuhnhäuser, Benedikt G., additional, Woudstra, Yannick, additional, and Kersey, Paul J., additional

Published
2021
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23. A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

Author

Baker, William J, Bailey, Paul, Barber, Vanessa, Barker, Abigail, Bellot, Sidonie, Bishop, David, Botigué, Laura, Brewer, Grace, Carruthers, Tom, Clarkson, James J, Cook, Jeffrey, Cowan, Robyn S, Dodsworth, Steven, Epitawalage, Niroshini, Françoso, Elaine, Gallego, Berta, Johnson, Matthew G, Kim, Jan T, Leempoel, Kevin, Maurin, Olivier, Mcginnie, Catherine, Pokorny, Lisa, Roy, Shyamali, Stone, Malcolm, Toledo, Eduardo, Wickett, Norman J, Zuntini, Alexandre R, Eiserhardt, Wolf L, Kersey, Paul J, Leitch, Ilia J, Forest, Félix, Baker, William J, Bailey, Paul, Barber, Vanessa, Barker, Abigail, Bellot, Sidonie, Bishop, David, Botigué, Laura, Brewer, Grace, Carruthers, Tom, Clarkson, James J, Cook, Jeffrey, Cowan, Robyn S, Dodsworth, Steven, Epitawalage, Niroshini, Françoso, Elaine, Gallego, Berta, Johnson, Matthew G, Kim, Jan T, Leempoel, Kevin, Maurin, Olivier, Mcginnie, Catherine, Pokorny, Lisa, Roy, Shyamali, Stone, Malcolm, Toledo, Eduardo, Wickett, Norman J, Zuntini, Alexandre R, Eiserhardt, Wolf L, Kersey, Paul J, Leitch, Ilia J, and Forest, Félix

Abstract

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. The primary goals of this article are to (i) document our methods, (ii) describe our first data release, and (iii) present a novel open data portal, the Kew Tree of Life Explorer (). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic data set for angiosperms to date, comprising 3099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96) and 2333 genera (17). A "first pass" angiosperm tree of life was inferred from the data, which totaled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns, for interactive presentation in the Kew Tree of Life Explorer. This species tree was generated using methods that were rigorous, yet tractable at our scale of operation. Despite limitations pertaining to taxon and gene sampling, gene recovery, models of sequence evolution and paralogy, the tree strongly supports existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated data set, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer and will be updated as

Published
2021

24. Supplementary Tables and Legends Standards Recommendations for the Earth BioGenome Project

Author

Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., Richards, Stephen, Lawniczak, Mara K. N., Durbin, Richard, Flicek, Paul, Lindblad-Toh, Kerstin, Wei, Xiaofeng, Archibald, John M., Baker, William J., Belov, Katherine, Blaxter, Mark, Marqués-Bonet, Tomàs, Childers, Anna K., Coddington, Jonathan A., Crandall, Keith A., Crawford, Andrew J., Davey, Robert P., Di Palma, Federica, Fang, Qi, Haerty, Wilfried, Hall, Neil, Hoff, Katharina J., Howe, Kerstin, Jarvis, Erich D., Johnson, Warren E., Johnson, Rebecca N., Kersey, Paul J., Liu, Xin, López, José Víctor, Myers, Eugene W., Vinnere Pettersson, Olga, Phillippy, Adam M., Poelchau, Monica F., Pruitt, kim D., Rhie, Arang, Castilla-Rubio, Juan Carlos, Kumar Sahu, Sunil, Salmon, Nicholas A., Soltis, Pamela S., Swarbreck, David, Thibaud-Nissen, Francoise, Wang, Sibo, Wegrzyn, Jill L., Zhang, Guojie, Zhang, He, Lewin, Harris A., and Richards, Stephen

Published
2021

25. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, DʼEustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, and Ware, Doreen

Published
2014
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26. Data management challenges for artificial intelligence in plant and agricultural research

Author

Williamson, Hugh F., primary, Brettschneider, Julia, additional, Caccamo, Mario, additional, Davey, Robert P., additional, Goble, Carole, additional, Kersey, Paul J., additional, May, Sean, additional, Morris, Richard J., additional, Ostler, Richard, additional, Pridmore, Tony, additional, Rawlings, Chris, additional, Studholme, David, additional, Tsaftaris, Sotirios A., additional, and Leonelli, Sabina, additional

Published
2021
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27. Selecting for useful properties of plants and fungi – Novel approaches, opportunities, and challenges

Author

Kersey, Paul J., Collemare, Jerome, Cockel, Christopher, Das, Dibakar, Dulloo, Ehsan M., Kelly, Laura J., Lettice, Eoin, Malécot, Valery, Maxted, Nigel, Metheringham, Carey, Thormann, Imke, Leitch, Ilia J., Kersey, Paul J., Collemare, Jerome, Cockel, Christopher, Das, Dibakar, Dulloo, Ehsan M., Kelly, Laura J., Lettice, Eoin, Malécot, Valery, Maxted, Nigel, Metheringham, Carey, Thormann, Imke, and Leitch, Ilia J.

Abstract

Societal Impact Statement For millennia, humans have used plants and fungi, as foods, fuels, fibers, and medicines; and have developed techniques for improving their usefulness to our species, mostly through selection of desirable traits. With human populations forecast to rise, the availability of arable land likely to fall amid climate change and increasing urbanization, and modern communications technologies accelerating the dispersal of pathogens, further improvement is urgently needed. However, ensuring long‐term resilience involves conservation of existing genetic diversity in addition to selection. New technologies, particularly those based on molecular biology, are increasingly driving conservation and improvement strategies. Summary Humans use plants and fungi for a wide range of purposes and, over millennia, have improved wild species by selecting for and combining genetic variation. Improvements in DNA sequencing technologies have enhanced our capacity to identify and manipulate genetic diversity, increasing the range of variation that can be utilized, and accelerating the breeding cycle to reduce the time taken to develop and put new varieties to use. Most recently, the CRISPR/Cas9 gene editing technology has greatly increased our capacity to directly introduce novel genetic variants without unwanted associated material. Moreover, increased knowledge of metabolic pathways resulting from genomic analysis can be used to design new varieties with desired properties with increased precision. Selecting for, or engineering, desirable variants has increased the usefulness of plants and fungi to humans, but at the cost of reducing their genetic diversity, decreasing their resilience and reducing the stock of variation available for future use. Conservation of genetic biodiversity is thus an essential counterpart of crop improvement and is essential to ensure that crop species retain resilience to emerging threats. Conservation efforts are focused on orphan crops

Published
2020

28. COPO : a metadata platform for brokering FAIR data in the life sciences

Author

Shaw, Felix, Etuk, Anthony, Minotto, Alice, Gonzalez-Beltran, Alejandra, Johnson, David, Rocca-Serra, Philippe, Laporte, Marie-Angélique, Arnaud, Elizabeth, Devare, Medha, Kersey, Paul J., Sansone, Susanna-Assunta, Davey, Robert P., Shaw, Felix, Etuk, Anthony, Minotto, Alice, Gonzalez-Beltran, Alejandra, Johnson, David, Rocca-Serra, Philippe, Laporte, Marie-Angélique, Arnaud, Elizabeth, Devare, Medha, Kersey, Paul J., Sansone, Susanna-Assunta, and Davey, Robert P.

Abstract

Scientific innovation is increasingly reliant on data and computational resources. Much of today’s life science research involves generating, processing, and reusing heterogeneous datasets that are growing exponentially in size. Demand for technical experts (data scientists and bioinformaticians) to process these data is at an all-time high, but these are not typically trained in good data management practices. That said, we have come a long way in the last decade, with funders, publishers, and researchers themselves making the case for open, interoperable data as a key component of an open science philosophy. In response, recognition of the FAIR Principles (that data should be Findable, Accessible, Interoperable and Reusable) has become commonplace. However, both technical and cultural challenges for the implementation of these principles still exist when storing, managing, analysing and disseminating both legacy and new data. COPO is a computational system that attempts to address some of these challenges by enabling scientists to describe their research objects (raw or processed data, publications, samples, images, etc.) using community-sanctioned metadata sets and vocabularies, and then use public or institutional repositories to share them with the wider scientific community. COPO encourages data generators to adhere to appropriate metadata standards when publishing research objects, using semantic terms to add meaning to them and specify relationships between them. This allows data consumers, be they people or machines, to find, aggregate, and analyse data which would otherwise be private or invisible, building upon existing standards to push the state of the art in scientific data dissemination whilst minimising the burden of data publication and sharing.

Published
2020
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29. Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Author

Tello-Ruiz, Marcela K, primary, Naithani, Sushma, additional, Gupta, Parul, additional, Olson, Andrew, additional, Wei, Sharon, additional, Preece, Justin, additional, Jiao, Yinping, additional, Wang, Bo, additional, Chougule, Kapeel, additional, Garg, Priyanka, additional, Elser, Justin, additional, Kumari, Sunita, additional, Kumar, Vivek, additional, Contreras-Moreira, Bruno, additional, Naamati, Guy, additional, George, Nancy, additional, Cook, Justin, additional, Bolser, Daniel, additional, D’Eustachio, Peter, additional, Stein, Lincoln D, additional, Gupta, Amit, additional, Xu, Weijia, additional, Regala, Jennifer, additional, Papatheodorou, Irene, additional, Kersey, Paul J, additional, Flicek, Paul, additional, Taylor, Crispin, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2020
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31. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Author

Kersey, Paul J., Staines, Daniel M., Lawson, Daniel, Kulesha, Eugene, Derwent, Paul, Humphrey, Jay C., Hughes, Daniel S. T., Keenan, Stephan, Kerhornou, Arnaud, Koscielny, Gautier, Langridge, Nicholas, McDowall, Mark D., Megy, Karine, Maheswari, Uma, Nuhn, Michael, Paulini, Michael, Pedro, Helder, Toneva, Iliana, Wilson, Derek, Yates, Andrew, and Birney, Ewan

Published
2012
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32. Mobilizing Crop Biodiversity

Author

McCouch, Susan, primary, Navabi, Zahra Katy, additional, Abberton, Michael, additional, Anglin, Noelle L., additional, Barbieri, Rosa Lia, additional, Baum, Michael, additional, Bett, Kirstin, additional, Booker, Helen, additional, Brown, Gerald L., additional, Bryan, Glenn J., additional, Cattivelli, Luigi, additional, Charest, David, additional, Eversole, Kellye, additional, Freitas, Marcelo, additional, Ghamkhar, Kioumars, additional, Grattapaglia, Dario, additional, Henry, Robert, additional, Valadares Inglis, Maria Cleria, additional, Islam, Tofazzal, additional, Kehel, Zakaria, additional, Kersey, Paul J., additional, King, Graham J., additional, Kresovich, Stephen, additional, Marden, Emily, additional, Mayes, Sean, additional, Ndjiondjop, Marie Noelle, additional, Nguyen, Henry T., additional, Paiva, Samuel Rezende, additional, Papa, Roberto, additional, Phillips, Peter W.B., additional, Rasheed, Awais, additional, Richards, Christopher, additional, Rouard, Mathieu, additional, Amstalden Sampaio, Maria Jose, additional, Scholz, Uwe, additional, Shaw, Paul D., additional, Sherman, Brad, additional, Staton, S. Evan, additional, Stein, Nils, additional, Svensson, Jan, additional, Tester, Mark, additional, Montenegro Valls, Jose Francisco, additional, Varshney, Rajeev, additional, Visscher, Stephen, additional, von Wettberg, Eric, additional, Waugh, Robbie, additional, Wenzl, Peter, additional, and Rieseberg, Loren H., additional

Published
2020
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33. Conservation Policy: Helping or hindering science to unlock properties of plants and fungi

Author

Williams, China, primary, Walsh, Alexandra, additional, Vaglica, Valentina, additional, Sirakaya, Aysegül, additional, Silva, Manuela, additional, Dalle, Gemedo, additional, Winterton, Deborah, additional, Annecke, Wendy, additional, Smith, Paul, additional, Kersey, Paul J., additional, Way, Michael, additional, Antonelli, Alexandre, additional, and Cowell, Carly, additional

Published
2020
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34. Selecting for useful properties of plants and fungi – Novel approaches, opportunities, and challenges

Author

Kersey, Paul J., primary, Collemare, Jerome, additional, Cockel, Christopher, additional, Das, Dibakar, additional, Dulloo, Ehsan M., additional, Kelly, Laura J., additional, Lettice, Eoin, additional, Malécot, Valery, additional, Maxted, Nigel, additional, Metheringham, Carey, additional, Thormann, Imke, additional, and Leitch, Ilia J., additional

Published
2020
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36. Uses and benefits of digital sequence information from plant genetic resources: Lessons learnt from botanical collections.

Author

Cowell, Carly, Paton, Alan, Borrell, James S., Williams, China, Wilkin, Paul, Antonelli, Alexandre, Baker, William J., Buggs, Richard, Fay, Michael F., Gargiulo, Roberta, Grace, Olwen M., Kuhnhäuser, Benedikt G., Woudstra, Yannick, and Kersey, Paul J.

Subjects
GENETIC resources utilization, PLANT germplasm, BIODIVERSITY, DNA, GERMPLASM conservation, NATURAL resources
Abstract

Societal Impact Statement: Digitized molecular data are vital to numerous aspects of scientific research and genetic resource use. The Convention on Biological Diversity currently refers to this as "Digital Sequence Information" (DSI), a term not widely adopted by science and lacking a clear definition. There are concerns over the access to genetic resources and absence of benefit sharing by provider countries. Open access to DSI might exacerbate this, which is leading to increasing policy interventions and restricted access to genetic resources and DSI. We analyze current international debate and proposed solutions and provide case studies of DSI use producing tangible benefits for the provider countries and scientific research, demonstrating the importance of open access DSI to achieving conservation goals. Summary: Substantial advances in DNA sequencing over the last decades hold great potential to enhance food security and sustainable use of global biodiversity, benefiting the world's poorest people. Digital Sequence Information (DSI) plays a crucial role in catalyzing research applications that can contribute to international societal and biodiversity conservation targets. However, benefit sharing relating to DSI is difficult to identify and hindered by the lack of clear international governance and legislation, which in turn has led to a reluctance to make DSI publicly and freely available. Critically, no precise definition exists under the Convention on Biological Diversity (CBD), the Nagoya Protocol (NP), or the International Treaty for Plant Genetic Resources for Food and Agriculture (ITPGRFA). The key difference between DSI and biological resources, for which access and use are highly regulated under those frameworks, is that information is nonphysical. Information can be replicated and used without movement of, or access to, physical specimens. Thus, regulating the use of DSI is extremely challenging and remains controversial. Here, we review the regulation of DSI and the possible future steps by the international community, in the context of the benefit‐sharing obligations of the CBD, NP, and ITPGRFA. We highlight how multilateral agreements work in practice and are a solution to this impasse. We provide case studies demonstrating how the Royal Botanic Gardens, Kew, and its collaborators address the uncertainty surrounding the use of DSI, illustrating tangible and equitable benefits that have arisen from such use. We conclude that open access to DSI is needed for scientific research and international policy. [ABSTRACT FROM AUTHOR]

Published
2022
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38. Data standards for plant phenotyping: MIAPPE and its implementations

Author

Pommier, Cyril, Cornut, Guillaume, Letellier, Thomas, Michotey, Célia, Neveu, Pascal, Ruiz, Manuel, Larmande, Pierre, Kersey, Paul J., Cwiek Kupczynska, Hanna, Krajewski, Paweł, Coppens, Frederik, Finkers, Richard, Laporte, Marie-Angélique, Faria, Daniel, Miguel, Célia M., Chavez, Inês, Adam Blondon, Anne-Françoise, Costa, Bruno, Unité de Recherche Génomique Info (URGI), Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Mathématiques, Informatique et STatistique pour l'Environnement et l'Agronomie (MISTEA), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD), European Molecular Biology Laboratory European Bioinformatics Institute, Institute of Plant Genetics, Polska Akademia Nauk = Polish Academy of Sciences (PAN), Polish Academy of Sciences (PAN), Department of plant systems biology, Flanders Institute for Biotechnology, Plant Breeding, Wageningen University and Research [Wageningen] (WUR), Bioversity International [Montpellier], Bioversity International [Rome], Consultative Group on International Agricultural Research [CGIAR] (CGIAR)-Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Instituto Gulbenkian de Ciência, Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Phenome Emphasis France, and European Project: 211601,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2007-1,ELIXIR(2007)

Subjects
[SDV]Life Sciences [q-bio], [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [INFO]Computer Science [cs], [MATH]Mathematics [math]
Abstract

International audience; Plant Phenotyping data management following the FAIR (Findable, Accessible, Interoperable, Resusable) is highly challenging because of its heterogenity. Thus, simply integrating and consolidating data within a single dataset like a phenotyping network is already a complicated task which is even more complex when trying to link different datasets together. To adress this problem, the Minimal Information About Plant Phenotyping Experiment standard construction has been initiated four years ago, with the help of experts from European infrastructures and institutes like Elixir, Emphasis, INRA, WUR, iBet, IPK, EBI and IPG PAS. It adresses the need of data publication and reuse through a checklist that formalize and document the minimal metadata necessary to ensure long term FAIRness of field or greenhouse datasets, including high througputs phenotyping ones. This list has been implemented in several databases like GnpIS or eDale, in a file format, ISA Tab, in a web service, the Breeding API and an RDF implementation is under construction. We will review those implementations, show its current adoption state and detail the plans for the future evolutions of the standard.

Published
2018

39. Data standards for plant phenotyping: MIAPPE and its implementations [W785]

Author

Pommier, Cyril, Cornut, Guillaume, Letellier, Thomas, Michotey, Célia, Neveu, Pascal, Manuel Ruiz, Larmande, Pierre, Kersey, Paul J., Cwiek, Hanna, Krajewski, Pawel, Coppens, Frederik, Finkers, Richard, Laporte, Marie-Angélique, Faria, Daniel, Miguel, Célia M., Chavez, Ines, Adam-Blondon, Anne-Françoise, and Costa, Bruno

Subjects
F30 - Génétique et amélioration des plantes
Abstract

Plant Phenotyping data management following the FAIR (Findable, Accessible, Interoperable, Resusable) is highly challenging because of its heterogenity. Thus, simply integrating and consolidating data within a single dataset like a phenotyping network is already a complicated task which is even more complex when trying to link different datasets together. To adress this problem, the Minimal Information About Plant Phenotyping Experiment standard construction has been initiated four years ago, with the help of experts from European infrastructures and institutes like Elixir, Emphasis, INRA, WUR, iBet, IPK, EBI and IPG PAS. It adresses the need of data publication and reuse through a checklist that formalize and document the minimal metadata necessary to ensure long term FAIRness of field or greenhouse datasets, including high througputs phenotyping ones. This list has been implemented in several databases like GnpIS or eDale, in a file format, ISA Tab, in a web service, the Breeding API and an RDF implementation is under construction. We will review those implementations, show its current adoption state and detail the plans for the future evolutions of the standard.

Published
2018

40. Ensembl Genomes 2020—enabling non-vertebrate genomic research

Author

Howe, Kevin L, primary, Contreras-Moreira, Bruno, additional, De Silva, Nishadi, additional, Maslen, Gareth, additional, Akanni, Wasiu, additional, Allen, James, additional, Alvarez-Jarreta, Jorge, additional, Barba, Matthieu, additional, Bolser, Dan M, additional, Cambell, Lahcen, additional, Carbajo, Manuel, additional, Chakiachvili, Marc, additional, Christensen, Mikkel, additional, Cummins, Carla, additional, Cuzick, Alayne, additional, Davis, Paul, additional, Fexova, Silvie, additional, Gall, Astrid, additional, George, Nancy, additional, Gil, Laurent, additional, Gupta, Parul, additional, Hammond-Kosack, Kim E, additional, Haskell, Erin, additional, Hunt, Sarah E, additional, Jaiswal, Pankaj, additional, Janacek, Sophie H, additional, Kersey, Paul J, additional, Langridge, Nick, additional, Maheswari, Uma, additional, Maurel, Thomas, additional, McDowall, Mark D, additional, Moore, Ben, additional, Muffato, Matthieu, additional, Naamati, Guy, additional, Naithani, Sushma, additional, Olson, Andrew, additional, Papatheodorou, Irene, additional, Patricio, Mateus, additional, Paulini, Michael, additional, Pedro, Helder, additional, Perry, Emily, additional, Preece, Justin, additional, Rosello, Marc, additional, Russell, Matthew, additional, Sitnik, Vasily, additional, Staines, Daniel M, additional, Stein, Joshua, additional, Tello-Ruiz, Marcela K, additional, Trevanion, Stephen J, additional, Urban, Martin, additional, Wei, Sharon, additional, Ware, Doreen, additional, Williams, Gary, additional, Yates, Andrew D, additional, and Flicek, Paul, additional

Published
2019
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41. Factors Affecting Targeted Sequencing of 353 Nuclear Genes From Herbarium Specimens Spanning the Diversity of Angiosperms

Author

Brewer, Grace E., primary, Clarkson, James J., additional, Maurin, Olivier, additional, Zuntini, Alexandre R., additional, Barber, Vanessa, additional, Bellot, Sidonie, additional, Biggs, Nicola, additional, Cowan, Robyn S., additional, Davies, Nina M. J., additional, Dodsworth, Steven, additional, Edwards, Sara L., additional, Eiserhardt, Wolf L., additional, Epitawalage, Niroshini, additional, Frisby, Sue, additional, Grall, Aurélie, additional, Kersey, Paul J., additional, Pokorny, Lisa, additional, Leitch, Ilia J., additional, Forest, Félix, additional, and Baker, William J., additional

Published
2019
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42. Gramene 2018: unifying comparative genomics and pathway resources for plant research

Author

Tello-Ruiz, Marcela K, primary, Naithani, Sushma, additional, Stein, Joshua C, additional, Gupta, Parul, additional, Campbell, Michael, additional, Olson, Andrew, additional, Wei, Sharon, additional, Preece, Justin, additional, Geniza, Matthew J, additional, Jiao, Yinping, additional, Lee, Young Koung, additional, Wang, Bo, additional, Mulvaney, Joseph, additional, Chougule, Kapeel, additional, Elser, Justin, additional, Al-Bader, Noor, additional, Kumari, Sunita, additional, Thomason, James, additional, Kumar, Vivek, additional, Bolser, Daniel M, additional, Naamati, Guy, additional, Tapanari, Electra, additional, Fonseca, Nuno, additional, Huerta, Laura, additional, Iqbal, Haider, additional, Keays, Maria, additional, Munoz-Pomer Fuentes, Alfonso, additional, Tang, Amy, additional, Fabregat, Antonio, additional, D’Eustachio, Peter, additional, Weiser, Joel, additional, Stein, Lincoln D, additional, Petryszak, Robert, additional, Papatheodorou, Irene, additional, Kersey, Paul J, additional, Lockhart, Patti, additional, Taylor, Crispin, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2017
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43. Advancing vector biology research : a community survey for future directions, research applications and infrastructure requirements

Author

Kohl, Alain, Pondeville, Emilie, Schnettler, Esther, Crisanti, Andrea, Supparo, Clelia, Christophides, George K., Kersey, Paul J., Maslen, Gareth L., Takken, Willem, Koenraadt, Constantianus J.M., Oliva, Clelia F., Busquets, Núria, Abad, F.X., Failloux, Anna Bella, Levashina, Elena A., Wilson, Anthony J., Veronesi, Eva, Pichard, Maëlle, Arnaud Marsh, Sarah, Simard, Frédéric, Vernick, Kenneth D., Kohl, Alain, Pondeville, Emilie, Schnettler, Esther, Crisanti, Andrea, Supparo, Clelia, Christophides, George K., Kersey, Paul J., Maslen, Gareth L., Takken, Willem, Koenraadt, Constantianus J.M., Oliva, Clelia F., Busquets, Núria, Abad, F.X., Failloux, Anna Bella, Levashina, Elena A., Wilson, Anthony J., Veronesi, Eva, Pichard, Maëlle, Arnaud Marsh, Sarah, Simard, Frédéric, and Vernick, Kenneth D.

Abstract

Vector-borne pathogens impact public health, animal production, and animal welfare. Research on arthropod vectors such as mosquitoes, ticks, sandflies, and midges which transmit pathogens to humans and economically important animals is crucial for development of new control measures that target transmission by the vector. While insecticides are an important part of this arsenal, appearance of resistance mechanisms is increasingly common. Novel tools for genetic manipulation of vectors, use of Wolbachia endosymbiotic bacteria, and other biological control mechanisms to prevent pathogen transmission have led to promising new intervention strategies, adding to strong interest in vector biology and genetics as well as vector–pathogen interactions. Vector research is therefore at a crucial juncture, and strategic decisions on future research directions and research infrastructure investment should be informed by the research community. A survey initiated by the European Horizon 2020 INFRAVEC-2 consortium set out to canvass priorities in the vector biology research community and to determine key activities that are needed for researchers to efficiently study vectors, vector-pathogen interactions, as well as access the structures and services that allow such activities to be carried out. We summarize the most important findings of the survey which in particular reflect the priorities of researchers in European countries, and which will be of use to stakeholders that include researchers, government, and research organizations.

Published
2016

44. Advancing vector biology research: a community survey for future directions, research applications and infrastructure requirements

Author

Kohl, Alain, primary, Pondeville, Emilie, additional, Schnettler, Esther, additional, Crisanti, Andrea, additional, Supparo, Clelia, additional, Christophides, George K., additional, Kersey, Paul J., additional, Maslen, Gareth L., additional, Takken, Willem, additional, Koenraadt, Constantianus J. M., additional, Oliva, Clelia F., additional, Busquets, Núria, additional, Abad, F. Xavier, additional, Failloux, Anna-Bella, additional, Levashina, Elena A., additional, Wilson, Anthony J., additional, Veronesi, Eva, additional, Pichard, Maëlle, additional, Arnaud Marsh, Sarah, additional, Simard, Frédéric, additional, and Vernick, Kenneth D., additional

Published
2016
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45. transPLANT Resources for Triticeae Genomic Data

Author

Spannagl, Manuel, primary, Alaux, Michael, additional, Lange, Matthias, additional, Bolser, Daniel M., additional, Bader, Kai C., additional, Letellier, Thomas, additional, Kimmel, Erik, additional, Flores, Raphael, additional, Pommier, Cyril, additional, Kerhornou, Arnaud, additional, Walts, Brandon, additional, Nussbaumer, Thomas, additional, Grabmuller, Christoph, additional, Chen, Jinbo, additional, Colmsee, Christian, additional, Beier, Sebastian, additional, Mascher, Martin, additional, Schmutzer, Thomas, additional, Arend, Daniel, additional, Thanki, Anil, additional, Ramirez‐Gonzalez, Ricardo, additional, Ayling, Martin, additional, Ayling, Sarah, additional, Caccamo, Mario, additional, Mayer, Klaus F.X., additional, Scholz, Uwe, additional, Steinbach, Delphine, additional, Quesneville, Hadi, additional, and Kersey, Paul J., additional

Published
2016
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46. Gramene 2016: comparative plant genomics and pathway resources

Author

Tello-Ruiz, Marcela K., primary, Stein, Joshua, additional, Wei, Sharon, additional, Preece, Justin, additional, Olson, Andrew, additional, Naithani, Sushma, additional, Amarasinghe, Vindhya, additional, Dharmawardhana, Palitha, additional, Jiao, Yinping, additional, Mulvaney, Joseph, additional, Kumari, Sunita, additional, Chougule, Kapeel, additional, Elser, Justin, additional, Wang, Bo, additional, Thomason, James, additional, Bolser, Daniel M., additional, Kerhornou, Arnaud, additional, Walts, Brandon, additional, Fonseca, Nuno A., additional, Huerta, Laura, additional, Keays, Maria, additional, Tang, Y. Amy, additional, Parkinson, Helen, additional, Fabregat, Antonio, additional, McKay, Sheldon, additional, Weiser, Joel, additional, D'Eustachio, Peter, additional, Stein, Lincoln, additional, Petryszak, Robert, additional, Kersey, Paul J., additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2015
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47. PomBase 2015: updates to the fission yeast database

Author

McDowall, Mark D., primary, Harris, Midori A., additional, Lock, Antonia, additional, Rutherford, Kim, additional, Staines, Daniel M., additional, Bähler, Jürg, additional, Kersey, Paul J., additional, Oliver, Stephen G., additional, and Wood, Valerie, additional

Published
2014
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48. Gramene 2013: comparative plant genomics resources

Author

Monaco, Marcela K., primary, Stein, Joshua, additional, Naithani, Sushma, additional, Wei, Sharon, additional, Dharmawardhana, Palitha, additional, Kumari, Sunita, additional, Amarasinghe, Vindhya, additional, Youens-Clark, Ken, additional, Thomason, James, additional, Preece, Justin, additional, Pasternak, Shiran, additional, Olson, Andrew, additional, Jiao, Yinping, additional, Lu, Zhenyuan, additional, Bolser, Dan, additional, Kerhornou, Arnaud, additional, Staines, Dan, additional, Walts, Brandon, additional, Wu, Guanming, additional, D’Eustachio, Peter, additional, Haw, Robin, additional, Croft, David, additional, Kersey, Paul J., additional, Stein, Lincoln, additional, Jaiswal, Pankaj, additional, and Ware, Doreen, additional

Published
2013
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49. Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

Author

Kersey, Paul J., primary, Staines, Daniel M., additional, Lawson, Daniel, additional, Kulesha, Eugene, additional, Derwent, Paul, additional, Humphrey, Jay C., additional, Hughes, Daniel S. T., additional, Keenan, Stephan, additional, Kerhornou, Arnaud, additional, Koscielny, Gautier, additional, Langridge, Nicholas, additional, McDowall, Mark D., additional, Megy, Karine, additional, Maheswari, Uma, additional, Nuhn, Michael, additional, Paulini, Michael, additional, Pedro, Helder, additional, Toneva, Iliana, additional, Wilson, Derek, additional, Yates, Andrew, additional, and Birney, Ewan, additional

Published
2011
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50. Assemblathon 1: A competitive assessment of de novo short read assembly methods

Author

Earl, Dent, primary, Bradnam, Keith, additional, St. John, John, additional, Darling, Aaron, additional, Lin, Dawei, additional, Fass, Joseph, additional, Yu, Hung On Ken, additional, Buffalo, Vince, additional, Zerbino, Daniel R., additional, Diekhans, Mark, additional, Nguyen, Ngan, additional, Ariyaratne, Pramila Nuwantha, additional, Sung, Wing-Kin, additional, Ning, Zemin, additional, Haimel, Matthias, additional, Simpson, Jared T., additional, Fonseca, Nuno A., additional, Birol, İnanç, additional, Docking, T. Roderick, additional, Ho, Isaac Y., additional, Rokhsar, Daniel S., additional, Chikhi, Rayan, additional, Lavenier, Dominique, additional, Chapuis, Guillaume, additional, Naquin, Delphine, additional, Maillet, Nicolas, additional, Schatz, Michael C., additional, Kelley, David R., additional, Phillippy, Adam M., additional, Koren, Sergey, additional, Yang, Shiaw-Pyng, additional, Wu, Wei, additional, Chou, Wen-Chi, additional, Srivastava, Anuj, additional, Shaw, Timothy I., additional, Ruby, J. Graham, additional, Skewes-Cox, Peter, additional, Betegon, Miguel, additional, Dimon, Michelle T., additional, Solovyev, Victor, additional, Seledtsov, Igor, additional, Kosarev, Petr, additional, Vorobyev, Denis, additional, Ramirez-Gonzalez, Ricardo, additional, Leggett, Richard, additional, MacLean, Dan, additional, Xia, Fangfang, additional, Luo, Ruibang, additional, Li, Zhenyu, additional, Xie, Yinlong, additional, Liu, Binghang, additional, Gnerre, Sante, additional, MacCallum, Iain, additional, Przybylski, Dariusz, additional, Ribeiro, Filipe J., additional, Yin, Shuangye, additional, Sharpe, Ted, additional, Hall, Giles, additional, Kersey, Paul J., additional, Durbin, Richard, additional, Jackman, Shaun D., additional, Chapman, Jarrod A., additional, Huang, Xiaoqiu, additional, DeRisi, Joseph L., additional, Caccamo, Mario, additional, Li, Yingrui, additional, Jaffe, David B., additional, Green, Richard E., additional, Haussler, David, additional, Korf, Ian, additional, and Paten, Benedict, additional

Published
2011
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