Genome sequence of the coffee root-knot nematode Meloidogyne exigua

Andrews, S. 2010. FastQC: a quality control tool for high throughput sequence data Babraham Bioinformatics, The Babraham Institute, Cambridge, available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed March 15, 2020). Andrews S. 2010 . FastQC: a quality control tool for high throughput sequence data Babraham Bioinformatics, The Babraham Institute, Cambridge, available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed March 15, 2020) . Search in Google Scholar

Anzueto, F., Bertrand, B. and Dufour, M. 1995. “Nemaya”, desarrollo de una variedad porta-injerto resistente a los principales nemátodos de América Central. Programa Cooperativo para el Desarrollo Tecnológico y la Modernización de la Caficultura (PROMECAFE) Boletín PROCAFE-IICA-CATIE, No. 66-67, available at: http://repositorio.iica.int/handle/11324/7910. Anzueto F. Bertrand B. and Dufour M. 1995 . “Nemaya”, desarrollo de una variedad porta-injerto resistente a los principales nemátodos de América Central. Programa Cooperativo para el Desarrollo Tecnológico y la Modernización de la Caficultura (PROMECAFE) Boletín PROCAFE-IICA-CATIE, No. 66-67, available at: http://repositorio.iica.int/handle/11324/7910 . Search in Google Scholar

Bali, S., Hu, S., Vining, K., Brown, C. R., Majtahedi, H., Zhang, L., Gleason, C. and Sathuvalli, V. 2021. Nematode genome announcement: draft genome of Meloidogyne chitwoodi, an economically important pest of potato in the Pacific Northwest IS-MPMI Congress. Bali S. Hu S. Vining K. Brown C. R. Majtahedi H. Zhang L. Gleason C. and Sathuvalli V. 2021 . Nematode genome announcement: draft genome of Meloidogyne chitwoodi, an economically important pest of potato in the Pacific Northwest IS-MPMI Congress . 10.1094/MPMI-12-20-0337-A33779267 Search in Google Scholar

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A. and Pevzner, P. A. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology 19:455–477. Bankevich A. Nurk S. Antipov D. Gurevich A. A. Dvorkin M. Kulikov A. S. Lesin V. M. Nikolenko S. I. Pham S. Prjibelski A. D. Pyshkin A. V. Sirotkin A. V. Vyahhi N. Tesler G. Alekseyev M. A. and Pevzner P. A. 2012 . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing . Journal of Computational Biology 19 : 455 – 477 . 10.1089/cmb.2012.0021334251922506599 Search in Google Scholar

Barbosa, D. H. S. G., Duarte, H., Souza, R., Viana, A. P. and Silva, C. P. 2004. Field estimates of coffee yield losses and damage threshold by Meloidogyne exigua. Nematologia Brasileira 28:49–54. Barbosa D. H. S. G. Duarte H. Souza R. Viana A. P. and Silva C. P. 2004 . Field estimates of coffee yield losses and damage threshold by Meloidogyne exigua . Nematologia Brasileira 28 : 49 – 54 . Search in Google Scholar

Bernt, M., Donath, A., Jühling, F., Externbrink, F., Florentz, C., Fritzsch, G., Pütz, J., Middendorf, M. and Stadler, P. F. 2013. MITOS: improved de novo metazoan mitochondrial genome annotation. Molecular Phylogenetics and Evolution 69:313–319. Bernt M. Donath A. Jühling F. Externbrink F. Florentz C. Fritzsch G. Pütz J. Middendorf M. and Stadler P. F. 2013 . MITOS: improved de novo metazoan mitochondrial genome annotation . Molecular Phylogenetics and Evolution 69 : 313 – 319 . 10.1016/j.ympev.2012.08.02322982435 Search in Google Scholar

Besnard, G., Jühling, F., Chapuis, É., Zedane, L., Lhuillier, É., Mateille, T. and Bellafiore, S. 2014. Fast assembly of the mitochondrial genome of a plant parasitic nematode Meloidogyne graminicola using next generation sequencing. Comptes Rendus Biologies 337:295–301. Besnard G. Jühling F. Chapuis É. Zedane L. Lhuillier É. Mateille T. and Bellafiore S. 2014 . Fast assembly of the mitochondrial genome of a plant parasitic nematode Meloidogyne graminicola using next generation sequencing . Comptes Rendus Biologies 337 : 295 – 301 . 10.1016/j.crvi.2014.03.00324841955 Search in Google Scholar

Blanc-Mathieu, R., Perfus-Barbeoch, L., Aury, J. -M., Rocha, M. D., Gouzy, J., Sallet, E., Martin-Jimenez, C., Bailly-Bechet, M., Castagnone-Sereno, P., Flot, J. -F., Kozlowski, D. K., Cazareth, J., Couloux, A., Silva, C. D., Guy, J., Kim-Jo, Y. -J., Rancurel, C., Schiex, T., Abad, P., Wincker, P. and Danchin, E. G. J. 2017. Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics 13:e1006777. Blanc-Mathieu R. Perfus-Barbeoch L. Aury J. -M. Rocha M. D. Gouzy J. Sallet E. Martin-Jimenez C. Bailly-Bechet M. Castagnone-Sereno P. Flot J. -F. Kozlowski D. K. Cazareth J. Couloux A. Silva C. D. Guy J. Kim-Jo Y. -J. Rancurel C. Schiex T. Abad P. Wincker P. and Danchin E. G. J. 2017 . Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLOS Genetics 13 : e1006777 . 10.1371/journal.pgen.1006777546596828594822 Search in Google Scholar

Campos, V. P. and Villain, L. 2005. Nematode parasites of coffee and cocoa. In Luc, M., Sikora, R. A. and Bridge, J. (Eds), Plant parasitic nematodes in subtropical and tropical agriculture, Wallingford: CABI, pp. 529–579. Campos V. P. and Villain L. 2005 . Nematode parasites of coffee and cocoa . In Luc M. Sikora R. A. and Bridge J. (Eds), Plant parasitic nematodes in subtropical and tropical agriculture , Wallingford : CABI , pp. 529 – 579 . Search in Google Scholar

Castagnone-Sereno, P., Mulet, K., Danchin, E. G. J., Koutsovoulos, G. D., Karaulic, M., Rocha, M. D., Bailly-Bechet, M., Pratx, L., Perfus-Barbeoch, L. and Abad, P. 2019. Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita. Molecular Ecology 28:2559–2572. Castagnone-Sereno P. Mulet K. Danchin E. G. J. Koutsovoulos G. D. Karaulic M. Rocha M. D. Bailly-Bechet M. Pratx L. Perfus-Barbeoch L. and Abad P. 2019 . Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita . Molecular Ecology 28 : 2559 – 2572 . 10.1111/mec.1509530964953 Search in Google Scholar

Danchin, G. J. E., Guzeeva, A. E., Mantelin, S., Berepiki, A. and Jones, T. J. 2016. Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose. Molecular Biology and Evolution 33:1571–1579. Danchin G. J. E. Guzeeva A. E. Mantelin S. Berepiki A. and Jones T. J. 2016 . Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose . Molecular Biology and Evolution 33 : 1571 – 1579 . 10.1093/molbev/msw04126915958 Search in Google Scholar

De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. and Van Broeckhoven, C. 2018. NanoPack: visualizing and processing long-read sequencing data. Bioinformatics 34:2666–2669. De Coster W. D’Hert S. Schultz D. T. Cruts M. and Van Broeckhoven C. 2018 . NanoPack: visualizing and processing long-read sequencing data . Bioinformatics 34 : 2666 – 2669 . 10.1093/bioinformatics/bty149606179429547981 Search in Google Scholar

Donath, A., Jühling, F., Al-Arab, M., Bernhart, S. H., Reinhardt, F., Stadler, P. F., Middendorf, M. and Bernt, M. 2019. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Research 47:10543–10552. Donath A. Jühling F. Al-Arab M. Bernhart S. H. Reinhardt F. Stadler P. F. Middendorf M. and Bernt M. 2019 . Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes . Nucleic Acids Research 47 : 10543 – 10552 . 10.1093/nar/gkz833684786431584075 Search in Google Scholar

Goeldi, E. A. 1892. Relatoria sobre a molestia do cafeeiro na provincia do Rio de Janeiro. Archivos do Museu Nacional do Rio de Janeiro 8:1–121. Goeldi E. A. 1892 . Relatoria sobre a molestia do cafeeiro na provincia do Rio de Janeiro . Archivos do Museu Nacional do Rio de Janeiro 8 : 1 – 121 . Search in Google Scholar

Jaron, K. S., Bast, J., Nowell, R. W., Ranallo-Benavidez, T. R., Robinson-Rechavi, M. and Schwander, T. 2020. Genomic features of parthenogenetic animals. Journal of Heredity 1:19–33. Jaron K. S. Bast J. Nowell R. W. Ranallo-Benavidez T. R. Robinson-Rechavi M. and Schwander T. 2020 . Genomic features of parthenogenetic animals . Journal of Heredity 1 : 19 – 33 . Search in Google Scholar

Jiang, H., Lei, R., Ding, S.-W. and Zhu, S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182. Jiang H. Lei R. Ding S.-W. and Zhu S. 2014 . Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads . BMC Bioinformatics 15 : 182 . 10.1186/1471-2105-15-182407438524925680 Search in Google Scholar

Jones, J. T., Haegeman, A., Danchin, E. G. J., Gaur, H. S., Helder, J., Jones, M. G. K., Kikuchi, T., Manzanilla-López, R., Palomares-Rius, J. E., Wesemael, W. M. L. and Perry, R. N. 2013. Top 10 plant-parasitic nematodes in molecular plant pathology. Molecular Plant Pathology 14:946–961. Jones J. T. Haegeman A. Danchin E. G. J. Gaur H. S. Helder J. Jones M. G. K. Kikuchi T. Manzanilla-López R. Palomares-Rius J. E. Wesemael W. M. L. and Perry R. N. 2013 . Top 10 plant-parasitic nematodes in molecular plant pathology . Molecular Plant Pathology 14 : 946 – 961 . 10.1111/mpp.12057663876423809086 Search in Google Scholar

Kokot, M., Długosz, M. and Deorowicz, S. 2017. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33:2759–2761. Kokot M. Długosz M. and Deorowicz S. 2017 . KMC 3: counting and manipulating k-mer statistics . Bioinformatics 33 : 2759 – 2761 . 10.1093/bioinformatics/btx30428472236 Search in Google Scholar

Koutsovoulos, G. D., Poullet, M., Ashry, A. E., Kozlowski, D. K., Sallet, E., Rocha, M. D., Perfus-Barbeoch, L, Martin-Jimenez, C., Frey, J. E., Ahrens, C. H., Kiewnick, S. and Danchin, E. G. J. 2020. The polyploid genome of the mitotic parthenogenetic root-knot nematode Meloidogyne enterolobii. Scientific Data 7:324. Koutsovoulos G. D. Poullet M. Ashry A. E. Kozlowski D. K. Sallet E. Rocha M. D. Perfus-Barbeoch L Martin-Jimenez C. Frey J. E. Ahrens C. H. Kiewnick S. and Danchin E. G. J. 2020 . The polyploid genome of the mitotic parthenogenetic root-knot nematode Meloidogyne enterolobii . Scientific Data 7 : 324 . 10.1038/s41597-020-00666-0753618533020495 Search in Google Scholar

Koren, S., Walenz, B. P., Berlin, K., Miller, J. R., Bergman, N. H. and Phillippy, A. M. 2017. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research 27:722–736. Koren S. Walenz B. P. Berlin K. Miller J. R. Bergman N. H. and Phillippy A. M. 2017 . Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation . Genome Research 27 : 722 – 736 . 10.1101/gr.215087.116541176728298431 Search in Google Scholar

Kozlowski, D. K., Hassanaly-Goulamhoussen, R., Rocha, M. D., Koutsovoulos, G. D., Bailly-Bechet, M. and Danchin, E. G. J. 2020. Transposable elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita. bioRxiv2020.04.30.069948. Kozlowski D. K. Hassanaly-Goulamhoussen R. Rocha M. D. Koutsovoulos G. D. Bailly-Bechet M. and Danchin E. G. J. 2020 . Transposable elements are an evolutionary force shaping genomic plasticity in the parthenogenetic root-knot nematode Meloidogyne incognita . bioRxiv2020.04.30.069948 . 10.1101/2020.04.30.069948 Search in Google Scholar

Kumar, S., Jones, M., Koutsovoulos, G., Clarke, M. and Blaxter, M. 2013. Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots. Frontiers in Genetics 4:237. Kumar S. Jones M. Koutsovoulos G. Clarke M. and Blaxter M. 2013 . Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots . Frontiers in Genetics 4 : 237 . Search in Google Scholar

Laetsch, D. R. and Blaxter, M. L. 2017. BlobTools: interrogation of genome assemblies. F1000Research 6:1287. Laetsch D. R. and Blaxter M. L. 2017 . BlobTools: interrogation of genome assemblies . F1000Research 6 : 1287 . 10.12688/f1000research.12232.1 Search in Google Scholar

Liu, Y., Schröder, J. and Schmidt, B. 2013. Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics 29:308–315. Liu Y. Schröder J. and Schmidt B. 2013 . Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data . Bioinformatics 29 : 308 – 315 . 10.1093/bioinformatics/bts69023202746 Search in Google Scholar

Marçais, G. and Kingsford, C. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770. Marçais G. and Kingsford C. 2011 . A fast, lock-free approach for efficient parallel counting of occurrences of k-mers . Bioinformatics 27 : 764 – 770 . 10.1093/bioinformatics/btr011305131921217122 Search in Google Scholar

Muniz de, M. F., Carneiro, R., Almeida, M. R., Campos, V. P., Castagnone-Sereno, P. and Castro, J. M. C. 2008. Diversity of Meloidogyne exigua (Tylenchida: Meloidogynidae) populations from coffee and rubber tree. Nematology 10:897–910. Muniz de M. F. Carneiro R. Almeida M. R. Campos V. P. Castagnone-Sereno P. and Castro J. M. C. 2008 . Diversity of Meloidogyne exigua (Tylenchida: Meloidogynidae) populations from coffee and rubber tree . Nematology 10 : 897 – 910 . 10.1163/156854108786161418 Search in Google Scholar

Opperman, C. H., Bird, D. M., Williamson, V. M., Rokhsar, D. S., Burke, M., Cohn, J., Cromer, J., Diener, S., Gajan, J., Graham, S., Houfek, T. D., Liu, Q., Mitros, T., Schaff, J., Schaffer, R., Scholl, E., Sosinski, B. R., Thomas, V. P. and Windham, E. 2008. Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences of the United States of America 105:14802–14807. Opperman C. H. Bird D. M. Williamson V. M. Rokhsar D. S. Burke M. Cohn J. Cromer J. Diener S. Gajan J. Graham S. Houfek T. D. Liu Q. Mitros T. Schaff J. Schaffer R. Scholl E. Sosinski B. R. Thomas V. P. and Windham E. 2008 . Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism . Proceedings of the National Academy of Sciences of the United States of America 105 : 14802 – 14807 . 10.1073/pnas.0805946105254741818809916 Search in Google Scholar

Parra, G., Bradnam, K. and Korf, I. 2007. CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067. Parra G. Bradnam K. and Korf I. 2007 . CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes . Bioinformatics 23 : 1061 – 1067 . 10.1093/bioinformatics/btm07117332020 Search in Google Scholar

Phan, N. T., Orjuela, J., Danchin, E. G. J., Klopp, C., Perfus-Barbeoch, L., Kozlowski, D. K., Koutsovoulos, G. D., Lopez-Roques, C., Bouchez, O., Zahm, M., Besnard, G. and Bellafiore, S. 2020. Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola). Ecology and Evolution 10:11006–11021. Phan N. T. Orjuela J. Danchin E. G. J. Klopp C. Perfus-Barbeoch L. Kozlowski D. K. Koutsovoulos G. D. Lopez-Roques C. Bouchez O. Zahm M. Besnard G. and Bellafiore S. 2020 . Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola) . Ecology and Evolution 10 : 11006 – 11021 . 10.1002/ece3.6680759317933144944 Search in Google Scholar

Ranallo-Benavidez, T. R., Jaron, K. S. and Schatz, M. C. 2020. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nature Communications 11:1432. Ranallo-Benavidez T. R. Jaron K. S. and Schatz M. C. 2020 . GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes . Nature Communications 11 : 1432 . 10.1038/s41467-020-14998-3708079132188846 Search in Google Scholar

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V. and Zdobnov, E. M. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31:3210–3212. Simão F. A. Waterhouse R. M. Ioannidis P. Kriventseva E. V. and Zdobnov E. M. 2015 . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs . Bioinformatics 31 : 3210 – 3212 . 10.1093/bioinformatics/btv35126059717 Search in Google Scholar

Triantaphyllou, A. C., Sasser, J. N. and Carter, C. C. 1985. Cytogenetics, cytotaxonomy and phylogeny of root-knot nematodes. An advanced treatise on Meloidogyne biology and control Raleigh: North Carolina State University, 113–126. Triantaphyllou A. C. , Sasser J. N. and Carter C. C. 1985 . Cytogenetics, cytotaxonomy and phylogeny of root-knot nematodes . An advanced treatise on Meloidogyne biology and control Raleigh : North Carolina State University , 113 – 126 . Search in Google Scholar

Vaser, R., Sovic, I., Nagarajan, N. and Sikic, M. 2017. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research 27:737–746. Vaser R. Sovic I. Nagarajan N. and Sikic M. 2017 . Fast and accurate de novo genome assembly from long uncorrected reads . Genome Research 27 : 737 – 746 . 10.1101/gr.214270.116541176828100585 Search in Google Scholar

Vurture, G. W., Sedlazeck, F. J., Nattestad, M., Underwood, C. J., Fang, H., Gurtowski, J. and Schatz, M. C. 2017. GenomeScope: fast reference-free genome profiling from short reads. Bioinformatics 33:2202–2204. Vurture G. W. Sedlazeck F. J. Nattestad M. Underwood C. J. Fang H. Gurtowski J. and Schatz M. C. 2017 . GenomeScope: fast reference-free genome profiling from short reads . Bioinformatics 33 : 2202 – 2204 . 10.1093/bioinformatics/btx153587070428369201 Search in Google Scholar

Walker, B. J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C. A., Zeng, Q., Wortman, J., Young, S.K. and Earl, A. M. 2014. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9:e112963. Walker B. J. Abeel T. Shea T. Priest M. Abouelliel A. Sakthikumar S. Cuomo C. A. Zeng Q. Wortman J. Young S.K. and Earl A. M. 2014 . Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement . PLoS ONE 9 : e112963 . 10.1371/journal.pone.0112963423734825409509 Search in Google Scholar

Wick, R. 2019. Porechop [C++], available at: https://github.com/rrwick/Porechop (original work published 2017). Wick R. 2019 . Porechop [C++], available at: https://github.com/rrwick/Porechop (original work published 2017) . Search in Google Scholar