This work is licensed under the Creative Commons Attribution 4.0 International License.
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).AndrewsS.2010.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.AnzuetoF.BertrandB. and DufourM.1995.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.BaliS.HuS.ViningK.BrownC. R.MajtahediH.ZhangL.GleasonC. and SathuvalliV.2021.IS-MPMI Congress.10.1094/MPMI-12-20-0337-A33779267Search 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.BankevichA.NurkS.AntipovD.GurevichA. A.DvorkinM.KulikovA. S.LesinV. M.NikolenkoS. I.PhamS.PrjibelskiA. D.PyshkinA. V.SirotkinA. V.VyahhiN.TeslerG.AlekseyevM. A. and PevznerP. A.2012.SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.19:455–477.10.1089/cmb.2012.0021334251922506599Search 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.BarbosaD. H. S. G.DuarteH.SouzaR.VianaA. P. and SilvaC. P.2004.Field estimates of coffee yield losses and damage threshold by Meloidogyne exigua.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.BerntM.DonathA.JühlingF.ExternbrinkF.FlorentzC.FritzschG.PützJ.MiddendorfM. and StadlerP. F.2013.MITOS: improved de novo metazoan mitochondrial genome annotation.69:313–319.10.1016/j.ympev.2012.08.02322982435Search 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.BesnardG.JühlingF.ChapuisÉ.ZedaneL.LhuillierÉ.MateilleT. and BellafioreS.2014.Fast assembly of the mitochondrial genome of a plant parasitic nematode Meloidogyne graminicola using next generation sequencing.337:295–301.10.1016/j.crvi.2014.03.00324841955Search 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-MathieuR.Perfus-BarbeochL.AuryJ. -M.RochaM. D.GouzyJ.SalletE.Martin-JimenezC.Bailly-BechetM.Castagnone-SerenoP.FlotJ. -F.KozlowskiD. K.CazarethJ.CoulouxA.SilvaC. D.GuyJ.Kim-JoY. -J.RancurelC.SchiexT.AbadP.WinckerP. and DanchinE. G. J.2017.Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes.13:e1006777.10.1371/journal.pgen.1006777546596828594822Search 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.CamposV. P.and VillainL.2005.Nematode parasites of coffee and cocoa. InLucM.SikoraR. A. and BridgeJ.(Eds),,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-SerenoP.MuletK.DanchinE. G. J.KoutsovoulosG. D.KaraulicM.RochaM. D.Bailly-BechetM.PratxL.Perfus-BarbeochL. and AbadP.2019.Gene copy number variations as signatures of adaptive evolution in the parthenogenetic, plant-parasitic nematode Meloidogyne incognita.28:2559–2572.10.1111/mec.1509530964953Search 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.DanchinG. J. E.GuzeevaA. E.MantelinS.BerepikiA. and JonesT. J.2016.Horizontal gene transfer from bacteria has enabled the plant-parasitic nematode Globodera pallida to feed on host-derived sucrose.33:1571–1579.10.1093/molbev/msw04126915958Search 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 CosterW.D’HertS.SchultzD. T.CrutsM. and Van BroeckhovenC.2018.NanoPack: visualizing and processing long-read sequencing data.34:2666–2669.10.1093/bioinformatics/bty149606179429547981Search 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.DonathA.JühlingF.Al-ArabM.BernhartS. H.ReinhardtF.StadlerP. F.MiddendorfM. and BerntM.2019.Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes.47:10543–10552.10.1093/nar/gkz833684786431584075Search 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.GoeldiE. A.1892.Relatoria sobre a molestia do cafeeiro na provincia 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.JaronK. S.BastJ.NowellR. W.Ranallo-BenavidezT. R.Robinson-RechaviM. and SchwanderT.2020.Genomic features of parthenogenetic animals.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.JiangH.LeiR.DingS.-W. and ZhuS.2014.Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.15:182.10.1186/1471-2105-15-182407438524925680Search 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.JonesJ. T.HaegemanA.DanchinE. G. J.GaurH. S.HelderJ.JonesM. G. K.KikuchiT.Manzanilla-LópezR.Palomares-RiusJ. E.WesemaelW. M. L. and PerryR. N.2013.Top 10 plant-parasitic nematodes in molecular plant pathology.14:946–961.10.1111/mpp.12057663876423809086Search in Google Scholar
Kokot, M., Długosz, M. and Deorowicz, S. 2017. KMC 3: counting and manipulating k-mer statistics. Bioinformatics 33:2759–2761.KokotM.DługoszM. and DeorowiczS.2017.KMC 3: counting and manipulating k-mer statistics.33:2759–2761.10.1093/bioinformatics/btx30428472236Search 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.KoutsovoulosG. D.PoulletM.AshryA. E.KozlowskiD. K.SalletE.RochaM. D.Perfus-BarbeochLMartin-JimenezC.FreyJ. E.AhrensC. H.KiewnickS. and DanchinE. G. J.2020.The polyploid genome of the mitotic parthenogenetic root-knot nematode Meloidogyne enterolobii.7:324.10.1038/s41597-020-00666-0753618533020495Search 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.KorenS.WalenzB. P.BerlinK.MillerJ. R.BergmanN. H. and PhillippyA. M.2017.Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation.27:722–736.10.1101/gr.215087.116541176728298431Search 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.KozlowskiD. K.Hassanaly-GoulamhoussenR.RochaM. D.KoutsovoulosG. D.Bailly-BechetM. and DanchinE. G. J.2020..bioRxiv2020.04.30.069948.10.1101/2020.04.30.069948Search 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.KumarS.JonesM.KoutsovoulosG.ClarkeM. and BlaxterM.2013.Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots.4:237.Search in Google Scholar
Laetsch, D. R. and Blaxter, M. L. 2017. BlobTools: interrogation of genome assemblies. F1000Research 6:1287.LaetschD. R. and BlaxterM. L.2017.BlobTools: interrogation of genome assemblies.6:1287.10.12688/f1000research.12232.1Search 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.LiuY.SchröderJ. and SchmidtB.2013.Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data.29:308–315.10.1093/bioinformatics/bts69023202746Search 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.MarçaisG. and KingsfordC.2011.A fast, lock-free approach for efficient parallel counting of occurrences of k-mers.27:764–770.10.1093/bioinformatics/btr011305131921217122Search 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 deM. F.CarneiroR.AlmeidaM. R.CamposV. P.Castagnone-SerenoP. and CastroJ. M. C.2008.Diversity of Meloidogyne exigua (Tylenchida: Meloidogynidae) populations from coffee and rubber tree.10:897–910.10.1163/156854108786161418Search 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.OppermanC. H.BirdD. M.WilliamsonV. M.RokhsarD. S.BurkeM.CohnJ.CromerJ.DienerS.GajanJ.GrahamS.HoufekT. D.LiuQ.MitrosT.SchaffJ.SchafferR.SchollE.SosinskiB. R.ThomasV. P. and WindhamE.2008.Sequence and genetic map of Meloidogyne hapla: a compact nematode genome for plant parasitism.105:14802–14807.10.1073/pnas.0805946105254741818809916Search 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.ParraG.BradnamK. and KorfI.2007.CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.23:1061–1067.10.1093/bioinformatics/btm07117332020Search 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.PhanN. T.OrjuelaJ.DanchinE. G. J.KloppC.Perfus-BarbeochL.KozlowskiD. K.KoutsovoulosG. D.Lopez-RoquesC.BouchezO.ZahmM.BesnardG. and BellafioreS.2020.Genome structure and content of the rice root-knot nematode (Meloidogyne graminicola).10:11006–11021.10.1002/ece3.6680759317933144944Search 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-BenavidezT. R.JaronK. S. and SchatzM. C.2020.GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes.11:1432.10.1038/s41467-020-14998-3708079132188846Search 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.SimãoF. A.WaterhouseR. M.IoannidisP.KriventsevaE. V. and ZdobnovE. M.2015.BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.31:3210–3212.10.1093/bioinformatics/btv35126059717Search 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.TriantaphyllouA. C.,SasserJ. N. and CarterC. C.1985.Cytogenetics, cytotaxonomy and phylogeny of root-knot nematodes.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.VaserR.SovicI.NagarajanN. and SikicM.2017.Fast and accurate de novo genome assembly from long uncorrected reads.27:737–746.10.1101/gr.214270.116541176828100585Search 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.VurtureG. W.SedlazeckF. J.NattestadM.UnderwoodC. J.FangH.GurtowskiJ. and SchatzM. C.2017.GenomeScope: fast reference-free genome profiling from short reads.33:2202–2204.10.1093/bioinformatics/btx153587070428369201Search 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.WalkerB. J.AbeelT.SheaT.PriestM.AbouellielA.SakthikumarS.CuomoC. A.ZengQ.WortmanJ.YoungS.K. and EarlA. M.2014.Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement.9:e112963.10.1371/journal.pone.0112963423734825409509Search in Google Scholar
Wick, R. 2019. Porechop [C++], available at: https://github.com/rrwick/Porechop (original work published 2017).WickR.2019.(original work published 2017).Search in Google Scholar