Identification of Suitable Meloidogyne spp. Housekeeping Genes

Abad P. , Gouzy J. , Aury J. M. , Castagnone-Sereno P. , Danchin E. G. J. , Deleury E. , Perfus-Barbeoch L. , Anthouard V. , Artiguenave F. , Blok V. C. , Caillaud M. C. , Coutinho P. M. , Dasilva C. , De Luca F. , Deau F. , Esquibet M. , Flutre T. , Goldstone J. V. , Hamamouch N. , Hewezi T. , Jaillon O. , Jubin C. , Leonetti P. , Magliano M. , Maier T. R. , Markov G. V. , McVeigh P. , Pesole G. , Poulain J. , Robinson-Rechavi M. , Sallet E. , Segurens B. , Steinbach D. , Tytgat T. , Ugarte E. , van Ghelder C. , Veronico P. , Baum T. J. , Blaxter M. , Bleve-Zacheo T. , Davis E. L. , Ewbank J. J. , Favery B. , Grenier E. , Henrissat B. , Jones J. T. , Laudet V. , Maule A. G. , Quesneville H. , Rosso M. N. , Schiex T. , Smant G. , Weissenbach J. and Wincker P. 2008. Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita . Nature Biotechnology 26:909–15.10.1038/nbt.148218660804 Search in Google Scholar

Bustin S. A. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25:169–93.10.1677/jme.0.025016911013345 Search in Google Scholar

Butte A. J. , Dzau V. J. and Glueck S. B. 2001. Further defining housekeeping, or ‘maintenance’, genes focus on ‘a compendium of gene expression in normal human tissues’. Physiological Genomics 7:95–6.10.1152/physiolgenomics.2001.7.2.9511773595 Search in Google Scholar

Cha S. 2016. Is the biology of M. chitwoodi and M. hapla reflected in their genomes? North Carolina State University, Raleigh, NC. Search in Google Scholar

Czechowski T. 2005. Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant physiology. 139 (1):5–17. Search in Google Scholar

de Jesus Miranda V. , Coelho R. R. , Viana A. A. B. , de Oliveira Neto O. B. , Carneiro R. M. D. G. , Rocha T. L. , de Sa M. F. G. and Fragoso R. R. 2013. Validation of reference genes aiming accurate normalization of qPCR data in soybean upon nematode parasitism and insect attack. BMC Research Notes 6:196.10.1186/1756-0500-6-196366016623668315 Search in Google Scholar

Duarte A. , Maleita C. , Tiago I. , Curtis R. and Abrantes I. 2016. Molecular characterization of putative parasitism genes in the plant-parasitic nematode Meloidogyne hispanica . Journal of Helminthology 90:28–38.10.1017/S0022149X1400073X25319213 Search in Google Scholar

Exposito-Rodriguez M. , Borges A. A. , Borges-Perez A. and Perez J. A. 2008. Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biology 8 (1):131.10.1186/1471-2229-8-131262947419102748 Search in Google Scholar

Gal A. B. , Carnwath J. W. , Dinnyes A. , Herrmann D. , Niemann H. and Wrenzycki C. 2006. Comparison of real-time polymerase chain reaction and end-point polymerase chain reaction for the analysis of gene expression in preimplantation embryos. Reproduction Fertility and Development 18:365–71.10.1071/RD0501216554012 Search in Google Scholar

Gleason C. , Polzin F. , Habash S. S. , Zhang L. , Utermark J. , Grundler F. M. W. and Elashry A. 2017. Identification of two Meloidogyne hapla genes and an investigation of their roles in the plant–nematode interaction. Molecular Plant–Microbe Interactions 30:101–12.10.1094/MPMI-06-16-0107-R28301312 Search in Google Scholar

Hofmann J. and Grundler F. M. W. 2007. Identification of reference genes for qRT-PCR studies of gene expression in giant cells and syncytia induced in Arabidopsis thaliana by Meloidogyne incognita and Heterodera schachtii . Nematology 9:317–23.10.1163/156854107781352034 Search in Google Scholar

Howe K. L. , Bolt B. J. , Shafie M. , Kersey P. and Berriman M. 2017. WormBase ParaSite - a comprehensive resource for helminth genomics. Molecular and Biochemical Parasitology 215:2–10.10.1016/j.molbiopara.2016.11.005548635727899279 Search in Google Scholar

Huggett J. , Dheda K. , Bustin S. and Zumla A. 2005. Real-time RT-PCR normalisation; strategies and considerations. Genes and Immunity 6:279–84.10.1038/sj.gene.636419015815687 Search in Google Scholar

Jensen J. and Ørntoft T. 2004. Normalization of real-time quantitative RT-PCR data: a model based variance estimation approach to identify genes suited for normalization-applied to bladder-and colon-cancer data-sets. Cancer Research 64:5245–50.10.1158/0008-5472.CAN-04-049615289330 Search in Google Scholar

Jian B. , Liu B. , Bi Y. R. , Hou W. S. , Wu C. X. and Han T. F. 2008. Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Molecular Biology, 9. Search in Google Scholar

Jongsik C. . 2007 . EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. International journal of systematic and evolutionary microbiology 57 (10):2259–61.10.1099/ijs.0.64915-017911292 Search in Google Scholar

Kanehisa M. and Goto S. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28:27–30.10.1093/nar/28.1.2710240910592173 Search in Google Scholar

McCarthy D. J. , Chen Y. S. and Smyth G. K. 2012. Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Research 40:4288–97.10.1093/nar/gks042337888222287627 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. and Graham S. 2008. Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proceedings of the National Academy of Sciences 105:14802–7.10.1073/pnas.0805946105254741818809916 Search in Google Scholar

Petersen T. N. , Brunak S. , von Heijne G. and Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods 8:785–6. Search in Google Scholar

Sahu A. R. , Wani S. A. , Saxena S. , Rajak K. K. , Chaudhary D. , Sahoo A. P. , Khanduri A. , Pandey A. , Mondal P. , Malla W. A. , Khan R. I. N. , Tiwari A. K. , Mishra B. , Muthuchelvan D. , Mishra B. P. , Singh R. K. and Gandham R. K. 2018. Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection. Scientific reports 8.10.1038/s41598-018-34236-7620603230374051 Search in Google Scholar

Sasser J. and Freckman D. 1987. W 1987 A world perspective on nematology. The role of the society. Vistas on Nematology a Commemoration of the Twenty Fifth Anniversary M A Siddiqai and MM Alam. Search in Google Scholar

Team R. C . 2014. A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL: (https://www. R-project. org). Search in Google Scholar

Vandesompele J. , De Preter K. , Pattyn F. , Poppe B. , Van Roy N. , De Paepe A. and Speleman F. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biology 3 (7):research0034-1.10.1186/gb-2002-3-7-research003412623912184808 Search in Google Scholar