Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species

Kamrul Islam; Mohammad Jakir Hosen; Sourav Chakraborty; Auditi Purkaystha; Mahmudul Hasan; Bonhi Elora

doi:doi:10.11648/j.cbb.20200801.11

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Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species

Kamrul Islam, Mohammad Jakir Hosen, Sourav Chakraborty, Auditi Purkaystha, Mahmudul Hasan, Bonhi Elora

Published in Computational Biology and Bioinformatics (Volume 8, Issue 1)

Received: 17 September 2019 Accepted: 30 December 2019 Published: 3 February 2020

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Abstract

Among the root-knot nematodes three Meloidogyne species namely Meloidogyne incognita, M. javanica, and M. arenaria are emerging as an important pest of many cultivated plants, and recognized as the most economically destructive plant parasitic nematodes species of all over the world. Although other root-knot nematodes may virulent for plant but limited information is available. Thus, a comprehensive bioinformatics analysis including sequence acquisition, multiple sequence alignment and the phylogenetic tree construction for well-known Meloidogyne species was employed to predict the emerging virulent species. About eighty seven (87) 18S rRNA sequences of three damaging Meloidogyne species (M. javanica, M. arenaria and M. incognita) were retrieved from NCBI database, and allowed to construct phylogenetic trees using both NJ and ME methods of Molecular Evolution Genetic Analysis (MEGA) tools. Phylogeny analysis revealed that M. enterolobii_1, M. sp._Mi_c3a, M. sp_Mj_c1a and M._sp._Mj_c3a are genetically as well as evolutionally related to existing well recognized virulent nematodes. Moreover, evolutionally emerging strains of existing virulent species of M. javanica, M. arenaria and M. incognita along with the predicted virulence nematodes could become a great challenge to agriculture. The study could initiate the further analysis for novel insights in the pathogenesis of emerging virulence species of Meloidogyne that must be needed for future crop management strategies.

Published in	Computational Biology and Bioinformatics (Volume 8, Issue 1)
DOI	10.11648/j.cbb.20200801.11
Page(s)	1-8
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2020. Published by Science Publishing Group

Keywords

Meloidogyne, Virulence, Phylogenetic Analysis, Plant Parasite, 18S rRNA

References

[1]	C. Wang, S. Lower, V. P. Thomas and V. M. Williamson, “Root-knot nematodes exhibit strain-specific clumping behavior that is inherited as a simple genetic trait,” PloS One, vol. 5 (12), pp. e15148, December 2010.
[2]	Mantelin, S., Bellafiore, S. and Kyndt, T., “Meloidogyne graminicola: a major threat to rice agriculture,” Molecular plant pathology, 18 (1), p. 3, 2017.
[3]	Archidona-Yuste, A., Cantalapiedra-Navarrete, C., Liébanas, G., Rapoport, H. F., Castillo, P. and Palomares-Rius, J. E., “Diversity of root-knot nematodes of the genus Meloidogyne Göeldi, 1892 (Nematoda: Meloidogynidae) associated with olive plants and environmental cues regarding their distribution in southern Spain” PloS one, 13 (6), p. e0198236, 2018.
[4]	J. N. Sasser, “Economic importance of Meloidogyne in tropical countries,” Root-knot nematodes, pp. 359-374, 1979.
[5]	R. A. Sikora and E. Fernandez, “Nematode parasites of vegetables,” Plant Parasitic Nematodes in Subtropical and Tropical Agriculture, pp. 319, 2005.
[6]	W. M. Wesemael, N. Viaene and M. Moens, “Root-knot nematodes (Meloidogyne spp.) in Europe,” Nematology, vol. 13 (1), pp. 3-16, January 2011.
[7]	Janssen, T., Karssen, G., Topalović, O., Coyne, D. and Bert, W., “Integrative taxonomy of root-knot nematodes reveals multiple independent origins of mitotic parthenogenesis” PloS one, 12 (3), p. e0172190, 2017.
[8]	Janssen, T., Karssen, G., Verhaeven, M., Coyne, D. and Bert, W., “Mitochondrial coding genome analysis of tropical root-knot nematodes (Meloidogyne) supports haplotype based diagnostics and reveals evidence of recent reticulate evolution” Scientific Reports, 6, p. 22591, 2016.
[9]	Hamza, M. A., Ali, N., Tavoillot, J., Fossati-Gaschignard, O., Boubaker, H., El Mousadik, A. and Mateille, T., “Diversity of root-knot nematodes in Moroccan olive nurseries and orchards: does Meloidogyne javanica disperse according to invasion processes?” BMC ecology, 17 (1), p. 41, 2017.
[10]	M. Moens, R. N. Perry and J. L. Starr, “Meloidogyne species–a diverse group of novel and important plant parasites,” Root-knot nematodes, vol. 1, pp. 483, 2009.
[11]	A. C. Triantaphyllou, “Cytogenetics, cytotaxonomy and phylogeny of root-knot nematodes,” 1985.
[12]	Sun, L., Zhuo, K., Lin, B., Wang, H. and Liao, J., “The complete mitochondrial genome of Meloidogyne graminicola (Tylenchina): a unique gene arrangement and its phylogenetic implications” Plos one, 9 (6), p. e98558, 2014.
[13]	T. Powers, “Nematode molecular diagnostics: From bands to barcodes,” Annu. Rev. Phytopathol, vol. 42, pp. 367-383, September 2004.
[14]	I. T. De Ley, P. De Ley, A. Vierstraete, G. Karssen, M. Moens and J. Vanfleteren, “Phylogenetic analyses of Meloidogyne small subunit rDNA,” Journal of Nematology, vol. 34 (4), pp. 319, December 2002.
[15]	R. Nakacwa, A. Kiggundu, H. Talwana, J. Namaganda, C. Lilley, W. Tushemereirwe and H. Atkinson, “Nematode 18S rRNA gene is a reliable tool for environmental biosafety assessment of transgenic banana in confined field trials,” Transgenic research, vol. 22 (5), pp. 1003-1010, October 2013.
[16]	J. Brito, T. O. Powers, P. G. Mullin, R. N. Inserra, D. W. Dickson, “Morphological and molecular characterization of Meloidogyne mayaguensis isolates from Florida,” Journal of Nematology, vol. 36 (3), pp. 232, September 2004.
[17]	N. Vovlas, D. Mifsud, B. B. Landa and P. Castillo, “Pathogenicity of the root-knot nematode Meloidogyne javanica on potato,” Plant Pathology, vol. 54 (5), pp. 657-664, October 2005.
[18]	Ali, M. A., Azeem, F., Abbas, A., Joyia, F. A., Li, H. and Dababat, A. A., “Transgenic strategies for enhancement of nematode resistance in plants” Frontiers in plant science, 8, p. 750, 2017.
[19]	Sultana, T., Kim, J., Lee, S. H., Han, H., Kim, S., Min, G. S., Nadler, S. A. and Park, J. K., “Comparative analysis of complete mitochondrial genome sequences confirms independent origins of plant-parasitic nematodes” BMC evolutionary biology, 13 (1), p. 12, 2013.
[20]	E. K. Tomaszewski, M. A. M. Khalil, A. A. Er- Deeb, T. O. Powers, J. L. Starr, “Meloidogyne javanica parasitic on peanut,” Journal of Nematology, vol. 26 (4), pp. 436-441, December 1994.
[21]	F. Lamberti and R. C. Baines, “Pathogenicity of four species of Meloidogyne on three varieties of olive trees,” Journal of Nematology, vol. 1, pp. 111-115, April 1969.
[22]	N. Sasanelli, G. Fontanazza, F. D. Lamberti, T. D’ Addabbo, M. Patumi and G. Vergari, “Reaction of olive cultivars to Meloidogyne species,” Nematol. Mediterr., vol. 25, pp. 183-190, December 1997.
[23]	I. A. Udo, M. I. Uguru and R. O. Ogbuji, “Pathogenicity of Meloidogyne incognita race 1 on tomato as influenced by different arbuscular mycorrhizal fungi and bioformulated Paecilomyces lilacinus in dysteric cambisol soil,” Journal of Plant Protection Research, vol. 53 (1), pp. 71-78, January 2013.
[24]	C. M., Maleita, M. J. Simões, C. Egas, R. H. C. Curtis & I. M. De O. Abrantes. Biometrical, biochemical, and molecular diagnosis of Portuguese Meloidogyne hispanica isolates. Plant Disease, 96 (6): 865-874, 2012.
[25]	Y. F. Wang, S. Xiao, Y. K. Huang, X. Zhou, S. S. Zhang and G. K. Liu, "First Report of Meloidogyne enterolobii on carrot in China," APS journal, vol. 98 (7), pp. 1019, June 2014.
[26]	Hasan, M., Hakim, A., Iqbal, A., Bhuiyan, F. R., Begum, M. K., Sharmin, S. and Abir, R. A.,”Computational study and homology modeling of phenol hydroxylase: key enzyme for phenol degradation” Int J Comput Bioinfo In Silico Model. 2015b, 4 (4), pp. 691-698, 2015.
[27]	Hasan, M., Ghosh, P. P., Azim, K. F., Mukta, S., Abir, R. A., Nahar, J. and Khan, M. M. H., “Reverse vaccinology approach to design a novel multi-epitope subunit vaccine against avian influenza A (H7N9) virus. Microbial pathogenesis, 130, pp. 19-37, 2019.
[28]	Das, K., Chakraborty, S., Hasan, M. and Shovo, A. M., “In silico analysis to elect superior bacterial alkaline protease for detergent and leather industries” Journal of Advances In Biotechnology, 5 (3), pp. 685-698, 2016.
[29]	K. Tamura, G. Stecher, D. Peterson, A. Filipski and S. Kumar, “MEGA6: molecular evolutionary genetics analysis version 6. 0,” Molecular Biology and Evolution, vol. 30 (12), pp. 2725-2729, October 2013.
[30]	K. Tamura, M. Nei and S. Kumar, “Prospects for inferring very large phylogenies by using the neighbor-joining method,” Proceedings of the National Academy of Sciences (USA), vol. 101, pp. 11030-11035, July 2004.
[31]	J. N. Sasser, “Plant-parasitic nematodes: the farmer's hidden enemy. Plant-parasitic nematodes: the farmer's hidden enemy,” 1989.
[32]	Tian, B. Y., Cao, Y. and Zhang, K. Q., “Metagenomic insights into communities, functions of endophytes, and their associates with infection by root-knot nematode, Meloidogyne incognita, in tomato roots” Scientific reports, 5, p. 17087, 2015.
[33]	Warmerdam, S., Sterken, M. G., van Schaik, C., Oortwijn, M. E., Sukarta, O. C., Lozano‐Torres, J. L., Dicke, M., Helder, J., Kammenga, J. E., Goverse, A. and Bakker, J., “Genome‐wide association mapping of the architecture of susceptibility to the root‐knot nematode Meloidogyne incognita in Arabidopsis thaliana”. New Phytologist, 218 (2), pp. 724-737, 2018.
[34]	B. B. Landa, J. E. P. Rius, N. Vovlas, R. M. Carneiro, C. M. Maleita, I. M. de O. Abrantes and P. Castillo, “Molecular characterization of Meloidogyne hispanica (Nematoda, Meloidogynidae) by Phylogenetic Analysis of Genes Within the rDNA in Meloidogyne spp,” Plant Disease, vol. 92 (7), pp. 1104-1110, July 2008.
[35]	M. L. Blaxter, P. De Ley, J. R. Garey, L. X. Liu, P. Scheldeman, A. Vierstraete, J. R. Vanfleteren, L. Y. Mackey, M. Dorris, L. M. Frisse and J. T. Vida, “A molecular evolutionary framework for the phylum Nematoda,” Nature, vol. 392 (6671), pp. 71-75, March 1998.
[36]	M. L. Blaxter, “Nematoda: genes, genomes and the evolution of parasitism,” Advances in Parasitology, vol. 54, pp. 101-195, January 2003.
[37]	Teillet, A., Dybal, K., Kerry, B. R., Miller, A. J., Curtis, R. H. and Hedden, P., “Transcriptional changes of the root-knot nematode Meloidogyne incognita in response to Arabidopsis thaliana root signals”. PloS one, 8 (4), p. e61259, 2013.
[38]	Tao, Y., Xu, C., Yuan, C., Wang, H., Lin, B., Zhuo, K. and Liao, J., “Meloidogyne aberrans sp. nov. (Nematoda: Meloidogynidae), a new root-knot nematode parasitizing kiwifruit in China”. PloS one, 12 (8), p. e0182627, 2017.
[39]	K. Kiontke, N. P. Gavin, Y. Raynes, C. Roehrig, F. Piano and D. H. Fitch, “Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101 (24), pp. 9003-9008, June 2004.
[40]	M. Mitreva, G. Smant and J. Helder, “Role of horizontal gene transfer in the evolution of plant parasitism among nematodes,” Methods Mol. Biol, vol. 532, pp. 517-535, 2009.
[41]	E. H., Scholl, J. L., Thorne, J. P. McCarterand, D. M., Bird, (2003). Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol, 4 (6), p. R39.

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Kamrul Islam, Mohammad Jakir Hosen, Sourav Chakraborty, Auditi Purkaystha, Mahmudul Hasan, et al. (2020). Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Computational Biology and Bioinformatics, 8(1), 1-8. https://doi.org/10.11648/j.cbb.20200801.11

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ACS Style

Kamrul Islam; Mohammad Jakir Hosen; Sourav Chakraborty; Auditi Purkaystha; Mahmudul Hasan, et al. Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Comput. Biol. Bioinform. 2020, 8(1), 1-8. doi: 10.11648/j.cbb.20200801.11

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AMA Style

Kamrul Islam, Mohammad Jakir Hosen, Sourav Chakraborty, Auditi Purkaystha, Mahmudul Hasan, et al. Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Comput Biol Bioinform. 2020;8(1):1-8. doi: 10.11648/j.cbb.20200801.11

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@article{10.11648/j.cbb.20200801.11,
  author = {Kamrul Islam and Mohammad Jakir Hosen and Sourav Chakraborty and Auditi Purkaystha and Mahmudul Hasan and Bonhi Elora},
  title = {Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species},
  journal = {Computational Biology and Bioinformatics},
  volume = {8},
  number = {1},
  pages = {1-8},
  doi = {10.11648/j.cbb.20200801.11},
  url = {https://doi.org/10.11648/j.cbb.20200801.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20200801.11},
  abstract = {Among the root-knot nematodes three Meloidogyne species namely Meloidogyne incognita, M. javanica, and M. arenaria are emerging as an important pest of many cultivated plants, and recognized as the most economically destructive plant parasitic nematodes species of all over the world. Although other root-knot nematodes may virulent for plant but limited information is available. Thus, a comprehensive bioinformatics analysis including sequence acquisition, multiple sequence alignment and the phylogenetic tree construction for well-known Meloidogyne species was employed to predict the emerging virulent species. About eighty seven (87) 18S rRNA sequences of three damaging Meloidogyne species (M. javanica, M. arenaria and M. incognita) were retrieved from NCBI database, and allowed to construct phylogenetic trees using both NJ and ME methods of Molecular Evolution Genetic Analysis (MEGA) tools. Phylogeny analysis revealed that M. enterolobii_1, M. sp._Mi_c3a, M. sp_Mj_c1a and M._sp._Mj_c3a are genetically as well as evolutionally related to existing well recognized virulent nematodes. Moreover, evolutionally emerging strains of existing virulent species of M. javanica, M. arenaria and M. incognita along with the predicted virulence nematodes could become a great challenge to agriculture. The study could initiate the further analysis for novel insights in the pathogenesis of emerging virulence species of Meloidogyne that must be needed for future crop management strategies.},
 year = {2020}
}

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TY - JOUR
T1 - Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species
AU - Kamrul Islam
AU - Mohammad Jakir Hosen
AU - Sourav Chakraborty
AU - Auditi Purkaystha
AU - Mahmudul Hasan
AU - Bonhi Elora
Y1 - 2020/02/03
PY - 2020
N1 - https://doi.org/10.11648/j.cbb.20200801.11
DO - 10.11648/j.cbb.20200801.11
T2 - Computational Biology and Bioinformatics
JF - Computational Biology and Bioinformatics
JO - Computational Biology and Bioinformatics
SP - 1
EP - 8
PB - Science Publishing Group
SN - 2330-8281
UR - https://doi.org/10.11648/j.cbb.20200801.11
AB - Among the root-knot nematodes three Meloidogyne species namely Meloidogyne incognita, M. javanica, and M. arenaria are emerging as an important pest of many cultivated plants, and recognized as the most economically destructive plant parasitic nematodes species of all over the world. Although other root-knot nematodes may virulent for plant but limited information is available. Thus, a comprehensive bioinformatics analysis including sequence acquisition, multiple sequence alignment and the phylogenetic tree construction for well-known Meloidogyne species was employed to predict the emerging virulent species. About eighty seven (87) 18S rRNA sequences of three damaging Meloidogyne species (M. javanica, M. arenaria and M. incognita) were retrieved from NCBI database, and allowed to construct phylogenetic trees using both NJ and ME methods of Molecular Evolution Genetic Analysis (MEGA) tools. Phylogeny analysis revealed that M. enterolobii_1, M. sp._Mi_c3a, M. sp_Mj_c1a and M._sp._Mj_c3a are genetically as well as evolutionally related to existing well recognized virulent nematodes. Moreover, evolutionally emerging strains of existing virulent species of M. javanica, M. arenaria and M. incognita along with the predicted virulence nematodes could become a great challenge to agriculture. The study could initiate the further analysis for novel insights in the pathogenesis of emerging virulence species of Meloidogyne that must be needed for future crop management strategies.
VL - 8
IS - 1
ER -

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Author Information

Kamrul Islam

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
Mohammad Jakir Hosen

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
Sourav Chakraborty

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
Auditi Purkaystha

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
Mahmudul Hasan

Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
Bonhi Elora

Anandaniketan, Sylhet, Bangladesh

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Kamrul Islam, Mohammad Jakir Hosen, Sourav Chakraborty, Auditi Purkaystha, Mahmudul Hasan, et al. (2020). Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Computational Biology and Bioinformatics, 8(1), 1-8. https://doi.org/10.11648/j.cbb.20200801.11

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ACS Style

Kamrul Islam; Mohammad Jakir Hosen; Sourav Chakraborty; Auditi Purkaystha; Mahmudul Hasan, et al. Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Comput. Biol. Bioinform. 2020, 8(1), 1-8. doi: 10.11648/j.cbb.20200801.11

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AMA Style

Kamrul Islam, Mohammad Jakir Hosen, Sourav Chakraborty, Auditi Purkaystha, Mahmudul Hasan, et al. Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species. Comput Biol Bioinform. 2020;8(1):1-8. doi: 10.11648/j.cbb.20200801.11

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@article{10.11648/j.cbb.20200801.11,
  author = {Kamrul Islam and Mohammad Jakir Hosen and Sourav Chakraborty and Auditi Purkaystha and Mahmudul Hasan and Bonhi Elora},
  title = {Comprehensive Phylogenetic Analysis of Root-knot Nematodes Predicts Emerging Virulent Species},
  journal = {Computational Biology and Bioinformatics},
  volume = {8},
  number = {1},
  pages = {1-8},
  doi = {10.11648/j.cbb.20200801.11},
  url = {https://doi.org/10.11648/j.cbb.20200801.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20200801.11},
  abstract = {Among the root-knot nematodes three Meloidogyne species namely Meloidogyne incognita, M. javanica, and M. arenaria are emerging as an important pest of many cultivated plants, and recognized as the most economically destructive plant parasitic nematodes species of all over the world. Although other root-knot nematodes may virulent for plant but limited information is available. Thus, a comprehensive bioinformatics analysis including sequence acquisition, multiple sequence alignment and the phylogenetic tree construction for well-known Meloidogyne species was employed to predict the emerging virulent species. About eighty seven (87) 18S rRNA sequences of three damaging Meloidogyne species (M. javanica, M. arenaria and M. incognita) were retrieved from NCBI database, and allowed to construct phylogenetic trees using both NJ and ME methods of Molecular Evolution Genetic Analysis (MEGA) tools. Phylogeny analysis revealed that M. enterolobii_1, M. sp._Mi_c3a, M. sp_Mj_c1a and M._sp._Mj_c3a are genetically as well as evolutionally related to existing well recognized virulent nematodes. Moreover, evolutionally emerging strains of existing virulent species of M. javanica, M. arenaria and M. incognita along with the predicted virulence nematodes could become a great challenge to agriculture. The study could initiate the further analysis for novel insights in the pathogenesis of emerging virulence species of Meloidogyne that must be needed for future crop management strategies.},
 year = {2020}
}

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