The map-1 gene family in root-knot nematodes, Meloidogyne spp.: A set of taxonomically restricted genes specific to clonal species

PLoS ONE

Volumn 7, Issue 6, 2012, Pages

  Tomalova, Iva ^a,b,c,d   Iachia, Cathy ^a,b,c   Mulet, Karine ^a,b,c   Castagnone Sereno, Philippe ^a,b,c  

^a CEMAGREF   (France)

^b UNIVERSITÉ CÔTE D'AZUR   (France)

^c CNRS   (France)

^d MASARYK UNIVERSITY   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

MICROTUBULE ASSOCIATED PROTEIN 1; PATULIN;

ARTICLE; BIOINFORMATICS; CLONAL SPECIES; GENE; GENE DUPLICATION; GENE FUNCTION; GENE IDENTIFICATION; GENE LOSS; GENETIC SELECTION; GENETIC VARIABILITY; MAP 1 GENE; MEIOSIS; MELOIDOGYNE; MELOIDOGYNE FLORIDENSIS; MELOIDOGYNE INCOGNITA; MITOSIS; MOLECULAR BIOLOGY; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PARTHENOGENESIS; PHYLOGENY; SEQUENCE ANALYSIS; TAXONOMICALLY RESTRICTED GENE; TYLENCHOIDEA;

AMINO ACID SEQUENCE; ANIMALS; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; TYLENCHOIDEA;

EID: 84862496333     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0038656     Document Type: Article

References (55)

1. Blaxter ML, (2003) Nematoda: Genes, genomes and the evolution of parasitism. Adv Parasitol 54: 101-195.
2. Blok VC, Jones JT, Phillips MS, Trudgill DL, (2008) Parasitism genes and host range disparities in biotrophic nematodes: the conundrum of polyphagy versus specialisation. BioEssays 30: 249-259.
3. Abad P, Favery B, Rosso MN, Castagnone-Sereno P, (2003) Root-knot nematode parasitism and host response: molecular basis of a sophisticated interaction. Mol Plant Pathol 4: 217-224.
4. Triantaphyllou AC, (1985) Cytogenetics, cytotaxonomy and phylogeny of root-knot nematodes. In: Sasser JN, Carter CC, editors. Raleigh: North Carolina State University Graphics pp. 113-126 eds. An Advanced Treatise on Meloidogyne. Vol. 1.
5. Castagnone-Sereno P, (2006) Genetic variability and adaptive evolution in parthenogenetic root-knot nematodes. Heredity 96: 282-289.
6. Lunt DH, (2008) Genetic tests of ancient asexuality in root-knot nematodes reveal recent hybrid origins. BMC Evol Biol 8: 194.
7. Fargette M, Berthier K, Richaud M, Lollier V, Franck P, et al. (2010) Crosses prior to parthenogenesis explain the current genetic diversity of tropical plant-parasitic Meloidogyne species (Nematoda: Tylenchida). Infect Genet Evol 10: 807-814.
8. Semblat JP, Rosso MN, Hussey RS, Abad P, Castagnone-Sereno P, (2001) Molecular cloning of a cDNA encoding an amphid-secreted putative avirulence protein from the root-knot nematode Meloidogyne incognita. Mol Plant Microbe Interact 14: 72-79.
9. Danchin EGJ, Rosso MN, Vieira P, de Almeida-Engler J, Coutinho PM, et al. (2010) Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes. Proc Natl Acad Sci USA 107: 17651-17656.
10. Qin L, Kudla U, Roze EHA, Goverse A, Popeijus H, et al. (2004) A nematode expansin acting on plants. Nature 427: 30.
11. Rosso MN, Vieira P, de Almeida-Engler J, Castagnone-Sereno P, (2011) Proteins secreted by root-knot nematodes accumulate in the extracellular compartment during root infection. Plant Signal Behav 6: 1232-1234.
12. Vieira P, Danchin EGJ, Neveu C, Crozat C, Jaubert S, et al. (2011) The plant apoplasm is an important recipient compartment for nematode secreted proteins. J Exp Bot 62: 1241-1253.
13. Castagnone-Sereno P, Semblat JP, Castagnone C, (2009) Modular architecture and evolution of the map-1 gene family in the root-knot nematode Meloidogyne incognita. Mol Genet Genomics 282: 547-554.
14. Wilson GA, Bertrand N, Patel Y, Hughes JB, Feil EJ, et al. (2005) Orphans as taxonomically restricted and ecologically important genes. Microbiology 151: 2499-2501.
15. Khalturin K, Hemmrich G, Fraune S, Augustin R, Bosch TCG, (2009) More than just orphans: are taxonomically-restricted genes important in evolution? Trends Genet 25: 404-413.
16. Johnson BR, Tsutsui ND, (2011) Taxonomically restricted genes are associated with the evolution of sociality in the honey bee. BMC Genomics 12: 164.
17. Abad P, Gouzy J, Aury JM, Castagnone-Sereno P, Danchin EG, et al. (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol 26: 909-915.
18. Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, et al. (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci USA 105: 14802-14807.
19. Tigano M, Carneiro R, Jeyaprakash A, Dickson D, Adams B, (2005) Phylogeny of Meloidogyne spp. based on 18S rDNA and mitochondrial DNA partial sequences Nematology 7: 851-862.
20. Holterman M, Karssen G, van den Elsen S, van Megen H, Bakker J, et al. (2009) Small subunit rDNA-based phylogeny of the Tylenchida sheds light on relationships among some high-impact plant-parasitic nematodes and the evolution of plant feeding. Phytopathology 99: 227-235.
21. Van Megen H, van den Elsen S, Holterman M, Karssen G, Mooyman P, et al. (2009) A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences. Nematology 11: 927-950.
22. Adam MAM, Phillips MS, Tzortzakakis EA, Blok VC, (2009) Characterisation of mjap genes encoding novel secreted proteins from the root-knot nematode Meloidogyne javanica. Nematology 11: 253-265.
23. Domazet-Loso T, Josip Brajkovic J, Tautz D, (2007) A phylostratigraphy approach to uncover the genomic history of major adaptations in metazoan lineages. Trends Genet 23: 533-539.
24. Tautz D, Domazet-Loso T, (2011) The evolutionary origin of orphan genes. Nature Rev Genet 12: 692-702.
25. Haegeman A, Jones JT, Danchin EGJ, (2011) Horizontal gene transfer in nematodes: a catalyst for plant parasitism? Mol Plant Microbe Interact 24: 879-887.
26. Denver DR, Clark KA, Raboin MJ, (2011) Reproductive mode evolution in nematodes: Insights from molecular phylogenies and recently discovered species. Mol Phylogenet Evol 61: 584-592.
27. Hunt DJ, Handoo ZA, (2009) Taxonomy, identification and principal species. In: Perry RN, Moens M, Starr JL, editors. eds. Root-knot nematodes: CABI, Wallingford, UK. Pp 55-97.
28. Apic G, Huber W, Teichmann SA, (2003) Multi-domain protein families and domain pairs: comparison with known strutures and a random model of domain recombination. J Struct Funct Genomics 4: 67-78.
29. Garb JE, Hayashi CY, (2005) Modular evolution of egg case silk genes across orb-weaving spider superfamilies. Proc Natl Acad Sci USA 102: 11379-11384.
30. Rasteiro R, Pereira-Leal JB, (2007) Multiple domain insertions and losses in the evolution of the Rab prenylation complex. BMC Evol Biol 7: 140.
31. Wu YC, Rasmussen MD, Kellis M, (2012) Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny. Mol Biol Evol 29: 689-705.
32. Moore AD, Björklund AK, Ekman D, Bornberg-Bauer E, Elofsson A, (2008) Arrangements in the modular evolution of proteins. Trends Biochem Sci 33: 444-451.
33. Katju V, Lynch M, (2006) On the formation of novel genes by duplication in the Caenorhabditis elegans genome. Mol Biol Evol 23: 1056-1067.
34. Lipinski KJ, Farslow JC, Fitzpatrick KA, Lynch M, Katju V, et al. (2011) High spontaneous rate of gene duplication in Caenorhabditis elegans. Curr Biol 21: 306-310.
35. Casewell NR, Wagstaff SC, Harrison RA, Renjifo C, Wuester W, (2011) Domain loss facilitates accelerated evolution and neofunctionalization of duplicate snake venom metalloproteinase toxin genes. Mol Biol Evol 28: 2637-2649.
36. Tadepally HD, Burger G, Aubry M, (2008) Evolution of C2H2-zinc finger genes and subfamilies in mammals: Species-specific duplication and loss of clusters, genes and effector domains. BMC Evol Biol 8: 176.
37. Podlaha O, Webb DM, Zhang J, (2006) Accelerated evolution and loss of a domain of the sperm-egg-binding protein SED1 in ancestral primates. Mol Biol Evol 23: 1828-1831.
38. Trudgill DL, Blok VC, (2001) Apomictic, polyphagous root-knot nematodes: exceptionally successful and damaging biotrophic root pathogens. Annu Rev Phytopathol 39: 53-77.
39. Moens M, Perry RN, Starr JL, (2009) Meloidogyne species - a diverse group of novel and important plant parasites. In: Perry RN, Moens M, Starr JL, editors. eds. Root-knot nematodes: CABI, Wallingford, UK. Pp 1-17.
40. Sambrook J, Fritsch E F, Maniatis T, (1989) Molecular cloning: a laboratory manual (2nd ed). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
41. Tigano M, de Siqueira K, Castagnone-Sereno P, Mulet K, Queiroz P, et al. (2010) Genetic diversity of the root-knot nematode Meloidogyne enterolobii and development of a SCAR marker for this guava-damaging species. Plant Pathol 59: 1054-1061.
42. Holterman M, Van der Wurff A, Van den Elsen S, Van Megen H, Bongers T, et al. (2006) Phylum-wide analysis of SSU rDNA reveals deep phylogenetic relationships among nematodes and accelerated evolution toward crown clades. Mol Biol Evol 23: 1792-1800.
43. Carneiro RMDG, Almeida MRA, Quénéhervé P, (2000) Enzyme phenotype of Meloidogyne spp. populations. Nematology 2: 645-654.
44. Randig O, Bongiovanni M, Carneiro MDG, Castagnone-Sereno P, (2002) Genetic diversity of root-knot nematodes from Brasil and development of SCAR markers specific for the coffee-damaging species. Genome 45: 862-870.
45. Zijlstra C, (2000) Identification of Meloidogyne chitwoodi, M. fallax and M. hapla based on SCAR-PCR: a powerful way of enabling reliable identification of populations or individuals that share common traits. Eur J Plant Pathol 106: 283-290.
46. Zijlstra C, Donkers-Venne DTHM, Fargette M, (2000) Identification of Meloidogyne incognita, M. javanica and M. arenaria using sequence characterised amplified regions (SCAR) based PCR assays. Nematology 2: 847-853.
47. Zhang Z, Schwartz S, Wagner L, Miller W, (2000) A greedy algorithm for aligning DNA sequences. J Comput Biol 7: 203-14.
48. Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, et al. (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res 37: D571-D578.
49. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, et al. (2005) Protein identification and analysis tools on the ExPASy server. In: Walker JM, editors. pp. 571-607 ed. The Proteomics Protocols Handbook: Humana Press.
50. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32: 1792-1797.
51. Swofford DL, (1998) PAUP*: (Phylogenetic Analysis Using Parsimony *) and other methods Version 4 Sinauer Associates, Sunderland Mass.
52. Felsenstein J, (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791.
53. Siddiqi MR, (2000) Tylenchida: Parasites of plants and insects. Second edition. Wallingford, UK: CAB International Publishing. 833 p.
54. De Ley P, Blaxter ML, (2004) A new system for Nematoda: combining morphological characters with molecular trees, and translating clades into ranks and taxa. In: Cook R, Hunt DJ, editors. 2: 633-653 editors. Nematology Monographs and Perspectives, vol.
55. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, et al. (1998) A molecular evolutionary framework for the phylum Nematoda. Nature 392: 71-75.