Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S Rdna
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University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications from the Harold W. Manter Laboratory of Parasitology Parasitology, Harold W. Manter Laboratory of February 1997 Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA Luma Al-Banna University of Jordan, [email protected] Valerie M. Williamson University of California, Davis, [email protected] Scott Lyell Gardner University of Nebraska - Lincoln, [email protected] Follow this and additional works at: https://digitalcommons.unl.edu/parasitologyfacpubs Part of the Parasitology Commons Al-Banna, Luma; Williamson, Valerie M.; and Gardner, Scott Lyell, "Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA" (1997). Faculty Publications from the Harold W. Manter Laboratory of Parasitology. 52. https://digitalcommons.unl.edu/parasitologyfacpubs/52 This Article is brought to you for free and open access by the Parasitology, Harold W. Manter Laboratory of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications from the Harold W. Manter Laboratory of Parasitology by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Published in Molecular Phylogenetics and Evolution (ISSN: 1055-7903), vol. 7, no. 1 (February 1997): 94-102. Article no. FY960381. Copyright 1997, Academic Press. Used by permission. Phylogenetic Analysis of Nematodes of the Genus Pratylenchus Using Nuclear 26S rDNA Luma Al-Banna*, Valerie Williamson*, and Scott Lyell Gardner1 *Department of Nematology, University of California at Davis, Davis, California 95676-8668 1H. W. Manter Laboratory, Division of Parasitology, University of Nebraska State Museum, W-529 Nebraska Hall, University of Nebraska-Lincoln, Lincoln, NE 68588-0514; [email protected] Fax: (402) 472-8949. (Author to whom correspondence should be directed.) Submitted March 18, 1996; revised August 23, 1996. Abstract (1991) recognized only forty-six. These nematodes typi- cally have wide host ranges and are highly variable in We used nucleotide sequences of the large subunit ribo- their pathogenicity (Pinochet et al., 1993; Wheeler and somal genes (26S rDNA) to examine evolutionary rela- Riedel, 1994). tionships among species of the genus Pratylenchus (Or- Species in this genus are typically distinguished from der: Tylenchida, Family: Pratylenchidae), commonly each other by several characters such as number of an- known as root-lesion nematodes. Ten species of Praty- nuli in the lip region, presence or absence of a spermath- lenchus were studied including, P. penetrans, P. crena- eca in the female, presence or absence of males, num- tus, P. minyus, P. vulnus, P. thornei, P. musicale, P. coffeae, ber of lines in the lateral field, and the shape of the tail P. bexincisus, P. scribneri, and P. brachyurus. The species (Handoo and Golden, 1989; Loof, 1991). Hirschmanniella belli, Meloidogyne javanica, Heterorhab- Morphologically, Pratylenchus species are differen- ditis bacteriophora, Nacobbus eberruns, Radopholus similis, tiated from the other 8 genera in the family Pratylenchi- and Xiphinema index were used as outgroups. Based on dae by the number of female gonads (one vs. two), parsimony analyses of approximately 307 aligned nucle- whether or not the caudal alae reach to the tip of the otides of the D3 expansion region of the 26S rDNA, it is tail, sexual dimorphism, presence or absence of deirids, clear that species of Pratylenchus are a paraphyletic as- and by the direction of overlap of the esophageal glands semblage. The outgroup taxon H. belli shares a common over the intestine (Luc, 1987). These diagnostic features ancestor with the clade that includes P. vulnus and P. applicable at the species or genus level are not based on crenatus while N. aberrans and R. similis share a common presence of synapomorphies, as determined by careful ancestor with 5 other species included in this study. studies of ancestor-descendant relationships (i.e., stud- ies of phylogeny), but on phenetic or morphological Introduction similarities. In this group of nematodes, multistate char- acters commonly have been used to classify nematodes Nematodes of the genus Pratylenchus Filipjev, 1936 are to one genus or another. However, species in one ge- common endoparasites of plants world-wide. Second nus (as defined by past researchers) may actually have only to root-knot nematodes in causing economic losses all states present. For example, the direction of overlap in agricultural systems (Sasser and Freckman, 1987), of the esophageal gland over the intestine (dorsal, ven- these nematodes are migratory parasites that invade tral, or lateral) is used as a diagnostic character to de- the cortex of roots, tubers, and bulbs of plants, result- fine all genera in the family Pratylenchidae. However, ing in necrotic lesions. This causes reduction of yields several species, each with a different state of this char- (Lownsberry, 1956; McKenry, 1989) or lowering of the acter (esophageal gland overlap) have been included in market value of crops (Bernard and Laughlin, 1976), one genus (Pratylenchoides). Therefore, we decided to Filipjev (1936) first erected the genus Pratylenchus when perform a phylogenetic analysis on species of the ge- he recognized the group of nematodes possessing a ty- nus Pratylenchus based on ribosomal DNA (rDNA) se- lenchoid esophagus overlapping the anterior por-tion quences. Evolution of rDNA is relatively independent of the intestine and a uniovarial gonad in adult females. of changes in morphology, and analysis of these genetic Ninety species of Pratylenchus have been described data have been shown to provide good phylogenetic res- worldwide (Jatala and Bridge, 1990); however, Loof olution (Nadler, 1992; Heise et al., 1995). In fact, several 94 P HYLOGENETIC AN A LYSIS OF NEM A TODES OF THE GENUS P RATYLENCHUS 95 recent studies of eukaryotes used rDNA sequences in phylogenetic analyses to make strong inferences of an- TABLE 1 cestor descendant relationships when analyses of mor- phological data only resulted in more unanswered ques- Nematode Species Studied with Collection tions (Carmean et al., 1992; Sidow and Thomas, 1994). In Localities and Hosts addition, the analysis of rDNA nucleotide sequences has recently been used to assess phylogenetic relationships Nematode species Locality Host among taxa of both higher and lower organisms (Hillis Pratylenchus brachyurus FL, U.S.A. Aster sp. and Dixon, 1991; Sidow and Thomas, 1994; Halanych et (Godfrey, 1929) al., 1995). P. crenatus Loof, 1960 OR, U.S.A. Rubus ditifolius Choosing the appropriate segment of DNA within the genome of an organism is a critical step in any phyloge- P. coffeae (Zimmermann, Guatemala Coffeea arabica 1898) netic study (Hillis and Dixon, 1991; Derr et al., 1992). The P. hexincisus Taylor and MD, U.S.A. Zea mays region of choice should have enough variability among Jenkins, 1957 the taxa in question to allow an estimation of their his- P. minyus Sher and Allen, Monterey Co., Pyrethrum sp. torical relationships. This variation must not be too great 1953 CA, U.S.A. so as to obscure past ancestor-descendant relationships. P. minyus Sher and Allen, Siskiyou Co., Solanum tubersom One of the rRNA genes that has been used in mo-lec- 1953 CA, U.S.A. ular systematics is the large subunit rRNA gene (23S in P. musicola (Cobb, 1919) HI, U.S.A. Aglonema sp. prokaryotes and 26S or 28S in eukaryotes). This rRNA gene has been shown to be useful in estimating phylog- P. musicola (Cobb, 1919) FL, U.S.A. Citrus sp. eny because it contains regions that evolve slowly and P. penetrans (Cobb, 1917) MD, U.S.A. Medicago sativa other regions that evolve more quickly. Thus this gene P. penetrans (Cobb, 1917) Monroe Co., Prunus avium can be used to infer both paleozoic and mesozoic diver- NY, U.S.A. gences (Hillis and Dixon, 1991; Nadler, 1992). Nadler P. penetrans (Cobb, 1917) OR, U.S.A. Lilium eximium (1992) used rDNA to examine the evolutionary relation- P. penetrans (Cobb, 1917) OR, U.S.A. Menta sp. ships among animal parasitic nematodes of the families P. scribneri Steiner, 1943 Kern Co., CA, Vitis sp. Ascarididae and Anisakidae. U.S.A. In the present study, phylogenetic relationships of P. scribneri Steiner, 1943 Wayne Co., Solanum tubersome several species of the genus Pratylenchus were investi- NY, U.S.A. gated using nucleotide sequences of the D3 expansion P. thornei Sher and Allen, Yolo Co., CA, Vicia faba region of 26S rDNA corresponding to the positions 1953 U.S.A. 3304-3648 in Caenorhabditis elegans (Maupas, 1900) (see P. thornei Sher and Allen, Yolo Co., CA, Carthamus tinctorius Ellis et al., 1986). 1953 U.S.A. P. thornei Sher and Allen, Yolo Co., CA, Triticum aestivum Materials and Methods 1953 U.S.A. P. thornei Sher and Allen, San Joaquin Co., Lycopersicon Collection of Nematode Species. 1953 CA, U.S.A. esculentum Nineteen populations representing 10 species of the P. vulnus Allen and Jensen, Yolo Co., CA, Juglans hindsii genus Pratylenchus were obtained from various hosts 1951 U.S.A. and from different localities from North and Central Hirschmanniella belli Sher, Yolo Co., CA, Typha sp. America (Table 1). Six outgroup taxa were used, in- 1968 U.S.A. cluding Hirschmanniella belli Sher, 1968. Radopholus Nacobbus aberrans (Thorne, NE, U.S.A. Beta vulgaris 1935) similis (Cobb, 1893), Nacobbus aberrans (Thorne, 1935), Meloidogyne javanica (Treub, 1885), Heterorhabditis bac- Radopholus similis (Cobb, FL, U.S.A. Citrus sp. 1893) teriophora (Poinar, 1975), and Xiphinema index Thorne and Allen, 1950. Meloidogyne javanica Yolo Co., CA, Lycopersicon (Treub, 1885) U.S.A. esculentum Heterorhabditis bacteriophora UT, U.S.A. Phyllophaga sp. Extraction and Culture. Poinar, 1975 Establishment of nematodes. Plant parasitic nematodes Xiphinema index Thorne Napa Co., CA, Vitis sp. were extracted from their hosts or from soil using either and Allen, 1950 U.S.A. centrifugation (Niblack and Hussey, 1985) or Baermann funnel techniques (Christie and Perry, 1951). Nematodes Note: Two individuals from each species from each host or local- recovered from the extractions were either were killed ity sequenced.