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Made available in DSpace on 2020-12-12T01:19:18Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-01 Crop losses due to viral diseases and pests are major constraints on food security and income for millions of households in sub-Saharan Africa (SSA). Such losses can be reduced if plant diseases and pests are correctly diagnosed and identified early. Currently, accurate diagnosis for definitive identification of plant viruses and their vectors in SSA mostly relies on standard PCR and next generation sequencing technologies (NGS). However, it can take up to 6 months before results generated using these approaches are available. The long time taken to detect or identify viruses impedes quick, within-season decision-making necessary for early action, crop protection advice and disease control measures by farmers. This ultimately compounds the magnitude of crop losses and food shortages suffered by farmers. The MinION portable pocket DNA sequencer was used, to our knowledge globally for the first time, to sequence whole plant virus genomes. We used this technology to identify the begomoviruses causing the devastating cassava mosaic virus, which is ravaging smallholder farmers’ crops in sub-Saharan Africa. School of Molecular Sciences The University of Western Australia School of Agriculture Dept. of Plant Protection São Paulo State University (UNESP) Crop Protection Branch Department of Agriculture and Food Western Australia Mikocheni Agricultural Research Institute (MARI) National Crops Resources Research Institute (NaCRRI) Jomo Kenyatta University of Agriculture and Technology (JKUAT) School of Agriculture Dept. of Plant Protection São Paulo State University (UNESP)

Hodda, Mike, Collins, Sarah J., Vanstone, Vivien A., Hartley, Diana, Wanjura, Wolfgang, Kehoe, Monica (2014): Pratylenchus quasitereoides n. sp. from cereals in Western Australia. Zootaxa 3866 (2): 277-288, DOI: http://dx.doi.org/10.11646/zootaxa.3866.2.6

Pratylenchus quasitereoides n. sp. (Table 1, Fig. 1) Measurements and morphometrics of the holotype female and paratypes are presented in Table 1. Adult female: Body vermiform, tapering to anterior and posterior ends, maximum diameter at about oesophago-intestinal junction, with slight reduction in diameter near vulva. Cuticle thin (about 0.5 ���1.0 ��m), with external transverse striae spaced about 1 ��m apart, lacking internal transverse striae, radial striation, punctation and longitudinal markings. Lateral field conspicuous, with three incisures from posterior end of stylet to about level of median oesophageal bulb, four incisures over most of body then two incisures at the phasmids; outer incisures straight, inner incisures straight and continuous; inner field without markings; outer fields of equal width to inner. Cuticular pores absent. Anterior cephalid just anterior to junction of conus and shaft, posterior cephalid just anterior to posterior end of shaft. Excretory pore just anterior to nerve ring, duct prominent, sclerotized. Hemizonid visible anterior to excretory pore, in similar longitudinal position to oesophago-intestinal junction. Hemizonion just posterior to excretory pore. Head 8 ��m long (0.28 times head diameter), tapering little anteriorly, flat, angular, not dorsoventrally flattened, lacking longitudinal division, consisting of three annules of which the middle is widest. A shallow, rounded constriction about 0.5 ��m deep located behind head, 2���2.5 ��m from anterior extremity. Cephalic framework thick, sclerotized, extending anteriorly to anterior-most annule. Stoma very thin walled, with stylet. Stylet 18���19 ��m long, straight. Conus and shaft lengths equal. Knobs at posterior of shaft large, rounded, with anterior face at slightly obtuse angle to shaft (105���115 ��), posterior face at slightly greater angle to shaft (120���130 ��), creating indentation at posterior end of stylet. Dorsal oesophageal gland orifice 3���4 ��m from posterior end of stylet. Median expansion of oesophagus spindle-shaped, diameter 11 ��m (50���60 % of body diameter), with sclerotized hemispheroid valves of diameter about 3 ��m (20���30 % of the oesophagus diameter), located 55���61 ��m from anterior of body (65���85 % of the distance to the oesophago-intestinal junction). Oesophageal glands large, free in body cavity, offset to ventral side, with three nuclei, dorsal cell and nucleus larger than subventrals. Circumoesophageal nerve ring located 15���20 ��m behind valves (80���90 % of distance between anterior of body and oesophago-intestinal junction). Intestinal fasciculi absent. Anus clearly visible. Post-anal sac absent. Anterior genital branch outstretched, located ventrally to the intestine, spermatheca not strongly differentiated, round, without constrictions, without sperm. Posterior genital branch short, 0.5���1.8 body diameters long, consisting of uterine sac and a small amount of incomplete or non-functional ovarial tissue. Vulva without cuticular thickening, indented from a small protuberance on the ventral body surface. Vaginal cuticle thickened, sclerotized over most of length, smooth, directed radially, lumen narrow over entire length. Tail cylindroid-ellipsoid, tapering very little in anterior half, more rapidly in posterior half, slightly concave ventrally, with slightly thickened cuticle on posterior surface only, with 20 to 28 external transverse striae extending around the rounded terminus. Phasmids pore-like, located nearly opposite each other, posterior to anus, in middle of lateral field. Adult male: Not found. Juvenile: Similar to adult female but lacking reproductive structures. Type locality and host. Katanning, Western Australia (33 �� 17 ���S 117 �� 35 ���E), cultivated wheat (Triticum aestivum L.). Collectors: I Riley & S Kelly. Collected on 0 1 October 1998. Type designations. Holotype adult female: specimen no 89, Australian National Insect Collection Nematode Collection, Canberra, Australia. Paratypes: 16 adult females: specimen nos 90-105, ANIC Nematode Collection, Canberra, Australia. a���in ��m. b���abbreviations follow Hooper (1986 b). c���diam at 50 % tail length / diam at anus. d���diam at 75 % tail length / diam at anus. TABLE 2. Tabular compendium of diagnostic features of P. quasitereoides n. sp. differing from other species or species populations from the genus Pratylenchus. Only species differing from P. quasitereoides in less than 4 primary characters are listed a. species or population head incisures Stylet length b lateral incisures V PUS length b Tail terminus Other differences c. quasitereoides 3 17���19 4 75���82 0.5���1.8 annulated . teres sensu Loof (1992) 3 16���18 6 69���78 1 annulated. teres Amritsar pop (Khan and 3 16���18 6 69���78 1.1���1.4 d annulated Singh, 1974) . flakkensis 2 17 4 73���77 1.3���1.6 annulated SF,OG. alleni 2 13���15 77 ��� 84 1���3 smooth ���annulated SF. loosi 2 14���18 79 ���85 0.8���1.3 smooth SF. wescolagricus 4 17���20 78 ���82 1 smooth ��� ���continued on the next page shaded cells represent differences from P. quasitereoides n. sp.; b in ��m; c SF=spermatheca full (of sperm), males common; OG=length of oesophageal gland overlap of intestine; SL=spermatheca length relative to diameter; TA=number of tail annules; LLC=lateral lines crenate; d calculated from diagram in original description; e Diagnosis. Pratylenchus quasitereoides n. sp. is characterized by having three annules (two external incisures) in the head cuticle, four lateral incisures at mid body, stylet 17���19 ��m long, morphometric index V greater than 75 %, PUS less than 2 body diameters long and tail terminus crenate. Morphological relationships. P. quasitereoides n. sp. differs from all other species in the genus by at least two morphological characters, except for the Amritsar population of P. t ere s (as documented by Khan and Singh 1974) and Loof���s (1992) concept of P. t e re s (Table 2). The main difference between P. quasitereoides n. sp. and these taxa is that P. quasitereoides n. sp. has 4 rather than 6 lateral lines. P. quasitereoides n. sp. differs from the Amritsar population of P. teres in the following characteristics additional to those presented in Table 2: ��� mean position of vulva relative to total body length (morphometric index V = 78 for P. quasitereoides n. sp. vs V = 70 for the Amritsar population of P. teres); and ��� mean body length (L = 656 ��m for P. quasitereoides n. sp. vs L = 550 ��m for the Amritsar population of P. teres). There is some small overlap in the ranges of the two characters, but the differences are based on 16 and 17 adult female specimens of the two species, so there is a high probability that the differences are real, particularly in the case of the morphometric index V (Geraert 1968). The species concept of P. t e re s implicit in the key of Loof (1992) encompasses a very broad range of characteristics. Not all characters were used in the key, so additional differences between the species concepts may exist, most notably in the mean position of the vulva and body size. The species concept of P. t eres was further expanded by Carta et al. (2002). The biological basis for such gradual expansion of species definitions and its implications for the taxonomy of the genus Pratylenchus will be discussed at length in a forthcoming publication. More general considerations of the relationships between morphological, biological, genetic and ecological species concepts in nematodes will also be discussed elsewhere. For identification at low magnifications, two species may be confused with P. quasitereoides n. sp.: P. thornei has the ventral side of the body indented between the vulva and anus, a longer PUS and a wider tail than P. quasitereoides n. sp.; P. crenatus is generally smaller (although there is some overlap), has a shorter oesophageal gland lobe, and a longer PUS. Pratylenchus quasitereoides n. sp. shares a very prominent excretory pore with P. crenatus (Karssen & Bolk 2000). Molecular relationships. Cladistic analyses of the sequences for P. quasitereoides n. sp. and 29 sequences from nine other species in the genus for which the same section of the genome was available used 180 positions in the final data set. All species were in separate, well-supported clades (Fig. 2). Identical consensus tree topologies were obtained from all methods, with support levels for the species clades only differing slightly (86���100 % for NJ- ND, 80���100 % for NJ - CML, 75���99 % for ML, and 86���100 % for ME). To put the genetic differences in context, P. quasitereoides n.sp. differed by 0���10 bp among 4 populations, which was similar to the differences among 8 populations of P. thornei and slightly less than the differences among 5 populations of P. penetrans (0���12 bp). Similar variation in this gene region has been observed in other species of Pratylenchus (Hodda pers. comm.). Ecological relationships. P. quasitereoides n. sp. has been found in Western Australia from Carnamah (29 �� 41 'S 115 �� 53 'E) to Tambellup (34 ��02'S 117 �� 38 'E) (Collins et al. 2013, Riley & Kelly 2002, Riley & Wouts 2001, Vanstone 2007), as well as in South Australia (J. Nobbs, SARDI, personal communication). All populations recorded previously as P. t ere s in Western Australia seem to be the new species P. quasitereoides. No known specimens from Western Australia or anywhere else in Australia should be called ��� P. t ere s ��� now that P. quasitereoides n. sp. has been described. P. t e re s has been found in widely separated locations elsewhere in the world (Carta et al. 2002, Khan & Singh 1974; van den Berg & Queneherve, 2000). No endemic species in the genus Pratylenchus are known in Australia other than P. quasitereoides n.sp (Hodda & Nobbs 2008). The genus Pratylenchus contains a few apparently widespread species and many species with geographic distributions apparently restricted to various small regions of the world (Ryss 2002, Siddiqi 2000). The restricted distribution is not unusual. P. quasitereoides n. sp. has been found on wheat (Triticum aestivum L.), oat (Avena sativa L.), barley (Hordeum vulgare L.), chickpea (Cicer arietinum L.), lupin (Lupinus angustifolius L.) and canola (Brassica napus L.) (Collins et al. 2013, Riley & Kelly 2002, Riley & Wouts 2001, Vanstone 2007). By contrast, P. teres has never been found on these hosts (Table 3). The sympatric congeners P. neglectus, P. thornei and P. penetrans have many of the same plant species as hosts as P. quasitereoides n.sp, but all have been found on additional hosts (Table 3). Multiplication factors for P. neglectus and P. t h or n e i on lupin and oats are generally less than 1, but generally greater than 1 for P. quasitereoides n. sp. (Vanstone et al. 2005). On the same varieties of lupin and oats, reproduction rates of P. quasitereoides n. sp. (1.6 and 8.1, respectively) were much greater than those of P. neglectus (1.0 and 1.6, repectively). However, different varieties have different host status to P. quasitereoides n.sp. as well as for P. n e gl e ct us and P. t h or n e i (Collins et al. 2013, Vanstone 2007, Vanstone et al. 2005). Etymology. The name indicates the similarity of the new species with P. t e re s from the suffix ���oides���, and that the species has been known as P. t e re s ���quasi���. The species epithet is mostly Latin neuter, but the suffix is Greek (as with the generic name), and chosen for euphony above the Latin ���similis���. Braun, A.L. & Loof, P.A.A. (1966) Pratylenchoides laticuada n. sp., a new endoparasitic phytonematode. Netherlands Journal of Plant Pathology, 72, 241 ��� 245. http://dx.doi.org/ 10.1007 /BF02650210 Cadet, P., van den Berg, E., Delatte, A. & Fiard, J.-P. 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Proceedings of the National Academy of Sciences (USA), 1, Published as part of Hodda, Mike, Collins, Sarah J., Vanstone, Vivien A., Hartley, Diana, Wanjura, Wolfgang & Kehoe, Monica, 2014, Pratylenchus quasitereoides n. sp. from cereals in Western Australia, pp. 277-288 in Zootaxa 3866 (2) on pages 279-288, DOI: 10.11646/zootaxa.3866.2.6, http://zenodo.org/record/230849, {"references":["Hooper, D. J. (1986 b) Drawing and measuring nematodes. In: Southey, J. F. (Ed.), Laboratory methods for work with plant and soil nematodes. 6 th ed. Her Majesty's Stationery Office, London, pp. 87 - 94.","Loof, P. A. A. (1992) The family Pratylenchidae Thorne, 1949. In: Nickle, W. R. (Ed.), Manual of Agricultural Nematology. Marcel Dekker, New York, pp 363 - 421.","Khan, E. & Singh, D. B. (1974) Five new species of Pratylenchus (Nematoda: Pratylenchidae) from India. Indian Journal of Nematology, 4, 199 - 211.","Ryss, A. Y. (1982) [New phyto nematode species of the genus Pratylenchus in the Estonian SSR, USSR.] Eesti NSV Teaduste Akadeemia Toimetised Bioloogia, 31, 22 - 29.","Ryss, A. Y. (2002) Genus Pratylenchus Filipjev: multientry and monoentry keys and diagnostic relationships (Nematoda: Tylenchida: Pratylenchidae). Zoosystematica Rossica, 10, 241 - 255.","Geraert, E. (1968) Morphometric relations in nematodes. Nematologica, 14, 171 - 182. http: // dx. doi. org / 10.1163 / 187529268 X 00390","Carta, L. K., Handoo, Z. A., Skantar, A. M., van Biljon, J. & Botha, M. (2002) Redescription of Pratylenchus teres Khan & Singh, 1974 (Nemata: Pratylenchidae), with the description of a new subspecies from South Africa, and a phylogenetic analysis of related species. African Plant Protection, 8, 13 - 24.","Karssen, G. & Bolk, R. J. (2000) An additional character useful for the identification of Pratylenchus crenatus Loof 1960 (Nematoda: Pratylenchidae). Nematology, 2, 695 - 697. http: // dx. doi. org / 10.1163 / 156854100509556","Collins, S. J., Kelly, S., Hunter, H., MacLeod, B., Debrincat, L., Teasdale, J., Versteeg, C. & Zhang, Z. (2013) P. teres - WA's home grown Root Lesion Nematode (RLN) and its unique impacts on broadacre crops. 2013 WA Crop Updates, GRDC & DAFWA, Perth., 4 pp.","Riley, I. T. & Kelly, S. J. (2002) Endoparasitic nematodes in cropping soils of Western Australia. Australian Journal of Experimental Agriculture, 42, 49 - 56. http: // dx. doi. org / 10.1071 / EA 01054","Riley, I. T. & Wouts, W. M. (2001) Pratylenchus and Radopholus species in agricultural soils and native vegetation in Southern Australia. Transactions of the Royal Society of South Australia, 125, 147 - 153.","Vanstone, V. A. (2007) Root Lesion and Burrowing Nematodes in Western Australian cropping systems. DAFWA Bulletin, 4698, 1 - 19.","van den Berg, E. & Queneherve, P. (2000) Hirschmanniella caribbeana sp. n. and new records of Pratylenchus spp. (Pratylenchidae: Nematoda) from Guadeloupe, French West Indies. Nematology, 2, 179 - 190. http: // dx. doi. org / 10.1163 / 156854100509079","Hodda, M. & Nobbs, J. M. (2008) A review of current knowledge on particular taxonomic features of the Australasian nematode fauna, with special emphasis on plant feeders. Australasian Plant Pathology, 37, 308 - 317. http: // dx. doi. org / 10.1071 / AP 08024","Siddiqi, M. R. (2000) Tylenchida: Parasites of plants and insects. CABI, New York, 833 pp.","Vanstone, V. A., Kelly, S. J., Hunter, H. F. & Gilchrist, M. C. (2005) Rotations for nematode management. 2005 WA Crop Updates, GRDC & DAFWA, Perth, 7 pp."]}