Description of Xiphinema parachambersi sp. n. (Nematoda: Longidoridae) from Imported Ornamental Plants in Japan with a Key to Xiphinema Species in Group 1.
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ABSTRACT:
SUBMITTER: Maria M
PROVIDER: S-EPMC6909363 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Mixed populations of Xiphinema americanum-group species were detected from a root zone soil sample of Japanese holly, Ilex crenata, during a survey for plant-parasitic nematodes of commercial ornamental plant nurseries in Chiba Prefecture, Japan. From the result of the morphological study, the species were identified as Xiphinema brevicolle and Xiphinema sp. This is the first record of Xiphinema brevicolle in Japan. Morphometrics of Xiphinema brevicolle generally agree with those of the type specimens and the topotype specimens. Xiphinema sp. morphometrically resembles Xiphinema paramonovi except for tail length. The mitochondrial COI region, the nuclear 18S rDNA and the nuclear large subunit rDNA D2/D3 region of the species were sequenced and compared in the molecular study. For the COI region, PCR primers were newly designed to obtain longer sequences, ca. 900 bp, than previously used. Sequence identities of COI, 18S and D2/D3 regions between these two populations were 84.0-84.1%, 99.9% and 98.1-98.2%, respectively. Phylogenetic analyses of maximum likelihood trees were carried out to compare genetic relationships among the group and some suggestions were made on the Xiphinema brevicolle-subgroup.
| S-EPMC3260796 | biostudies-literature
Project description:In October 1985 during a survey of fauna of the Great Smoky Mountains National Park, Ernest Bernard recovered a limited number of specimens of a non-described species of Xiphinema (Nematoda: Longidoridae) and sent them to the senior author. The species is distinct from other species by its large size and having Z-organs in the genital tract. During July 2006, Dr. Bernard's survey crew took samples in the area where the species was first found and was successful in finding it again. Without Dr. Bernard's efforts, this species could not have been described and thus the new species is named X. bernardi n. sp. in his honor. Several female and juvenile specimens of the new species were recovered in a sample from a mixed forest of maple, hemlock, and silverbell. It is distinct from all others in Xiphinema group 4 species (with Z-organs) by having a longer total stylet length, 259.8 to 284.2 μm vs < 253 μm for all other species in this group. Xiphinema bernardi n. sp. is distinctive because of its long body length (4.45 to 6.00 mm), tail shape, and c' ratio. Of the group 4 species, it most closely resembles X. phoenicis. Second, third and fourth stage juvenile descriptions and morphometrics are included. The polytomous key code for X. bernardi n. sp. is A4-B1-C6-D56-E56-F(4)5-G4-H2-I34-J5-K?-L1. Molecular approaches using the internal transcribed spacer 1 sequences of nuclear ribosomal DNA suggested that X. bakeri and X. diversicaudatum are the most closely related species from the species examined.
| S-EPMC3365308 | biostudies-literature
Project description:Longidorus chenisp. n., an amphimictic species recovered from the rhizosphere of Larix principis-rupprechtii and Pyracantha fortuneana in Shanxi and Beijing, China, is described and illustrated. The taxonomic position of L. chenisp. n. among other species within the genus was elucidated using morphometric and molecular data, and phylogenetic relationships were inferred using D2-D3 expansion domains of 28S and 18S rRNA genes by Bayesian Inference (BI) method. The new species is characterised by females with a medium body size (L = 4.9-6.6 mm), a lip region slightly expanded, broadly rounded frontally and laterally, the amphidial fovea broad and symmetrically bilobed at base, odontostyle long and slender (143-168 μm), odonthophore slightly swollen at the base, tail short bluntly conoid to rounded. Guide ring located far posterior from the oral aperture (70-93 μm). Males with two ad-cloacal pairs of supplements preceded by a row of 10-14 ventromedian supplements, with robust spicules measuring 111-126 μm along the median line. Three juvenile stages were present, tail shape of J1 elongate conoid while in J2 and J3 the tail gradually becomes bluntly rounded. Codes for identifying the new species are: A6-B3-C5-D2-E2-F3-G1-H1-I2-J2-K2. Longidorus chenisp. n. belongs to a group of species with a guide ring at the mid-odontostyle position that have a predominantly Asiatic origin. It differs from all of them by a combination of morphological characters and unique sequences of partial 18S and D2-D3 region of 28S rRNA genes. The percentage dissimilarities in partial 18S and D2-D3 28S rRNA genes of L. cheni to the closest species (L. litchii, L. fangi, L. jonesi and L. juglans) were 1.5 %-1.8 % and 16.8-18.3 %, respectively.
| S-EPMC5904558 | biostudies-literature
Project description:Dagger nematodes of the genus Xiphinema include a remarkable group of invertebrates of the phylum Nematoda comprising ectoparasitic animals of many wild and cultivated plants. Damage is caused by direct feeding on root cells and by vectoring nepoviruses that cause diseases on several crops. Precise identification of Xiphinema species is critical for launching appropriate control measures. We deciphered the cryptic diversity of the Xiphinema hispanum-species complex applying integrative taxonomical approaches that allowed us to verify a paradigmatic example of the morphostatic speciation and the description of a new species, Xiphinema malaka sp. nov. Detailed morphological, morphometrical, multivariate and genetic studies were carried out, and mitochondrial and nuclear haploweb analyses were used for species delimitation of this group. The new species belongs to morphospecies Group 5 from the Xiphinema nonamericanum-group species. D2-D3, ITS1, partial 18S, and partial coxI regions were used for inferring the phylogenetic relationships of X. malaka sp. nov. with other species within the genus Xiphinema. Molecular analyses showed a clear species differentiation not paralleled in morphology and morphometry, reflecting a clear morphostatic speciation. These results support the hypothesis that the biodiversity of dagger nematodes in southern Europe is greater than previously assumed.
| S-EPMC7761271 | biostudies-literature
Project description:Xiphinema barooghii n. sp. collected from the rhizosphere of common wheat (Triticum aestivum L.) in Roodghat area, Sufiyan, East-Azarbaijan province, northwest of Iran, is described on the basis of the morphological, morphometric and molecular data. The new species belongs to morphospecies group 6 of the polytomous key prepared by Loof and Luc, 1990. Xiphinema barooghii n. sp. is characterized by having two almost equally developed female reproductive branches with spines in the tubular portion of the uterus, a body length of 3.67-4.25?mm, a flat lip region, rounded cephalic region, separated from body contour by a shallow depression, a spear 215-225 ?m long, mid-body diameter of 60-79 ?m, vulva (46-48%), a short tail (30-38 µm, c = 103-133, c' = 0.7-0.9), conoid, dorsally convex, ventrally directed with a small terminal peg and a distinct terminal blind canal, the presence of four juvenile stages and the absence of males. The polytomous identification codes of the new species are: A4, B3, C5a, D6, E5, F4, G3, H2, I3, J4, K2, L1. In addition to morphological and morphometric data, molecular analyses of the D2-D3 expansion regions of the 28S rDNA gene placed the new species as a sister species of X. herakliense (Group 5) with 65% Bayesian posterior probability and further separated this species from the other members in group 6. In this study, X. index, X. pachtaicum and X. vuittenezi were also collected and additional data for the species were provided.Xiphinema barooghii n. sp. collected from the rhizosphere of common wheat (Triticum aestivum L.) in Roodghat area, Sufiyan, East-Azarbaijan province, northwest of Iran, is described on the basis of the morphological, morphometric and molecular data. The new species belongs to morphospecies group 6 of the polytomous key prepared by Loof and Luc, 1990. Xiphinema barooghii n. sp. is characterized by having two almost equally developed female reproductive branches with spines in the tubular portion of the uterus, a body length of 3.67–4.25?mm, a flat lip region, rounded cephalic region, separated from body contour by a shallow depression, a spear 215–225 ?m long, mid-body diameter of 60–79 ?m, vulva (46–48%), a short tail (30–38 µm, c = 103–133, c? = 0.7–0.9), conoid, dorsally convex, ventrally directed with a small terminal peg and a distinct terminal blind canal, the presence of four juvenile stages and the absence of males. The polytomous identification codes of the new species are: A4, B3, C5a, D6, E5, F4, G3, H2, I3, J4, K2, L1. In addition to morphological and morphometric data, molecular analyses of the D2–D3 expansion regions of the 28S rDNA gene placed the new species as a sister species of X. herakliense (Group 5) with 65% Bayesian posterior probability and further separated this species from the other members in group 6. In this study, X. index, X. pachtaicum and X. vuittenezi were also collected and additional data for the species were provided.
| S-EPMC6929665 | biostudies-literature
Project description:An intracellular bacterium, strain IAST, was observed to infect several species of the plant-parasitic nematode genus Xiphinema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts Mycoavidus cysteinexigens B1-EBT (92.9 % sequence identity) and 'Candidatus Glomeribacter gigasporarum' BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations supported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium. Ultrastructural analysis of the bacterium showed cells that appear as mostly irregular, slightly curved rods with rounded ends, 0.8-1.2 µm wide and 2.5-6.0 µm long, possessing a typical Gram-negative cell wall. The peptidoglycan layer is, however, evident only occasionally and not detectable by TEM in most cells. Another irregularly occurring shell surrounding the endosymbiont cells or the cell clusters was also revealed, probably originating from the host cell membrane. Flagella or spore-like cells do not occur and the nucleoid is diffusely distributed throughout the cell. This endosymbiont is transmitted vertically through nematode generations. These results support the proposal of IAST as a new species, although its obligate intracellular and obligate endosymbiont nature prevented isolation of a definitive type strain. Strain IAST is therefore proposed as representing 'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov.
| S-EPMC8489844 | biostudies-literature
Project description:Using ribosomal (18S, ITS1, ITS2, D2-D3 expansion segments of 28S rDNA) and mitochondrial (partial cox1 and nad4) DNA markers in a study of several populations of Xiphinema americanum-group from Europe and Morocco, two cryptic species Xiphinema browni sp. n. (formerly reported as Xiphinema pachtaicum) and Xiphinema penevi sp. n. were revealed. The species are described, illustrated and their phylogenetic relationships discussed. The first species is most similar to Xiphinema parasimile and is a member of Xiphinema simile species complex. The phylogenetic reconstructions inferred from three molecular markers (18S, D2-D3 28S rDNA and cox1) showed that Xiphinema penevi sp. n. is part of Xiphinema pachtaicum-subgroup and is closely related to Xiphinema incertum, Xiphinema pachtaicum, Xiphinema parapachydermum, Xiphinema plesiopachtaicum, Xiphinema astaregiense and Xiphinema pachydermum. Also, a separate "Xiphinema simile-subgroup", outside the Xiphinema pachtaicum-subgroup and so far consisting only of the parthenogenetic species Xiphinema simile, Xiphinema parasimile, Xiphinema browni sp. n. and probably Xiphinema vallense was formed. New primers for amplification and sequencing of part of the nad4 mitochondrial gene were designed and used.
| S-EPMC4829900 | biostudies-literature
Project description:A new needle nematode, Longidorus carniolensissp. n., recovered from the soil around the roots of grapevine Vitis vinifera L. from Slovenia, is described and illustrated. Longidorus carniolensisis an amphimictic species, characterised by females with a moderately long (L=5.6-8.2 mm) and plump (a=51-72.4, ave. 66.3) body, assuming a spiral to C-shape when heat relaxed. Head region continuous, anteriorly almost flat, lip region 23-25 µm wide; guiding ring situated posteriorly (42-47 μm, 43-50 μm in males), odontostyle long (ave. 146.6 (136-157) μm); pharyngeal glands with normal location, their nuclei of approximately equal size; tail bluntly conoidal to almost hemispherical. Males abundant, spicules slender and long (122-145 μm), ventromedian supplements 13-17, irregularly spaced, preceded by an adanal pair. Four juvenile stages present, the first stage juvenile with bluntly conoidal tail. Codes for identifying the new species when using the key by Chen et al. (1997) are: A 56, B 4, C 4, D 1, E 4, F 35, G 1, H 1, I 2. The new species is morphologically the most similar to Longidorus poessneckensis Altherr, 1974, Longidorus macrosoma Hooper, 1961, Longidorus caespiticola Hooper, 1961, Longidorus helveticus Lamberti et al., 2001, Longidorus macroteromucronatus Altherr, 1974, Longidorus pius Barsi & Lamberti, 2001, Longidorus raskii Lamberti & Agostinelli, 1993, Longidorus kheirii Pedram et al. 2008, Longidorus silvae Roca, 1993, Longidorus iuglandis Roca et al., 1985, Longidorus vinearum Bravo & Roca, 1995 and Longidorus major Roca & d'Erico, 1987, but differs from these species either by the body and odontostyle length, position of guide ring, head region and tail shape or the shape of the first stage juvenile tail. Sequence data from the D2-D3 region of the 28S rDNA distinguishes this new species from other speciesof the genus Longidorus with known sequences. Relationships of Longidorus carniolensissp. n. with other Longidorus species based on analysis of this DNA fragment and morphology are discussed.
| S-EPMC3252759 | biostudies-literature
Project description:The most prevalent dagger nematode recovered from rhizospheric soil samples of forest trees in the Afrātakhteh region of Golestan province (Iran) was Xiphinema afratakhtehnsis sp. nov. and it is described and illustrated with integrative approaches using both morphological and molecular criteria. It belongs to the morphospecies group 6 of the intragenic historical grouping of Xiphinema non-americanum species. The new species is characterized by females with 3.3-4.9 mm sized body, lip region separated from the rest of body by a depression, anteriorly expanded, 16-18 μm wide, vulva located at 47.2-58.5%, odontostyle 155-173 μm and odontophore 89-107 μm long, female genital system composed of two equally developed branches, the tubular part of each having spines, short symmetrically rounded female tail to symmetrically rounded with a small mucro-like projection at the end in a few females, rare males (n = 1 out of 74 females) with 83 μm long dorylaimoid spicules and four juvenile developmental stages. The third-stage juveniles (J3) have a characteristic tail shape (short, symmetrically conical with a club-shaped long mucro) demarcating the species, and being typologically useful for its separation from closely similar species (except X. cohni, with currently no data on its juvenile stages) viz. X. adenohystherum, X. iranicum, X. mazandaranense, X. nuragicum, X. pyrenaicum, X. robbinsi, X. sphaerocephalum and X. zagrosense. Molecular phylogenetic studies using genomic (partial large subunit and internal transcribed spacer 1 ribosomal RNA genes: D2-D3 and ITS1 rDNA) and mitochondrial cytochrome c oxidase subunit I gene (COI mtDNA) revealed the new species forming a unique lineage in all reconstructed trees using Bayesian inference (BI) and maximum likelihood (ML) methods. The sequenced isolates of the new species formed a monophyletic group in the D2-D3 tree. The sequenced isolates of the new species for their COI mtDNA formed four subclades in COI mtDNA phylogeny, and four haplotypes in corresponding analysis.
| S-EPMC6493718 | biostudies-literature
Project description:Genetic analyses using DNA sequences of nuclear ribosomal DNA ITS1 were conducted to determine the extent of genetic variation within and among Longidorus and Xiphinema species. DNA sequences were obtained from samples collected from Arkansas, California and Australia as well as 4 Xiphinema DNA sequences from GenBank. The sequences of the ITS1 region including the 3' end of the 18S rDNA gene and the 5' end of the 5.8S rDNA gene ranged from 1020 bp to 1244 bp for the 9 Longidorus species, and from 870 bp to 1354 bp for the 7 Xiphinema species. Nucleotide frequencies were: A = 25.5%, C = 21.0%, G = 26.4%, and T = 27.1%. Genetic variation between the two genera had a maximum divergence of 38.6% between X. chambersi and L. crassus. Genetic variation among Xiphinema species ranged from 3.8% between X. diversicaudatum and X. bakeri to 29.9% between X. chambersi and X. italiae. Within Longidorus, genetic variation ranged from 8.9% between L. crassus and L. grandis to 32.4% between L. fragilis and L. diadecturus. Intraspecific genetic variation in X. americanum sensu lato ranged from 0.3% to 1.9%, while genetic variation in L. diadecturus had 0.8% and L. biformis ranged from 0.6% to 10.9%. Identical sequences were obtained between the two populations of L. grandis, and between the two populations of X. bakeri. Phylogenetic analyses based on the ITS1 DNA sequence data were conducted on each genus separately using both maximum parsimony and maximum likelihood analysis. Among the Longidorus taxa, 4 subgroups are supported: L. grandis, L. crassus, and L. elongatus are in one cluster; L. biformis and L. paralongicaudatus are in a second cluster; L. fragilis and L. breviannulatus are in a third cluster; and L. diadecturus is in a fourth cluster. Among the Xiphinema taxa, 3 subgroups are supported: X. americanum with X. chambersi, X. bakeri with X. diversicaudatum, and X. italiae and X. vuittenezi forming a sister group with X. index. The relationships observed in this study correspond to previous genera and species defined by morphology.
| S-EPMC2620731 | biostudies-other