scholarly journals Phenotypic and genetic characterization of date palm cultivars resistant to bayoud disease

2021 ◽  
Vol 8 (4) ◽  
Author(s):  
Said Boudeffeur ◽  
Abdelkhader Ameur Ameur ◽  
M M Aci ◽  
Hafida Khelafi ◽  
Abdelkader Laaboudi ◽  
...  
Keyword(s):  
Date Palm ◽  
Phylogenetic Analyses ◽  
Principal Component ◽  
Natural Resistance ◽  
Sequence Comparisons ◽  
Bayoud Disease ◽  
Phenotypic And Genetic Characterization ◽  
Simple Sequence ◽  
Morphological And Molecular Characterization

Taqerbucht cultivars of date palm are well known by their natural resistance against devastating fungus Bayoud disease. In order to know, if these accessions have the same genetic and morphological profile or each of them constitutes a separate cultivar, we carried out a morphological and molecular characterization and we compared four Taqerbucht (Tq.) date palm cultivars from the southwestern region of Algeria: Tq.hamra cultivar (red fruits), Tq. safra cultivar (yellow fruits), Tq.beïda (white fruits) and Tq.kahla cultivar (black fruits). Seventy one phenotypic characteristics, including 33 quantitative and 38 qualitative traits, have been selected for comparison. Principal component analysis (PCA) and multi-component clustering were used to analyze and compare the data. The results suggest that the four cultivars can be classified into distinct groups. One group contains one cultivar, the Tq.kahla and another group contains the three other cultivars (Tq.safra, Tq.beïda and Tq. hamra). Based on phylogenetic analyses and sequence comparisons, the cultivar Tq. kahla seems to be divergent from the cultivar Tq.hamra, whereas the two cultivars Tq.Safra and Tq.beïda are close to each other. Using 16 Simple Sequence Repeat (SSR) genetic markers to analyze genetic diversity among the cultivars, we found that 13 markers were detectable in 31 allele's loci, and the number of alleles per locus varied from 1–4 with an average of 2.38 alleles per locus. Expected heterozygosity (He) values ranged from 0.375–0.500 and observed heterozygosity (Ho) values from 0.750–1.000.

scholarly journals Isolation and DNA characterization of a simian retrovirus 5 from a Japanese monkey (Macaca fuscata)

2013 ◽  
Vol 94 (5) ◽  
pp. 955-959 ◽  
Author(s):  
Jun-Ichiro Takano ◽  
Arlene Leon ◽  
Miyoko Kato ◽  
Yuko Abe ◽  
Koji Fujimoto
Keyword(s):  
Macaca Fuscata ◽  
Direct Sequencing ◽  
Phylogenetic Analyses ◽  
Japanese Monkey ◽  
Full Length ◽  
Universal Primers ◽  
Sequence Comparisons ◽  
Dna Characterization

An SRV-like virus was isolated from a colony-born Japanese monkey. To identify this SRV-like virus, we designed universal primers at regions that were conserved among the reported SRV sequences in the 5′-LTR and the short ORF and we obtained plasmid clones containing the complete gag, prt, pol and env genes. The full-length sequences of the isolate were determined from the plasmids and by direct sequencing. Sequence comparisons and phylogenetic analyses indicated that this SRV-like virus had a sequence identical to the reported 626 bp of SRV-5. In this study, we isolated SRV5/JPN/2005/V1 from a Japanese monkey and characterized the full-length SRV-5 sequence.

scholarly journals Analysis of Soybean mosaic virus genetic diversity in Iran allows the characterization of a new mutation resulting in overcoming Rsv4-resistance

2013 ◽  
Vol 94 (11) ◽  
pp. 2557-2568 ◽  
Author(s):  
Akbar Ahangaran ◽  
Mina Koohi Habibi ◽  
Gholam-Hossein Mosahebi Mohammadi ◽  
Stephan Winter ◽  
Fernando García-Arenal
Keyword(s):  
Genetic Diversity ◽  
Amino Acid ◽  
Mosaic Virus ◽  
Phylogenetic Analyses ◽  
Soybean Mosaic Virus ◽  
Biologically Active ◽  
Site Directed Mutagenesis ◽  
Sequence Comparisons ◽  
Strong Negative Selection

The genetic variation and population structure of Soybean mosaic virus (SMV) in Iran was analysed through the characterization of a set of isolates collected in the soybean-growing provinces of Iran. The partial nucleotide sequence of these isolates showed a single, undifferentiated population with low genetic diversity, highly differentiated from other SMV world populations. These traits are compatible with a population bottleneck associated with the recent introduction of SMV in Iran. Phylogenetic analyses suggest that SMV was introduced into Iran from East Asia, with at least three introduction events. The limited genetic diversification of SMV in Iran may be explained by strong negative selection in most viral genes eliminating the majority of mutations, together with recombination purging deleterious mutations. The pathogenicity of Iranian SMV isolates was typified on a set of soybean differential lines either susceptible or carrying different resistance genes or alleles to SMV. Two pathotypes were distinguished according to the ability to overcome Rsv4 resistance in line V94-5152. Amino acid sequence comparisons of virulent and avirulent isolates on V94-5152 (Rsv4), plus site-directed mutagenesis in a biologically active cDNA clone, identified mutation S1053N in the P3 protein as the determinant for virulence on V94-5152. Codon 1053 was shown to be under positive selection, and S1053N-determined Rsv4-virulence occurred in isolates with different genealogies. The V94-5152 (Rsv4)-virulence determinant in Iranian isolates maps into a different amino acid position in the P3 protein than those previously reported, indicating different evolutionary pathways towards resistance breaking that might be conditioned by sequence context.

Morphological and molecular characterization of Hemicycliophora subbotini n. sp. (Tylenchida: Hemicycliophoridae) from China

Zootaxa ◽  
2018 ◽  
Vol 4433 (1) ◽  
pp. 161 ◽  
Author(s):  
MUNAWAR MARIA ◽  
RUIHANG CAI ◽  
NAN QU ◽  
PABLO CASTILLO ◽  
JINGWU ZHENG
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Oral Disc ◽  
Pharyngeal Bulb ◽  
En Face ◽  
The Status ◽  
A New Species ◽  
Morphological And Molecular Characterization ◽  
Lateral Plates

Sheath nematodes of the genus Hemicycliophora are migratory root-ectoparasites of many crops, but the damage is documented for only a few species. Hemicycliophora subbotini n. sp., isolated in Hangzhou, Zhejiang, China, from the rhizosphere of camphor tree (Cinnamomum camphora (L.) Presl), is described and characterized morphologically and molecularly with important morphological details elucidated by SEM studies. The new species can be characterized by the conoid lip region, with bulging oral disc protruding beyond the first annulus in some specimens. Oral disc narrow ovate, amphidial apertures covered by lateral plates, lying in the same plane as oral disc when observed en face. Stylet 118 (108–125) μm long and flexible, stylet knobs concave shaped having a slight cavity. The excretory pore is located 1–2 annuli posterior to the base of pharyngeal bulb. Vulval lips slightly modified with small vulval sleeve, spermatheca rounded to oblong. Anus located 18 (15–22) annuli posterior to vulva. Tail elongated, with conoid or slightly offset spike having a narrowly rounded terminus. The study provides the first description of a new Hemicycliophora species from China. Phylogenetic analyses based on D2–D3 expansion segments of the 28S and ITS fragments revealed the new species forming a separate clade from other Hemicycliophora species which supported the status as a new species of this genus. 

scholarly journals Morphological and Molecular Characterization of Nothotylenchus medians and N. similis (Nematoda: Anguinidae) from Southern Alberta, Canada

Horticulturae ◽  
2022 ◽  
Vol 8 (1) ◽  
pp. 74
Author(s):  
Maria Munawar ◽  
Atta Ur Rahman ◽  
Pablo Castillo ◽  
Dmytro P. Yevtushenko
Keyword(s):  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Original Description ◽  
Distribution Data ◽  
Plant Parts ◽  
Full Diversity ◽  
Canadian Population ◽  
Inventory Survey ◽  
Morphological And Molecular Characterization

The nematode family, Anguinidae, is a diverse group of polyphagous nematodes, generally known as fungal feeders or parasites of aerial plant parts. Here, we present the morphological and molecular characterization of adult females of two Nothotylenchus species, N. medians and N. similis, along with host association and geographical distribution data of the genus. Both species are recorded as new reports from Canada and designated as reference populations for future studies. Morphological or morphometrical variation was not observed in the Canadian population of N. medians and N. similis, in comparison with the original description. Phylogenetic analyses based on 18S and D2–D3 of 28S genes placed both species within Anguinidae. Since the biology of the genus Nothotylenchus has not been rigorously characterized, the habitat and distribution information presented in this study will shed some light on the ecology of these nematodes. Notably, the detection of N. medians and N. similis in our nematode inventory survey indicates that considerable Nothotylenchus diversity is hidden in these soils. Consequently, increased surveys and more in-depth research are needed to explore the full diversity of anguinids inhabiting these cultivated areas.

A new Cosmocercoides species (Ascaridida: Cosmocercidae), C. wuyiensis n. sp., from the Asiatic frog Amolops wuyiensis (Amphibia: Anura)

2019 ◽  
Vol 94 ◽  
Author(s):  
Y. Liu ◽  
Q. Yu ◽  
Y.-L. Shu ◽  
J.-H. Zhao ◽  
J.-Y. Fang ◽  
...  
Keyword(s):  
18S Rdna ◽  
Phylogenetic Analyses ◽  
Nematode Species ◽  
Coi Gene ◽  
Male Body ◽  
Lizard Species ◽  
Nucleotide Divergence ◽  
Distinguishing Features ◽  
Morphological And Molecular Characterization

Abstract We identified and characterized a new cosmocercid nematode species, Cosmocercoides wuyiensis n. sp., through microscopic examination and sequencing of the partial small ribosomal RNA gene (18S rDNA), internal transcribed spacer (ITS) and mitochondrial cytochrome c oxidase subunit 1 (COI) genes. The new species was isolated from the intestine of the Asiatic frog Amolops wuyiensis Liu and Hu, 1975 captured from four localities of the Anhui province in south-east China. Among the 25 recorded species of the Cosmocercoides genus, the morphology of C. wuyiensis n. sp. is closest to that of C. kiliwai and C. malayensis, which were isolated from various Mexican frog and Malaysian lizard species, respectively. However, C. wuyiensis n. sp. displayed several distinguishing features, such as small size of the male body, two spicules of unequal lengths in the male, small gubernaculum, pre-, ad- and post-cloacal caudal rosette papillae in the ratio of 18–24:2:6 and simple papillae in the ratio of 14:multiple:4, circle and number of punctation in each rosette at 1:11–16, sharply conical tail-end and the presence of lateral alae and somatic papillae in both sexes. BLAST and the phylogenetic analyses of the 18S rDNA and ITS sequences indicated that C. wuyiensis n. sp. belonged to the genus Cosmocercoides, while that of the COI gene sequence of C. wuyiensis n. sp. showed 16.36% nucleotide divergence with C. pulcher and 47.99% nucleotide divergence with C. qingtianensis. The morphological and molecular characterization of C. wuyiensis n. sp. provides new taxonomic data for this genus.

scholarly journals Characterization of Tomato yellow spot virus, a novel tomato-infecting begomovirus in Brazil

2007 ◽  
Vol 42 (9) ◽  
pp. 1335-1343 ◽  
Author(s):  
Renata Faier Calegario ◽  
Sávio de Siqueira Ferreira ◽  
Eduardo Chumbinho de Andrade ◽  
Francisco Murilo Zerbini
Keyword(s):  
Host Range ◽  
Molecular Characterization ◽  
Phylogenetic Analyses ◽  
Datura Stramonium ◽  
Sweet Pepper ◽  
Yellow Spot ◽  
Spot Virus ◽  
Sequence Comparisons ◽  
Full Length Genome

The objective of this work was the biological and molecular characterization of a begomovirus detected in São Joaquim de Bicas, Minas Gerais, Brazil, named TGV-[Bi2], by determining its host range, complete nucleotide sequence and phylogenetic relationships with other begomoviruses. Biological characterization consisted of a host range study using either sap inoculation or particle bombardment as inoculation methods. The yellow spot virus can infect plants in Solanaceae and Amaranthaceae, including economically importat crops as sweet pepper, and weeds as Datura stramonium and Nicotiana silvestris. For the molecular characterization, the full-length genome (DNA-A and DNA-B) was amplified, cloned and completely sequenced. Sequence comparisons and phylogenetic analyses indicated that TGV-[Bi2] constitutes a novel begomovirus species named Tomato yellow spot virus (ToYSV), closely related to Sida mottle virus (SiMoV).

scholarly journals Morphological and Molecular Characterization of Three Endolichenic Isolates of Xylaria (Xylariaceae), from Cladonia curta Ahti & Marcelli (Cladoniaceae)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 399
Author(s):  
Ehidy Rocio Peña Cañón ◽  
Margeli Pereira de Albuquerque ◽  
Rodrigo Paidano Alves ◽  
Antonio Batista Pereira ◽  
Filipe de Carvalho Victoria
Keyword(s):  
Endophytic Fungi ◽  
Phylogenetic Relationships ◽  
Phylogenetic Analyses ◽  
Morphological Characteristics ◽  
Hyphal Growth ◽  
Endolichenic Fungi ◽  
Axenic Cultures ◽  
One Year ◽  
Morphological And Molecular Characterization

Endophyte biology is a branch of science that contributes to the understanding of the diversity and ecology of microorganisms that live inside plants, fungi, and lichen. Considering that the diversity of endolichenic fungi is little explored, and its phylogenetic relationship with other lifestyles (endophytism and saprotrophism) is still to be explored in detail, this paper presents data on axenic cultures and phylogenetic relationships of three endolichenic fungi, isolated in laboratory. Cladonia curta Ahti & Marcelli, a species of lichen described in Brazil, is distributed at three sites in the Southeast of the country, in mesophilous forests and the Cerrado. Initial hyphal growth of Xylaria spp. on C. curta podetia started four days after inoculation and continued for the next 13 days until the hyphae completely covered the podetia. Stromata formation and differentiation was observed, occurring approximately after one year of isolation and consecutive subculture of lineages. Phylogenetic analyses indicate lineages of endolichenic fungi in the genus Xylaria, even as the morphological characteristics of the colonies and anamorphous stromata confirm this classification. Our preliminary results provide evidence that these endolichenic fungi are closely related to endophytic fungi, suggesting that the associations are not purely incidental. Further studies, especially phylogenetic analyses using robust multi-locus datasets, are needed to accept or reject the hypothesis that endolichenic fungi isolated from Xylaria spp. and X. berteri are conspecific.

scholarly journals Isolation and characterization of Fusarium oxysporum f. Sp. albedinis causing bayoud disease of date palm tree from Gambat, district Khairpur, Sindh, Pakistan

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Mirza Hussain Samo ◽  
Noor Jehan Ismailli
Keyword(s):  
Fusarium Oxysporum ◽  
Date Palm ◽  
Preventive Measures ◽  
Morphological Characteristics ◽  
Palm Tree ◽  
Palm Trees ◽  
Isolation And Characterization ◽  
Significant Damage ◽  
Bayoud Disease

Among different diseases of dates, bayoud disease caused by Fusarium oxysporum f. sp. albedinis causes serious damage to date palm throughout the world. The disease has damaged numerous date groves and can sometimes take on spectacular proportions when the disease appears in epidemic form. The disease is widespread and results in significant damage and incurs huge losses. In Pakistan, date palm is mainly cultivated in Khairpur (Sindh) and Turbat (Balochistan) districts. Date palm holds a significant position in the socio-economic development at Khairpur where several thousand peoples are associated directly or indirectly with date palm cultivation, trade and market. As no information exists about the bayoud disease in Khairpur district, therefore, in the present study, the disease was characterized on date palm trees caused by Fusarium oxysporum f. sp. albedinis at college area of Gambat, District Khairpur, Sindh, Pakistan. Samples of infected date palm trees of different varieties were collected from experimental area at the time of harvesting. The fungus was isolated, purified and identified as Fusarium oxysporum f. sp. albedinis on the basis of morphological characteristics. In conclusion, bayoud disease is an epiphytic disease for which there is no known cure at present. Only preventive measures could protect healthy date plantations from this disease.

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