Genetic diversity among isolates of stemphylium solani from cotton

The fungus Stemphylium solani causes leaf blight of tomato (Lycopersicon esculentum) in Brazil. In recent years, severe epidemics of a new leaf blight of cotton (Gossipium hyrsutum) caused by S. solani occurred in three major cotton-growing Brazilian states (PR, MT and GO). Molecular analysis was performed to assess the genetic diversity among the S. solani isolates from cotton, and to verify their relationship with representative S. solani isolates from tomato. Random amplified polymorphic DNA (RAPD) markers and internal transcribed spacers of ribosomal DNA (rDNA) were used to compare 33 monosporic isolates of S. solani (28 from cotton and five from tomato). An isolate of Alternaria macrospora from cotton was also used for comparison. RAPD analysis showed the presence of polymorphism between the genera and the species. The A. macrospora and the S. solani isolates from cotton and tomato were distinct from each other, and fell into separate groups. Variation by geographic region was observed for the tomato isolates but not for the cotton isolates. Amplifications of the ITS region using the primer pair ITS4/ITS5 resulted in a single PCR product of approximately 600 bp for all the isolates. Similarly, when amplified fragments were digested with eight restriction enzymes, identical banding patterns were observed for all the isolates. Hence, rDNA analysis revealed no inter-generic or intra-specific variation. The genetic difference observed between the cotton and the tomato isolates provides evidence that S. solani attacking cotton in Brazil belongs to a distinct genotype.

Download Full-text

DNA sequencing and genetic diversity of the 18S–26S nuclear ribosomal internal transcribed spacers (ITS) in nine Antarctic moss species

Antarctic Science ◽

10.1017/s0954102005002816 ◽

2005 ◽

Vol 17 (3) ◽

pp. 377-384 ◽

Cited By ~ 15

Author(s):

M.L. SKOTNICKI ◽

A.M. MACKENZIE ◽

M.A. CLEMENTS ◽

P.M. SELKIRK

Keyword(s):

Dna Sequencing ◽

Simple Technique ◽

Ross Sea ◽

Random Amplified Polymorphic Dna ◽

Its Region ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Taxonomic Identification ◽

Moss Species ◽

Antarctic Moss

We have sequenced the 18S–26S nuclear ribosomal DNA ITS region from the genome of nine different moss species from the Ross Sea region of Antarctica. This relatively quick and simple technique enables these species to be readily distinguished, facilitating their taxonomic identification. Only a single moss shoot is required, and for identification of these bryophytes it is only necessary to determine a few hundred nucleotides of the DNA sequence in a single sequencing reaction. Several previously unidentified Antarctic moss specimens were readily characterized by comparison with ITS sequences of known moss species. The relationships between species and locations previously detected by the RAPD (Random Amplified Polymorphic DNA) technique were confirmed by DNA sequencing, demonstrating that the two techniques can be complementary for molecular analysis of the ecology of mosses in Antarctica.

Download Full-text

Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

Horticulturae ◽

10.3390/horticulturae6040087 ◽

2020 ◽

Vol 6 (4) ◽

pp. 87

Author(s):

Kumpei Shiragaki ◽

Shuji Yokoi ◽

Takahiro Tezuka

Keyword(s):

Genetic Diversity ◽

Phylogenetic Analysis ◽

Wild Species ◽

Morphological Characteristics ◽

Its Region ◽

Internal Transcribed Spacers ◽

Nuclear Ribosomal Dna ◽

Rdna Its ◽

Rdna Its Region ◽

Genus Capsicum

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

Download Full-text

Characterization of genetic diversity on tropical Trichoderma germplasm by sequencing of rRNA internal transcribed spacers

BMC Research Notes ◽

10.1186/s13104-019-4694-1 ◽

2019 ◽

Vol 12 (1) ◽

Cited By ~ 1

Author(s):

Yara Barros Feitosa ◽

Valter Cruz-Magalhães ◽

Ronaldo Costa Argolo-Filho ◽

Jorge Teodoro de Souza ◽

Leandro Lopes Loguercio

Keyword(s):

Genetic Diversity ◽

Molecular Level ◽

Its Region ◽

Internal Transcribed Spacers ◽

Plant Diseases ◽

Rrna Genes ◽

Physiological Data ◽

Biotic And Abiotic Stresses ◽

Beneficial Effects

Abstract Objective Trichoderma species are found in soil and in association with plants. They can act directly or indirectly in the biological control of plant diseases and in the promotion of plant growth, being among the most used fungi in the formulation of bioproducts applied to agricultural systems. The main objective of this study was to characterize at a first-tier level a collection of 67 Trichoderma isolates from various tropical sources, based solely on sequencing of the internal transcribed spacer (ITS) region of the rRNA genes. Our goal was to provide a preliminary idea of the baseline diversity in this collection, to combine this information later with an array of other isolate-specific physiological data. This study provides a required knowledge at molecular level for assessment of this germplasm potential as a source of biotechnological products for beneficial effects in plants. Results Sequencing of the ITS region showed that the 67 Trichoderma isolates belonged in 11 species: T. asperellum, T. atroviride, T. brevicompactum, T. harzianum, T. koningiopsis, T. longibrachiatum, T. pleuroticola, T. reesei, T. spirale, T. stromaticum and T. virens. A total of 40.3% of the isolates were very closely related to each other and similar to T. harzianum. The baseline genetic diversity found indicates that the collection has different genotypes, which can be exploited further as a source of bioproducts, aiming at providing beneficial effects to plants of interest to cope with biotic and abiotic stresses.

Download Full-text

PCR Amplification of Ribosomal DNA for Species Identification in the Plant Pathogen Genus Phytophthora

Applied and Environmental Microbiology ◽

10.1128/aem.64.3.948-954.1998 ◽

1998 ◽

Vol 64 (3) ◽

pp. 948-954 ◽

Cited By ~ 115

Author(s):

Jean B. Ristaino ◽

Michael Madritch ◽

Carol L. Trout ◽

Gregory Parra

Keyword(s):

Ribosomal Dna ◽

Plant Pathogen ◽

Pcr Amplification ◽

Its Region ◽

Restriction Enzymes ◽

Internal Transcribed Spacers ◽

Important Species ◽

Major Species ◽

Field Samples ◽

Taxonomic Groups

ABSTRACT We have developed a PCR procedure to amplify DNA for quick identification of the economically important species from each of the six taxonomic groups in the plant pathogen genusPhytophthora. This procedure involves amplification of the 5.8S ribosomal DNA gene and internal transcribed spacers (ITS) with the ITS primers ITS 5 and ITS 4. Restriction digests of the amplified DNA products were conducted with the restriction enzymesRsaI, MspI, and HaeIII. Restriction fragment patterns were similar after digestions with RsaI for the following species: P. capsici andP. citricola; P. infestans,P. cactorum, and P. mirabilis;P. fragariae, P. cinnamomi, andP. megasperma from peach; P. palmivora, P. citrophthora, P. erythroseptica, and P. cryptogea; andP. megasperma from raspberry and P. sojae. Restriction digests with MspI separatedP. capsici from P. citricola and separated P. cactorum from P. infestans and P. mirabilis. Restriction digests with HaeIII separated P. citrophthorafrom P. cryptogea, P. cinnamomi fromP. fragariae and P. megasperma on peach, P. palmivora from P. citrophthora, and P. megasperma on raspberry from P. sojae. P. infestans and P. mirabilis digests were identical and P. cryptogea and P. erythroseptica digests were identical with all restriction enzymes tested. A unique DNA sequence from the ITS region I in P. capsici was used to develop a primer called PCAP. The PCAP primer was used in PCRs with ITS 1 and amplified only isolates of P. capsici,P. citricola, and P. citrophthoraand not 13 other species in the genus. Restriction digests withMspI separated P. capsici from the other two species. PCR was superior to traditional isolation methods for detection of P. capsici in infected bell pepper tissue in field samples. The techniques described will provide a powerful tool for identification of the major species in the genusPhytophthora.

Download Full-text

Characterization of the Hyphal Swelling Group of Pythium: DNA Polymorphisms and Cultural and Morphological Characteristics

Plant Disease ◽

10.1094/pdis.1998.82.2.218 ◽

1998 ◽

Vol 82 (2) ◽

pp. 218-222 ◽

Cited By ~ 23

Author(s):

K. Kageyama ◽

H. Uchino ◽

M. Hyakumachi

Keyword(s):

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Morphological Characteristics ◽

Its Region ◽

Restriction Enzymes ◽

Dna Polymorphisms ◽

Banding Patterns ◽

Length Polymorphisms ◽

Polymerase Chain

The hyphal swelling (HS) group of Pythium species and P. ultimum were studied for cultural and morphological characteristics, restriction fragment length polymorphisms of the amplified internal transcribed spacer (ITS) region in nuclear rDNA, and random amplified polymorphic DNA (RAPD) analysis of genome DNA. The shape of sporangia was spherical to subspherical or lemoniform and averaged 18.1–23.0 μm. All isolates could grow at 5 to 35°C, and the rate at the optimal temperature, 30°C, was 29–34 mm/24 h. The size of the ITS region amplified by polymerase chain reaction and the banding patterns after digestion with the restriction enzymes showed no variation between the HS group and P. ultimum. No difference in banding patterns was shown between the HS group and P. ultimum by RAPD analysis with each of three primers. Isolates examined were from Japan, and results should be confirmed from other regions.

Download Full-text

RAPD profiling in detecting genetic variation in Stellaria L. (Caryophyllaceae)

Genetika ◽

10.2298/gensr2101349p ◽

2021 ◽

Vol 53 (1) ◽

pp. 349-362

Author(s):

Xiaobang Peng ◽

Majid Khayyatnezhad ◽

Leila Ghezeljehmeidan

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Rapd Markers ◽

Genetic Difference ◽

Random Amplified Polymorphic Dna ◽

Molecular Data ◽

Shannon Index ◽

Neighbor Joining ◽

Medicinal Value ◽

Main Center

Stellaria species are common herbs, preferred humid mountainously slopes, but some grew in desert. Main center of diversification for Stellaria is Eurasia, with a center of distribution in the mountains of central Asia. Some species are also cosmopolitan. It is represented by 9 species in Iran. The genus has high medicinal value. To determine the genetic diversity and understand the species? limits within the Iranian Stellaria, we produced molecular data using 139 randomly collected plants representing 8 species from five provinces of Iran. A total of 122 reproducible bands were generated by 10 of 25 random amplified polymorphic DNA (RAPD) primers, with an average of 12.2 bands/primer and 33% polymorphism. Largest number of effective alleles (Ne), genetic diversity (H), and Shannon Index (I) were shown by S. media. Our data depicted highest similarity between S. media and S. pallida and lowest between S. media and S. graminea. S. pallida showed relatively low level of genetic variation. Finally, the Neighbor Joining (NJ) trees based on RAPD markers data divided the populations into two different clusters, indicating their genetic difference which is discussed in details.

Download Full-text

Gene flow and genetic structure between populations of Hesperis L. (Brassicaceae) species using molecular markers

Genetika ◽

10.2298/gensr2102769m ◽

2021 ◽

Vol 53 (2) ◽

pp. 769-782

Author(s):

Kuanhong Meng ◽

Jia Yao ◽

Cong He ◽

Heravi Morabbi

Keyword(s):

Genetic Diversity ◽

Genetic Difference ◽

Random Amplified Polymorphic Dna ◽

Principal Component ◽

Shannon Index ◽

The Other ◽

Brassicaceae Species ◽

Close Relationship ◽

Geographical Populations ◽

Dna Primers

Genetic variability and populations, structure were studied in seven geographical populations of Hesperis L. Genetic diversity parameters were determined in these populations. 5 of 10 random amplified polymorphic DNA primers produced 62 reproducible bands with average of 7.1 bands per primer and 55% of polymorphism. Hesperis hyrcana showed the highest number of effective allele (Ne), Shannon index (I) and genetic diversity (H). The highest values of genetic diversity were obtained in Hesperis hyrcana. NJ trees grouped the populations in two different clusters/groups, indicating their genetic difference which is discussed in details. The results of this study showed that the level of genetic variation in Hesperis is relatively high. NJ-based dendrogram showed a close relationship between members of Hesperis straussii and Hesperis hyrcana while the Hesperis luristanica protected population differ the most from the other populations. Principal component analysis, however, showed some minor differences with NJ-based dendrograms.

Download Full-text

Genetic analysis of pathogenic and nonpathogenic Fusarium oxysporum from tomato plants

Canadian Journal of Botany ◽

10.1139/b02-004 ◽

2002 ◽

Vol 80 (3) ◽

pp. 271-279 ◽

Cited By ~ 29

Author(s):

Jian R Bao ◽

Deborah R Fravel ◽

Nichole R O'Neill ◽

George Lazarovits ◽

Peter van Berkum

Keyword(s):

Genetic Diversity ◽

Fusarium Oxysporum ◽

Geographic Origin ◽

Its Region ◽

Internal Transcribed Spacers ◽

Rrna Gene ◽

Aflp Data ◽

5.8S Rrna Gene ◽

Rdna Its ◽

Wide Range

Forty-three Fusarium oxysporum strains and one Fusarium solani strain were analyzed for genetic diversity. These strains represent a wide range of geographic locations and were collected primarily from tomato (Lycopersicon esculentum) roots. Among all 43 F. oxysporum strains, 21 were not pathogenic to tomato, 20 were pathogenic, including 13 strains of Fusarium oxysporum lycopersici and seven strains of Fusarium oxysporum radicis-lycopersici, and two were other formae speciales of the fungus. Genetic diversity of all 43 strains was assessed by vegetative compatibility group (VCG), sequence analysis of the rDNA internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene, and amplified fragment length polymorphism (AFLP). Most of the F. o. lycopersici strains were assigned to VCG 0030, while most nonpathogenic ones were incompatible with each other. ITS region analysis grouped the strains into four clusters. The nonpathogenic F. oxysporum strains were in two groups, while the pathogenic strains were placed in two different groups. Pathogenic and nonpathogenic strains were also separated into different clusters based on AFLP data, although some nonpathogenic strains grouped with pathogenic strains. The population of pathogenic strains was less diverse than that of the nonpathogenic strains, suggesting that the pathogenic strains were possibly of monophyletic origin. For both pathogenic and nonpathogenic F. oxysporum strains, no relationship was observed between the genetic profiles and geographic origin; this may indicate that pathogens did not originate independently at each locality.Key words: Fusarium oxysporum, VCG, rDNA (ITS) sequence, AFLP.

Download Full-text

Genetic diversity of Bartonella taylorii and Bartonella grahamii strains

Biologija ◽

10.6001/biologija.v65i2.4029 ◽

2019 ◽

Vol 65 (2) ◽

Author(s):

Dalytė Mardosaitė-Busaitienė ◽

Paulina Amšiejūtė ◽

Jana Radzijevskaja ◽

Algimantas Paulauskas

Keyword(s):

Genetic Diversity ◽

Sequence Analysis ◽

Geographic Distance ◽

Its Region ◽

Housekeeping Gene ◽

Geographic Region ◽

23S Rrna ◽

Wild Rodents ◽

Bacterial Strains ◽

Its Sequence Analysis

Bacterial strains are a characteristic feature of many bacterial pathogens, including the species of the genus Bartonella. These bacteria are associated with different vertebrate hosts and vectors and have been detected in North America, Australia, Asia, and Europe. This study presents molecular characterization of Bartonella strains circulating in wild rodents. B. taylorii and B. grahamii are detected with high prevalence in mice, voles, and rats. However, there is a lack of knowledge on the geographical distribution and genetic diversity of B. taylorii and B. grahamii strains in wild rodents. The objectives of this study were to characterize the genetic diversity of B. taylorii and B. grahamii strains by sequence analysis of the housekeeping gene (rpoB) and the 16S-23S rRNA intergenic species region (ITS). Sequence analysis of rpoB gene revealed the presence of 15 B. taylorii genotypes and four B. grahamii genotypes in mice and voles captured in Lithuania. Sequence analysis of the ITS region revealed the presence of six B. taylorii genotypes and four B. grahamii genotypes in Lithuanian voles and mice. Analysis of genetic diversity demonstrated that B. grahamii strains derived from the same geographic region or from regions of close proximity more conservative, while B. grahamii strains from more distant areas are more variable. Genetic diversity of B. taylorii strains seems not to depend on geographic distance.

Download Full-text

Comparative study of genetic diversity using RAPD markers in Salvia (Lamiaceae)

Caryologia ◽

10.36253/caryologia-1236 ◽

2021 ◽

Author(s):

Majid KHAYYATNEZHAD ◽

Sayed Afzal Shah2

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Genetic Difference ◽

Random Amplified Polymorphic Dna ◽

Molecular Data ◽

Shannon Index ◽

Neighbor Joining ◽

The World ◽

Morphological And Molecular Data ◽

High Degree

Salvia has a high degree of environmental compatibility and is widespread around the world, especially in tropical and temperate regions. It is represented by 61 species in Iran including 19 endemic species. Salvia species are mostly shrubs or subshrubs, occasionally herbs, typically perennial, sometimes biennial or annual, and often aromatic. The genus has high medicinal, commercial and horticultural value. It is the largest and one of the taxonomically complicated genus of Lamiaceae. To determine the genetic diversity and understand the species’ limits within the Iranian Salvia, we produced both morphological and molecular data using 145 randomly collected plants representing 30 species from 18 provinces of Iran. A total of 107 reproducible bands were generated by 10 of 25 random amplified polymorphic DNA (RAPD) primers, with an average of 10.7 bands/primer and 44% polymorphism. Largest number of effective alleles (Ne), genetic diversity (H), and Shannon Index (I) were shown by S. reuterana. Our data depicted highest similarity between S. suffruticosa and S. hydrangea and lowest between S. aristata and S. oligphylla. Salvia limbata showed relatively low level of genetic variation. Finally, the Neighbor Joining (NJ) trees based on RAPD markers data divided the populations into two different clusters, indicating their genetic difference which is discussed in details.

Download Full-text