scholarly journals Mitochondrial Genomics of Six Cacao Pathogens From the Basidiomycete Family Marasmiaceae

2021 ◽  
Vol 12 ◽  
Author(s):  
Shahin S. Ali ◽  
Ishmael Amoako-Attah ◽  
Jonathan Shao ◽  
Eric Kumi-Asare ◽  
Lyndel W. Meinhardt ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Relationships ◽  
Homing Endonuclease ◽  
Western Hemisphere ◽  
Divergent Evolution ◽  
Moniliophthora Perniciosa ◽  
Evolutionary Trajectory ◽  
Important Species ◽  
Core Proteins ◽  
Blight Disease

Thread blight disease has recently been described as an emerging disease on cacao (Theobroma cacao) in Ghana. In Ghana, thread blight disease is caused by multiple species of the Marasmiaceae family: Marasmius tenuissimus, M. crinis-equi, M. palmivorus, and Marasmiellus scandens. Interestingly, two additional members of the Marasmiaceae; Moniliophthora roreri (frosty pod rot) and Moniliophthora perniciosa (witches’ broom disease), are major pathogens of cacao in the Western hemisphere. It is important to accurately characterize the genetic relationships among these economically important species in support of their disease management. We used data from Illumina NGS-based genome sequencing efforts to study the mitochondrial genomes (mitogenomes) of the four cacao thread blight associated pathogens from Ghana and compared them with published mitogenomes of Mon. roreri and Mon. perniciosa. There is a remarkable interspecies variation in mitogenome size within the six cacao-associated Marasmiaceae species, ranging from 43,121 to 109,103 bp. The differences in genome lengths are primarily due to the number and lengths of introns, differences in intergenic space, and differences in the size and numbers of unidentified ORFs (uORF). Among seven M. tenuissimus mitogenomes sequenced, there is variation in size and sequence pointing to divergent evolution patterns within the species. The intronic regions show a high degree of sequence variation compared to the conserved sequences of the 14 core genes. The intronic ORFs identified, regardless of species, encode GIY-YIG or LAGLIDADG domain-containing homing endonuclease genes. Phylogenetic relationships using the 14 core proteins largely mimic the phylogenetic relationships observed in gene order patterns, grouping M. tenuissimus with M. crinis-equi, and M. palmivorus with Mon. roreri and Mon. perniciosa, leaving Mar. scandens as an outlier. The results from this study provide evidence of independent expansion/contraction events and sequence diversification in each species and establish a foundation for further exploration of the evolutionary trajectory of the fungi in Marasmiaceae family.

Phylogenetic relationships of five morphological groups of hexaploid wheat (Triticum aestivum L. em Thell.) based on RAPD analysis

Genome ◽  
2000 ◽  
Vol 43 (4) ◽  
pp. 724-727 ◽  
Author(s):  
Wenguang Cao ◽  
G Scoles ◽  
P Hucl ◽  
R N Chibbar
Keyword(s):  
Hexaploid Wheat ◽  
Phylogenetic Relationships ◽  
Genetic Similarity ◽  
Rapd Analysis ◽  
Genetic Relationships ◽  
Random Amplified Polymorphic Dna ◽  
Triticum Aestivum L ◽  
Similarity Coefficients ◽  
Morphological Classification ◽  
Wild Wheat

The genetic relationships among the five groups of hexaploid wheat: common, spelta, macha, vavilovii, and semi-wild wheat (SWW) are not clear. Random amplified polymorphic DNA (RAPD) analysis was used to assess phylogenetic relationships among these five morphological groups of hexaploid wheat. RAPD data were analyzed using the NTSYS-PC computer program to generate Jaccard genetic similarity coefficients. A dendrogram based on RAPD analysis grouped 15 accessions into five distinct clusters. These results are in agreement with those based on morphological classification, suggesting that common wheat is most closely related to SWW, followed by spelta, vavilovii, and macha.Key words: RAPD, macha, spelta, vavilovii, semi-wild wheat, phylogenetic relationships.

Potential of random amplified microsatellites (RAMS) to typify and discriminate varieties of Physalis ixocarpa Brot. ex Hornem.

2018 ◽  
pp. 396
Author(s):  
Eli Amanda Delgado-Alvarado, Norma Almaraz-Abarca ◽  
Cirenio Escamirosa- Tinoco ◽  
Jose Natividad Uribe-Soto, Jose Antonio Avila-Reyes ◽  
Rene Torres-Ricario, Ana Isabel Chaidez-Ayala
Keyword(s):  
Cluster Analysis ◽  
Genetic Variability ◽  
South America ◽  
Principal Components ◽  
Genetic Relationships ◽  
Important Species ◽  
Physalis Peruviana ◽  
Edible Species ◽  
Components Analysis ◽  
Genetic Closeness

Physalis ixocarpa is an edible species of Solanaceae. This is one of the few cultivated and economically important species of the genus in Mesoamerica. In Mexico, several varieties and landraces have been developed, which have not been molecularly characterized. In the current study, five RAMS primers were used to characterize and assess the genetic variability of two varieties and three landraces of this species. The capacity of these markers to discriminate between them was also evaluated. With comparative aims, Physalis peruviana, the most economically important species of the genus in South America, was analyzed in the same manner. The results revealed that the varieties and landraces of P. ixocarpa conserve important levels of genetic variability (21.75% > Polymorphism < 42.75%), which were higher than that found for P. peruviana (10.75% Polymorphism). RAMS were useful specific markers, as P. peruviana and P. ixocarpa were clearly distinguished one from each other by both cluster analysis and principal components analysis. Close genetic relationships were found between the landraces San Isidro Chihuiro and Verde Puebla, and between the varieties Diamante and Rendidora. In spite of the genetic closeness, the RAMS amplification profiles had a clear varietal-specific tendency, in such a way that they may represent varietal fingerprints, which can be used as authentication tool for varieties and landraces of P. ixocarpa.

scholarly journals Evaluation of Xylella fastidiosa genetic diversity by fAFPL markers

2008 ◽  
Vol 30 (1) ◽  
pp. 202-208 ◽  
Author(s):  
Luciano Takeshi Kishi ◽  
Ester Wickert ◽  
Eliana Gertrudes de Macedo Lemos
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationships ◽  
Host Plants ◽  
Geographical Origin ◽  
Xylella Fastidiosa ◽  
Genetic Relationships ◽  
Single Species ◽  
Bacterial Typing ◽  
Phytopathogenic Bacterium ◽  
Different Strains

The first phytopathogenic bacterium with its DNA entirely sequenced is being detected and isolated from different host plants in several geographic regions. Although it causes diseases in cultures of economic importance, such as citrus, coffee, and grapevine little is known about the genetic relationships among different strains. Actually, all strains are grouped as a single species, Xylella fastidiosa, despite colonizing different hosts, developing symptoms, and different physiological and microbiological observed conditions. The existence of genetic diversity among X. fastidiosa strains was detected by different methodological techniques, since cultural to molecular methods. However, little is know about the phylogenetic relationships developed by Brazilian strains obtained from coffee and citrus plants. In order to evaluate it, fAFLP markers were used to verify genetic diversity and phylogenetic relationships developed by Brazilian and strange strains. fAFLP is an efficient technique, with high reproducibility that is currently used for bacterial typing and classification. The obtained results showed that Brazilian strains present genetic diversity and that the strains from this study were grouped distinctly according host and geographical origin like citrus-coffee, temecula-grapevine-mulberry and plum-elm.

scholarly journals Neofusicoccum parvum Causing Stem and Branch Blight Disease of Zanthoxylum bungeanum in Sichuan, China

Plant Disease ◽  
2021 ◽  
Author(s):  
Jie Chen ◽  
Shujiang Li ◽  
Tianhui Zhu ◽  
Shan Han ◽  
Tianmin Qiao ◽  
...  
Keyword(s):  
Water Conservation ◽  
Morphological Characteristics ◽  
Post Inoculation ◽  
Pathogenicity Test ◽  
Conidial Suspension ◽  
Internal Transcribed Spacer Region ◽  
Important Species ◽  
Neofusicoccum Parvum ◽  
Blight Disease ◽  
Zanthoxylum Bungeanum

The Chinese pepper Zanthoxylum bungeanum Maxim is a special economically important species and a traditional spice in China. It is widely used in medicine, food, timber, tourism, soil and water conservation. In April 2019, A stem and branch blight disease of Z. bungeanum was discovered in Muli, Puge and Yanyuan counties, in Liangshan Prefecture (27°15′20″-27°19′38″N, 101°44′58″-102°04′10″E), causing approximately 15% yield loss in the three counties. Among all fields in Muli County, approximately 41.38%, 10.79% and 2% of Chinese peppers exhibited mild, moderate and severe branch blight, respectively. The symptoms started to occur from March to April. First, red-brown spots on the base of the stem, branches or main trunks of young trees observed but were not obvious. In May, the spots became gray-brown to dark brown ovals and gradually expanded into long strips (Figure 1a, b). When the spots surrounded the branches, the branches above them withered and died, and the spots gradually expanded downward. Around June or July, scattered black dot-shaped fruiting bodies were observed on the lesion. The branches of infected trees were sampled systematically by cutting the branch at the junction of infected and healthy areas in 5×5 mm sections. Each sample was surface-sterilized with 3% NaClO and 75% alcohol for 60 s before being rinsed three times with sterilized distilled water. The sterile filter paper was used to dry the tissue, and the samples were cultured on potato dextrose agar (PDA) amended with streptomycin sulfate (50 μg/ml). Plates were incubated at 25°C in the dark. From the five isolates obtained, four exhibited the morphology described by Yu et al. (2015) for Neofusicoccum parvum. The colonies were white fluffy at first and grew fast (Figure 1c). After five days, the colony diameter reached 75.2-84.8 mm, produced yellow pigment and the mycelium in the middle of the colony began to turn gray (Figure 1d). and the entire colony turned dark gray 7–8 days post culturing as observed previously (Javier-Alva et al. 2009) and formed a black fruiting body at 20 days (Figure 1e). The width of the mycelium measured 2.3-4.8 µm, and with the diaphragm (Figure 1f). The spores were round or fusiform, colorless, transparent, smooth, thin-walled, and measured 6.3-10.6×3.1-5.2 µm (Figure 1g, h), similar to N. parvum (Yu et al. 2013). For molecular identification, DNA was extracted from the mycelia of four fungal isolates using a plant genomic DNA extraction kit (Solarbio, Beijing). Polymerase Chain Reaction (PCR) was performed with the primers ITS1/ITS4 (White et al. 1990), EF446F/EF1035R (Inderbitzin et al. 2005), BTF/BTR2 and HspF3/HspR (Inderbitzin et al. 2010) for the ribosomal internal transcribed spacer region (ITS), elongation factor-1alpha (EF1-alpha), beta-tubulin (TUB) and heat shock protein (HSP) genes, respectively. BLAST searches in the GenBank database indicated that the ITS, TUB, HSP and EF-1α sequences had 100%, 99.0%, 99.7% and 99.7% identity to N. parvum, respectively. Representative sequences were deposited in GenBank (ITS: MT355871; TUB: MT409397; EF-1α: MT409399; HSP: MT460413). A pathogenicity test was performed using N. parvum on ten 2-year-old potted Z. bungeanum plants at 22-28°C and 60% humidity indoors. The conidial suspension (1×107 conidia/ml) collected 25 days old PDA cultures with 0.05% tween buffer was used for inoculation by brushing the wounded area of branch scratched by epidermis with a piece of sandpaper. Ten plants in pots were inoculated with sterile water and served as controls. Thirty days post-inoculation, the plants showed the same symptoms as the original diseased plants, and the controls remained asymptomatic. N. parvum was re-isolated from the infected tissues and identified by morphological characteristics and DNA sequence analysis. The pathogenicity test was repeated three times with similar results, confirming Koch’s postulates. This fungus is an important pathogen on a variety of woody hosts, and represents a serious problem in the vineyards worldwide (Mélanie, et al. 2017). To our knowledge, this is the first report of N. parvum causing stem and branch blight of Z. bungeanum trees in China.

scholarly journals Genetic diversity among toxigenic and nontoxigenicVibrio choleraeO1 isolated from the Western Hemisphere

1991 ◽  
Vol 107 (1) ◽  
pp. 225-233 ◽  
Author(s):  
F. Chen ◽  
G. M. Evins ◽  
W. L. Cook ◽  
R. Almeida ◽  
N. Hargrett-Bean ◽  
...  
Keyword(s):  
Gulf Coast ◽  
Genetic Relationships ◽  
Western Hemisphere ◽  
Enzyme Electrophoresis ◽  
Multilocus Enzyme Electrophoresis ◽  
The Us ◽  
Single Clone ◽  
Diverse Origin ◽  
Toxigenic Strains ◽  
Surrounding Areas

SUMMARYMultilocus enzyme electrophoresis was used to examine genetic relationships among and between toxigenic and non-toxigenic isolates ofVibrio choleraeO1 obtained from patients and the environment in the US Gulf Coast and surrounding areas. A total of 23 toxigenic and 23 non-toxigenic strains were examined. All the toxigenic and 7 of the non-toxigenic strains had the same alleles at 16 enzyme loci, whereas the balance of the nontoxigenic strains had 9 distinct combinations of alleles. This study suggests that all of the toxigenic strains belong to a single clone, and that while some of the non-toxigenic isolates were related, most were of diverse origin.

scholarly journals Genetic diversity assessment of neem (Azadirachta indica A. Juss) in northern Nigeria

2021 ◽  
Author(s):  
Barka Peter MSHELMBULA ◽  
Geoffrey Obinna Anoliefo ◽  
Beckley Ikhajiagbe ◽  
Boniface Edegbai
Keyword(s):  
Genetic Diversity ◽  
Germplasm Conservation ◽  
Western Hemisphere ◽  
Northern Nigeria ◽  
Important Species ◽  
Tropical Regions ◽  
Ecological Zones ◽  
Diversity Assessment ◽  
Wide Range ◽  
Agro Ecological Zones

Neem is a tropical tree that can adapt to a wide range of places and particularly to semi- arid conditions. As at present, it is grown in many Asian countries and also in the tropical regions of the western hemisphere. Genetic variability and diversity are a major requirement needed for both immediate results and the one ones thereafter adaptation of plant types in their original domain. The evaluation of genetic diversity of any species is extremely crucial for their sustainability, continuity, survival and gene manipulation. Major breakthroughs in the field of molecular biology was able to develop several tools for the investigation of genetic diversity at the genome level to determine phylogenetic relationships among inter or intra-species. The advent of molecular markers for the detection and exploitation of DNA polymorphism is one of the major breakthroughs in the world of molecular genetics. The importance of genetic diversity in plant germplasm conservation, especially in economically important species such as Azadirachtaindica, is enormous, particularly in Nigeria. The question is whether A. indica from different Agro-ecological zones have genetic variations or similarities. This was the bane of the current study, which used RAPD to look atgenetic diversity of 27 randomly selected neem trees within the agro-ecological zones in Northern Nigeria. A total of 9 primers were employed out of which only 5 were responsive (OPA-02, OPA-03, OPA-15 and OPA-19). These primers showed dissimilarities in the visible DNA bands among the various tree samples. There was evidence of genetic dissimilarities among the trees sampled. Differences in percentage polymorphism was reported, where it was reportedly highest among the Borno State tree samples (97.44%), compared to those in Yobe State with no polymorphism.

scholarly journals Amplified Fragment Length Polymorphism Analysis for Studying Genetic Relationships among Mangifera Species in Thailand

2000 ◽  
Vol 125 (2) ◽  
pp. 160-164 ◽  
Author(s):  
Wichan Eiadthong ◽  
Keizo Yonemori ◽  
Shinya Kanzaki ◽  
Akira Sugiura ◽  
Naoki Utsunomiya ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Fragment Length ◽  
Fragment Length Polymorphism ◽  
Genetic Relationships ◽  
Amplified Fragment Length Polymorphism ◽  
Interspecific Variation ◽  
Polymorphism Analysis ◽  
Important Species ◽  
Cashew Nut ◽  
Grouping Method

The phylogenetic relationships among 14 Mangifera L. species including three economically important species, i.e., common mango (M. indica L.), horse mango (M. foetida Lour.) and kwini (M. odorata Griff.), were analyzed by comparing 217 amplified fragment length polymorphism (AFLP) markers. The unweighted pair grouping method using arithmetic averages (UPGMA) and neighbor-joining (NJ) method were used and two outgroup taxa, cashew nut (Anacardium occidentale L.) and gandaria (Bouea macrophylla Griff.), were added to both analyses. The common mango was closely related to banana mango (M. sylvatica Roxb.), M. laurina Bl., and M. oblongifolia Hook.f. Intraspecific variation among seven cultivars of common mango was much smaller than interspecific variation and these cultivars were classified into one M. indica group using both methods. Mangifera macrocarpa Bl., M. foetida, and M. odorata were also related to M. indica in both UPGMA and NJ trees, although these three species are classified into a different subgenus (subgenus Limus) from the subgenus Mangifera to which M. indica belongs. Also, in both UPGMA and NJ trees, M. gedebe Miq. and M. griffithii Hk.f. were placed in distant positions among the Mangifera species tested, indicating these two species are related distantly to M. indica. The AFLP technique was confirmed to be useful for phylogenetic analysis.

scholarly journals Validation of Mixed-Genome Microarrays as a Method for Genetic Discrimination

2007 ◽  
Vol 73 (5) ◽  
pp. 1425-1432 ◽  
Author(s):  
Yan Wan ◽  
Shira L. Broschat ◽  
Douglas R. Call
Keyword(s):  
Phylogenetic Relationships ◽  
Genetic Relationships ◽  
Branch Length ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Single Genome ◽  
Lineage Markers ◽  
Unique Strain ◽  
Different Strains

ABSTRACT Comparative genomic hybridizations have been used to examine genetic relationships among bacteria. The microarrays used in these experiments may have open reading frames from one or more reference strains (whole-genome microarrays), or they may be composed of random DNA fragments from a large number of strains (mixed-genome microarrays [MGMs]). In this work both experimental and virtual arrays are analyzed to assess the validity of genetic inferences from these experiments with a focus on MGMs. Empirical data are analyzed from an Enterococcus MGM, while a virtual MGM is constructed in silico using sequenced genomes (Streptococcus). On average, a small MGM is capable of correctly deriving phylogenetic relationships between seven species of Enterococcus with accuracies of 100% (n = 100 probes) and 95% (n = 46 probes); more probes are required for intraspecific differentiation. Compared to multilocus sequence methods and whole-genome microarrays, MGMs provide additional discrimination between closely related strains and offer the possibility of identifying unique strain or lineage markers. Representational bias can have mixed effects. Microarrays composed of probes from a single genome can be used to derive phylogenetic relationships, although branch length can be exaggerated for the reference strain. We describe a case where disproportional representation of different strains used to construct an MGM can result in inaccurate phylogenetic inferences, and we illustrate an algorithm that is capable of correcting this type of bias. The bias correction algorithm automatically provides bootstrap confidence values and can provide multiple bias-corrected trees with high confidence values.

scholarly journals Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1493
Author(s):  
Gulnara Svishcheva ◽  
Olga Babayan ◽  
Bulat Lkhasaranov ◽  
Ariuntuul Tsendsuren ◽  
Abdugani Abdurasulov ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Allelic Richness ◽  
Common Ancestor ◽  
Bos Taurus ◽  
Genetic Relationships ◽  
High Variability ◽  
Brown Swiss ◽  
Native Cattle ◽  
Historical Origin ◽  
Geographic Regions

We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.

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