scholarly journals Genetic Structure and Biology of Xylella fastidiosa Strains Causing Disease in Citrus and Coffee in Brazil

2008 ◽  
Vol 74 (12) ◽  
pp. 3690-3701 ◽  
Author(s):  
Rodrigo P. P. Almeida ◽  
Fernanda E. Nascimento ◽  
John Chau ◽  
Simone S. Prado ◽  
Chi-Wei Tsai ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Host Range ◽  
Multilocus Sequence Typing ◽  
Phylogenetic Trees ◽  
Xylella Fastidiosa ◽  
Microsatellite Analysis ◽  
The Other ◽  
Plant Pathogenic Bacterium ◽  
Vector Borne ◽  
Coffee Plants

ABSTRACT Xylella fastidiosa is a vector-borne, plant-pathogenic bacterium that causes disease in citrus (citrus variegated chlorosis [CVC]) and coffee (coffee leaf scorch [CLS]) plants in Brazil. CVC and CLS occur sympatrically and share leafhopper vectors; thus, determining whether X. fastidiosa isolates can be dispersed from one crop to another and cause disease is of epidemiological importance. We sought to clarify the genetic and biological relationships between CVC- and CLS-causing X. fastidiosa isolates. We used cross-inoculation bioassays and microsatellite and multilocus sequence typing (MLST) approaches to determine the host range and genetic structure of 26 CVC and 20 CLS isolates collected from different regions in Brazil. Our results show that citrus and coffee X. fastidiosa isolates are biologically distinct. Cross-inoculation tests showed that isolates causing CVC and CLS in the field were able to colonize citrus and coffee plants, respectively, but not the other host, indicating biological isolation between the strains. The microsatellite analysis separated most X. fastidiosa populations tested on the basis of the host plant from which they were isolated. However, recombination among isolates was detected and a lack of congruency among phylogenetic trees was observed for the loci used in the MLST scheme. Altogether, our study indicates that CVC and CLS are caused by two biologically distinct strains of X. fastidiosa that have diverged but are genetically homogenized by frequent recombination.

Darwin's two competing phylogenetic trees: marsupials as ancestors or sister taxa?

2012 ◽  
Vol 39 (2) ◽  
pp. 217-233 ◽  
Author(s):  
J. David Archibald
Keyword(s):  
Fossil Record ◽  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Charles Darwin ◽  
The Other ◽  
Charles Lyell ◽  
Single Origin ◽  
Molecular Studies ◽  
Richard Owen ◽  
First Time

Studies of the origin and diversification of major groups of plants and animals are contentious topics in current evolutionary biology. This includes the study of the timing and relationships of the two major clades of extant mammals – marsupials and placentals. Molecular studies concerned with marsupial and placental origin and diversification can be at odds with the fossil record. Such studies are, however, not a recent phenomenon. Over 150 years ago Charles Darwin weighed two alternative views on the origin of marsupials and placentals. Less than a year after the publication of On the origin of species, Darwin outlined these in a letter to Charles Lyell dated 23 September 1860. The letter concluded with two competing phylogenetic diagrams. One showed marsupials as ancestral to both living marsupials and placentals, whereas the other showed a non-marsupial, non-placental as being ancestral to both living marsupials and placentals. These two diagrams are published here for the first time. These are the only such competing phylogenetic diagrams that Darwin is known to have produced. In addition to examining the question of mammalian origins in this letter and in other manuscript notes discussed here, Darwin confronted the broader issue as to whether major groups of animals had a single origin (monophyly) or were the result of “continuous creation” as advocated for some groups by Richard Owen. Charles Lyell had held similar views to those of Owen, but it is clear from correspondence with Darwin that he was beginning to accept the idea of monophyly of major groups.

scholarly journals Population Genetic Structure Analysis Reveals Decreased but Moderate Diversity for the Oriental Fire-Bellied Toad Introduced to Beijing after 90 Years of Independent Evolution

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1429
Author(s):  
Yang Teng ◽  
Jing Yang ◽  
Guofen Zhu ◽  
Fuli Gao ◽  
Yingying Han ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Structure Analysis ◽  
Phylogenetic Trees ◽  
Molecular Genetic ◽  
Genetic Research ◽  
Haplotype Diversity ◽  
Botanical Garden ◽  
Source Population ◽  
Independent Evolution ◽  
Loop Region

Detailed molecular genetic research on amphibian populations has a significant role in understanding the genetic adaptability to local environments. The oriental fire-bellied toads (Bombina orientalis) were artificially introduced to Beijing from Shandong Province in 1927, and since then, this separated population went through an independent evolution. To explore the differentiation of the introduced population with its original population, this study analyzed the genetic structure of the oriental fire-bellied toad, based on the mitochondrial genome control region and six microsatellite sites. The results showed that the haplotype diversity and nucleotide diversity of the mitochondrial D-loop region partial sequences of the Beijing Botanical Garden population and the Baiwangshan population were lower than those of the Shangdong Kunyushan population. Microsatellite marker analysis also showed that the observed heterozygosity and expected heterozygosity of the Beijing populations were lower than those of the Kunyushan population. The phylogenetic trees and network diagrams of haplotypes indicated that the three populations were not genetically separated. However, the structure analysis showed a genetic differentiation and categorized the sampling individuals into Beijing and Shandong genetic clusters, which indicated a tendency for isolated evolution in the Beijing population. Although the Beijing populations showed a decline in genetic diversity, it was still at a moderate level, which could maintain the survival of the population. Thus, there is no need to reintroduce new individuals from the Kunyushan source population.

Microsatellite analysis reveals genetic structure of Leishmania tropica

2006 ◽  
Vol 36 (2) ◽  
pp. 237-246 ◽  
Author(s):  
Jan M. Schwenkenbecher ◽  
Thierry Wirth ◽  
Lionel F. Schnur ◽  
Charles L. Jaffe ◽  
Henk Schallig ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Microsatellite Analysis ◽  
Leishmania Tropica

Microsatellite analysis of the genetic structure of captive forest musk deer populations and its implication for conservation

2009 ◽  
Vol 37 (3) ◽  
pp. 166-173 ◽  
Author(s):  
Ting-Long Guan ◽  
Bo Zeng ◽  
Que-Kun Peng ◽  
Bi-Song Yue ◽  
Fang-Dong Zou
Keyword(s):  
Genetic Structure ◽  
Microsatellite Analysis ◽  
Musk Deer

Molecular identification and phylogenetics of local pearl millet cultivars using internal-transcribed spacers of nuclear ribosomal DNA

2021 ◽  
pp. 1-8
Author(s):  
Zainab M. Almutairi
Keyword(s):  
Pearl Millet ◽  
Phylogenetic Trees ◽  
Secondary Structures ◽  
Its2 Sequence ◽  
Internal Transcribed Spacers ◽  
The Other ◽  
Nuclear Ribosomal Dna ◽  
Its2 Region ◽  
Local Cultivars ◽  
Pearl Millet Cultivars

Abstract Local cultivars of pearl millet in Saudi Arabia are known to tolerate extreme heat and drought stress. In the current study, the sequences of internal-transcribed spacers (ITSs) of six pearl millet cultivars were sequenced and analysed to investigate the genetic diversity among the local cultivars. The nucleotide polymorphism, secondary structures and phylogenetics were analysed for ITS sequences of the six local cultivars. The obtained sequences were 772–774 base pairs (bp) in length, including complete sequences of the ITS1–5.8S–ITS2 region and partial sequences of 18S and 26S rRNA. The nucleotide diversity among cultivars was higher in ITS2 sequences than ITS1 sequences. The ITS2 had four variable nucleotide sites in three native cultivars, whereas the ITS1 contained one base insertion. The secondary structures of the ITS1 and 5.8S region were highly conserved among the six cultivars and contained some motifs that are conserved across Viridiplantae. However, the ITS2 secondary structure for the two native cultivars, Sayah and Jazan, was distinct from the other cultivars, which confirms the applicability of the ITS2 sequence in distinguishing between genetically close taxa. Additionally, the phylogenetic analysis of the six investigated cultivars and 31 pearl millet accessions from the NCBI database showed close relationships between the local accessions and NCBI accessions from India and France. However, the local cultivar Sayah appeared to be distinct from the other cultivars in the phylogenetic trees. This study provides insights into the polymorphism within local pearl millet cultivars which is important for the identification and conservation of these cultivars.

A New Sharpshooter Threatens Both Crops and Ornamentals

2000 ◽  
Vol 1 (1) ◽  
pp. 4 ◽  
Author(s):  
Matthew J. Blua ◽  
Phil A. Phillips ◽  
Richard A. Redak
Keyword(s):  
Host Range ◽  
Potential Distribution ◽  
Xylella Fastidiosa ◽  
New Disease ◽  
Leaf Scorch ◽  
Economic Problems ◽  
The Future ◽  
Different Strains ◽  
Large Host ◽  
Almond Leaf Scorch

The glassy-winged sharpshooter (Homalodisca coagulate), an insect that has recently invaded California, and the smoke tree sharpshooter (Homalodisca lacerta) are creating serious new economic problems in both agricultural and ornamental plantings. The greatest threats surround their ability to spread the plantpathogenic bacterium Xylella fastidiosa, which induces Pierce's disease in grapevines, almond leaf scorch disease, and a new disease known as oleander leaf scorch. Because of the potential distribution and large host range of the glassywinged sharpshooter, other diseases caused by different strains of X. fastidiosa may have an even greater impact on the state's agricultural and ornamental landscape industries in the future. Posted 27 June 2000.

scholarly journals Population genetic structure of pedunculate oak (Quercus robur L.) in Belarus according to the analysis of chloroplast DNA

2021 ◽  
pp. 59-70
Author(s):  
Vladimir E. Padutov
Keyword(s):  
Genetic Structure ◽  
Chloroplast Dna ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Quercus Robur ◽  
Phylogenetic Trees ◽  
Rflp Analysis ◽  
Pedunculate Oak ◽  
Maximum Likelihood Methods ◽  
The Republic

Pedunculate oak (Quercus robur L.) is one of the main forest forming species in the Republic of Belarus. Its population genetic structure was formed under the influence of various migration processes. Six chloroplast DNA loci (µdt1, µdt3, µdt4, µcd4, µcd5 and µkk4) were used for the genogeographic study. The material for the analysis was collected in 100 oak forest stands (2325 samples); 18 allelic variants were identified, which are grouped into 17 different combinations (haplotypes). Five of them are widespread (the proportion of occurrence varies from 7 to 48 %, totalling 85 %). The remaining 12 are rare (the proportion of occurrence varies from 1 to 3 %, totalling 15 %). Phylogenetic trees constructed using the nearest neighbour and maximum likelihood methods show the presence of two groups (branches) of haplotypes. One of it comprises 8 variants including 2 dominant haplotypes and the other comprises 9 variants including 3 dominant haplotypes. PCR-RFLP analysis of chloroplast DNA showed that the pedunculate oak in Belarus originates from the Balkan refugium. Haplotype No. 1 (µdt189, µdt3123, µdt4142, µcd494, µcd574, µkk4109) is found almost everywhere in Belarus with the exception of the southwest and northeast, while haplotype No. 8 (µdt189, µdt3121, µdt4142, µcd494, µcd574, µkk4109) is mainly localised in the southwest and northeast. Haplotypes No. 3 (µdt189, µdt3120, µdt4141, µcd494, µcd575, µkk4109) and No. 7 (µdt189, µdt3122, µdt4142, µcd494, µcd574, µkk4109) predominantly found in the west of the country. Haplotype No. 2 (µdt190, µdt3120, µdt4141, µcd495, µcd574, µkk4109) is typical for the southeast.

Fusarium oxysporum f.sp. cubense tropical race 4 (TR4).

2021 ◽  
Author(s):  
Claire Curry
Keyword(s):  
Fusarium Oxysporum ◽  
Host Range ◽  
The Other ◽  
Race 4

Abstract TR4 is one of only six strains strains of F. oxysporum f.sp. cubense (Foc) that attack Cavendish bananas (AAA genome). It is much more aggressive on Cavendish than SR4. TR4 was first observed in Taiwan in 1989 but its importance as an invasive was identified in the 1990s when it was isolated from damaged Cavendish plants in Indonesia and Malaysia (Buddenhagen, 2009). TR4 is considered one of the most destructive Foc strains because it has a wider host range than other strains, attacking the important cultivar Cavendish, but also all the other cultivars that are sensitive to Foc (Cheng et al., 2019).

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