Related Experiment Video
Updated: May 23, 2025
08:56
Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
Published on: July 27, 2018
10.9K
Phylogenetic Analysis of Geminiviruses
1Laboratory of Entomology and Phytopathology, Molecular Plant Virology, State University of the North Fluminense Darcy Ribeiro, Rio de Janeiro, Brazil. ramosrs@uenf.br.
Methods in Molecular Biology (Clifton, N.J.)
|March 11, 2025
Summary
Geminiviridae viruses, known for causing crop losses, have diverse single-stranded DNA genomes. Phylogenetic analysis using coat protein and replication-associated protein sequences helps clarify their evolutionary relationships and diversity.
Area of Science:
- Virology
- Plant Pathology
- Bioinformatics
Background:
- Geminiviridae viruses possess single-stranded, circular DNA genomes within geminate particles.
- These viruses cause significant yield losses in economically important crops globally.
- Molecular characterization and bioinformatics have revealed extensive species diversity within Geminiviridae.
Purpose of the Study:
- To describe methods for reconstructing Geminiviridae phylogenetic relationships.
- To analyze diversity using coat protein (CP), replication-associated protein (Rep) sequences, and full-length genomes.
- To investigate phylogenetic congruence and potential recombination events.
Main Methods:
- Phylogenetic reconstruction using Maximum Likelihood (ML) and Bayesian Inference (BI) approaches.
- Analysis of amino acid sequences for CP and Rep.
- Utilizing full-length nucleotide genome sequences for phylogenetic analysis.
Main Results:
- Phylogenetic trees derived from CP, Rep, and genome sequences showed some topological incongruences.
- Evidence suggests potential inter-genera recombination within the Geminiviridae family.
- Despite incongruences, viruses generally clustered according to established genera.
Conclusions:
- Phylogenetic analyses are crucial for understanding Geminiviridae diversity and evolution.
- Recombination may play a role in the diversification of Geminiviridae.
- Current genus classifications are largely supported by sequence-based phylogenetic studies.
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
5.7K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
5.7K
02:05Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
01:23Phylogeny
43.5K
Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
43.5K
03:21Phylogenetic Trees
45.0K
Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
45.0K
02:33Retroviruses
12.2K
Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
12.2K
00:36Viral Mutations
32.1K
A mutation is a change in the sequence of bases of DNA or RNA in a genome. Some mutations occur during replication of the genome due to errors made by the polymerase enzymes that replicate DNA or RNA. Unlike DNA polymerase, RNA polymerase is prone to errors because it is not capable of “proofreading” its work. Viruses with RNA-based genomes, like HIV, therefore accrue mutations faster than viruses with DNA-based genomes. Because mutation and recombination provide the raw material...
32.1K