Related Experiment Video
Updated: Sep 9, 2025
10:41
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
Published on: May 9, 2017
9.3K
EASYstrata: an all-in-one workflow for genome annotation and genomic divergence analysis
Quentin Rougemont1, Elise Lucotte1, Loreleï Boyer1
1Ecologie Société et Evolution, CNRS, Universite Paris-Saclay, AgroParisTech, 91198 Gif-sur-Yvette, France.
NAR Genomics and Bioinformatics
|September 2, 2025
Summary
We introduce EASYstrata, a new workflow for evolutionary analyses that simplifies genome annotation and the detection of recombination suppression. This tool aids in understanding genomic rearrangements and transposable element accumulation across species.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Availability of new reference genomes and transcriptomes presents opportunities for evolutionary studies.
- Challenges remain in genome annotation, evolutionary inference, and methodological standardization.
Purpose of the Study:
- To develop a standardized, user-friendly workflow for evolutionary analyses.
- To facilitate the detection of recombination suppression and its genomic consequences.
Main Methods:
- The EASYstrata workflow integrates multiple bioinformatic tools.
- It detects transposable elements, annotates genomes, infers gene orthology, computes sequence divergence, and identifies evolutionary strata and structural rearrangements.
Main Results:
- EASYstrata was applied to reannotate 42 genomes from *Microbotryum* fungi.
- The workflow successfully recovered previously described evolutionary strata in plant and animal case studies.
Conclusions:
- EASYstrata streamlines the analysis of recombination suppression and its impact on genome evolution.
- The workflow is applicable to any haplotype pair and beneficial for studying non-model species with newly available phased diploid genomes.
More Related Videos
Related Concept Videos
03:36Genome Annotation and Assembly
19.3K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
19.3K
02:54Evolutionary Relationships through Genome Comparisons
6.1K
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...
6.1K
02:37Gene Duplication and Divergence
6.3K
The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
6.3K
02:05Gene Evolution - Fast or Slow?
7.4K
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...
7.4K