Related Experiment Video
Updated: May 28, 2026
10:23
A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
Published on: July 11, 2025
RhoMitoAnnotator and Polypods, Bioinformatics Tools for the Rhodiola Mitochondrial Gene Assembly, Annotation and
Erhuan Zang1,2, Yanda Zhu1, Tingyu Ma2
1State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.
International Journal of Molecular Sciences
|May 27, 2026
Summary
This study created a Rhodiola mitochondrial gene atlas and annotation tool, improving analysis of plant mitochondrial genomes. It reveals evolutionary insights and structural variations in Rhodiola species.
Area of Science:
- Plant genomics
- Mitochondrial DNA analysis
- Bioinformatics
Background:
- Plant mitochondrial genomes exhibit structural dynamism and annotation challenges.
- Accurate annotation of mitochondrial protein-coding genes (PCGs) is crucial for evolutionary studies.
- Existing methods struggle with complex features like trans-splicing and RNA editing in plant mitochondria.
Purpose of the Study:
- To develop a high-confidence mitochondrial reference library for Rhodiola.
- To create an accurate annotation pipeline (RhoMitoAnnotator) for plant mitochondrial genomes.
- To analyze mitochondrial genome structure and evolutionary patterns in Rhodiola.
Main Methods:
- Integrated transcriptomic data, public resources, and experimental validation for reference library construction.
- Developed novel algorithms (EBAnno, REAnno, NCAnno) for annotating trans-splicing, RNA editing, and non-canonical codons.
- Employed long-read sequencing and developed the Polypods pipeline for scalable short-read data analysis.
Main Results:
- Established a curated mitochondrial gene atlas for Rhodiola, defining 30 PCGs with corrected annotations.
- Completed and re-annotated mitogenomes of multiple Rhodiola species, identifying widespread structural misannotations.
- Identified variant genes, stop codon variations, and supported evolutionary hypotheses regarding dioecy in Rhodiola.
Conclusions:
- The RhoMitoAnnotator provides a robust framework for plant mitochondrial genome annotation.
- The study offers a comprehensive understanding of Rhodiola mitochondrial genome structure and evolution.
- The developed analytical framework is adaptable for other plant lineages with database and parameter optimization.
Related Concept Videos
03:36Genome Annotation and Assembly
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.
01:27Diversity of Protists III
Rhizaria are a diverse group of unicellular protists characterized by their threadlike cytoplasmic extensions known as pseudopodia. These structures aid in both locomotion and feeding, giving Rhizaria an amoeboid appearance. Their amoeboid morphology once led to taxonomic confusion, but molecular phylogenetics has clarified their evolutionary placement and emphasized their shared use of pseudopodia despite divergent lineages.This clade comprises diverse lineages such as Chlorarachniophyta,...
02:19Export of Mitochondrial and Chloroplast Genes
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred irrespective...
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
01:29Modern Molecular Taxonomy
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
02:54Evolutionary Relationships through Genome Comparisons
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...