Related Experiment Video
Updated: Sep 13, 2025
13:03
Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
10.7K
PlastidHub: An integrated analysis platform for plastid phylogenomics and comparative genomics
Na-Na Zhang1,2, Gregory W Stull3, Xue-Jie Zhang1,2
1College of Life Sciences, Shandong Normal University, Ji'nan 250358, China.
Plant Diversity
|July 30, 2025
Summary
PlastidHub is a new web application that simplifies the analysis of plant plastid genomes. This tool aids botanists and evolutionary biologists in phylogenetic studies by improving annotation and comparative genomics.
Area of Science:
- Plant molecular biology
- Evolutionary biology
- Bioinformatics
Background:
- The plastid genome (plastome) is crucial for plant phylogeny and evolution research.
- Annotating and utilizing plastome sequences efficiently remains a challenge.
- A streamlined pipeline for plastome annotation, phylogenetic reconstruction, and comparative genomics is needed.
Purpose of the Study:
- To develop PlastidHub, a novel web application for analyzing plastome sequences.
- To provide innovative tools for standardization, annotation, and comparative genomics.
- To facilitate research for botanists and evolutionary biologists.
Main Methods:
- Development of a cloud-based web application, PlastidHub.
- Implementation of novel functionalities including structure standardization, flexible annotation, and quantitative completeness assessment.
- Integration of tools for sequence extraction, marker screening, and gene-level visual comparison.
Main Results:
- PlastidHub offers cloud-based, user-friendly tools requiring no specialized computational skills.
- Key features include standardization of quadripartite structure, improved annotation consistency, and quantitative completeness assessment.
- The platform supports diverse sequence extraction, intelligent marker screening, and visual gene comparison.
Conclusions:
- PlastidHub streamlines plastome analysis, enhancing annotation, phylogenetic reconstruction, and comparative genomics.
- Its ease of use and comprehensive functionalities will benefit botanists and evolutionary biologists.
- The platform aims to improve and expedite research utilizing plant organellar genomes.
Related Concept Videos
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
13.5K
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...
13.5K
02:54Evolutionary Relationships through Genome Comparisons
6.2K
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...
6.2K
01:28Plasmids
125
Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
125
02:32Plasmodesmata
33.2K
The organs in a multicellular organism’s body are made up of tissues formed by cells. To work together cohesively, cells must communicate. One way that cells communicate is through direct contact with other cells. The points of contact that connect adjacent cells are called intercellular junctions.
33.2K
01:08The Anatomy of Chloroplasts
5.7K
Green algae and plants, including green stems and unripe fruit, harbor specialized organelles called chloroplasts to carry out photosynthesis. They coordinate both stages of photosynthesis — the light-dependent reactions and the light-independent reactions. The light-dependent reactions use sunlight to release oxygen and produce chemical energy in the form of ATP and NADPH, and the light-independent reactions capture CO2 and use ATP and NADPH to produce sugar.
Structure of...
Structure of...
5.7K
02:19Export of Mitochondrial and Chloroplast Genes
3.8K
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...
3.8K