Related Experiment Video
Updated: Jun 29, 2025
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
9.5K
Karyotype and LTR-RTs analysis provide insights into oak genomic evolution
Rui-Bin Cao1, Ran Chen1, Ke-Xin Liao1
1The Laboratory of Forestry Genetics, Central South University of Forestry and Technology, 410004, Changsha, Hunan, China.
BMC Genomics
|April 2, 2024
Summary
Oak karyotype evolution involved chromosome rearrangements after ancient triplication. Long terminal repeat retrotransposons (LTR-RTs) amplified recently, varying in abundance and suppressing gene expression, offering insights into oak evolutionary history.
Area of Science:
- Genomics
- Evolutionary Biology
- Plant Science
Background:
- Whole-genome duplication and long terminal repeat retrotransposons (LTR-RTs) amplification are key drivers of speciation and adaptation.
- Understanding karyotype and LTR-RTs evolution is crucial for deciphering evolutionary history.
- Oaks, a dominant Northern Hemisphere forest lineage, were studied to compare karyotype and LTR-RTs evolution.
Purpose of the Study:
- To compare karyotype and LTR-RTs evolution in eight oak genomes.
- To investigate the impact of chromosomal evolution and LTR-RTs amplification on oak diversification.
- To understand the functional role of LTR-RTs in gene expression and genomic organization.
Main Methods:
- Comparative genomics analysis of eight oak species.
- Karyotype projection to reconstruct chromosomal evolution.
- Identification and quantification of full-length LTR-RTs across oak genomes.
- Analysis of LTR-RTs insertion sites and their impact on gene expression.
Main Results:
- Oak karyotype evolution was conservative, with modern chromosomes formed by fusions, fissions, and rearrangements post-triplication.
- Species-specific rearrangements suggest fragments preserved by natural selection.
- 441,449 full-length LTR-RTs were identified, with higher abundance in section Cyclobalanopsis.
- Recent LTR-RTs amplification caused significant variation in abundance and composition.
- LTR-RTs insertion suppresses gene expression, particularly in gene regions, and is enriched in centromere and rearrangement regions.
- Distinct centromeric repeat units were found on different *Q. glauca* chromosomes.
Conclusions:
- Oak karyotypes are shaped by chromosome fusions and arm exchanges.
- Recent LTR-RTs amplification significantly impacts their composition and abundance.
- LTR-RTs retrotransposition suppresses gene expression and localizes to centromeric and rearrangement regions.
- This study provides novel insights into oak karyotype evolution and LTR-RTs organization, amplification, and function.
Keywords:
Chromosomal structureGenomic evolutionKaryotypeLong terminal repeat retrotransposonsOakWhole-genome duplicationMore Related Videos
10:40Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine
Published on: December 22, 2017
10.5K
13:03Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens
Published on: March 8, 2018
10.6K
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
03:08LTR Retrotransposons
17.5K
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
17.5K
02:37Gene Duplication and Divergence
6.1K
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...
6.1K
03:18Non-LTR Retrotransposons
11.5K
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.5K
02:31Synteny and Evolution
3.3K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.3K
02:05Gene Evolution - Fast or Slow?
7.1K
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...
7.1K