Related Experiment Video
Updated: Aug 16, 2025
07:09
A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
9.7K
Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution
Chunyan Chen1, Yuan Yin1, Haorong Li1
1School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
Science Bulletin
|December 22, 2022
Summary
Researchers identified 1064 ruminant-specific genes, revealing their role in rumen evolution and development. These new genes, alongside older ones, shaped this unique mammalian organ, offering insights into organogenesis.
Area of Science:
- Genomics
- Evolutionary Biology
- Mammalian Physiology
Background:
- Ruminants possess unique morphological traits, notably the rumen, crucial for their ecological success.
- Species-specific or lineage-specific genes, termed new genes, are recognized drivers of phenotypic evolution across mammals.
Purpose of the Study:
- To identify and characterize ruminant-specific genes using newly assembled high-quality genomes.
- To investigate the evolutionary patterns and expression profiles of these new genes in ruminants.
- To understand the contribution of both new and old genes to rumen evolution and development.
Main Methods:
- Genome assembly of representative ruminant species.
- Comparative genomics to identify ruminant-specific genes.
- Analysis of gene evolutionary patterns and tissue-specific expression (including rumen development).
- Identification of genes under positive selection, such as the PRD-SPRRII family.
Main Results:
- Identification of 1064 ruminant-specific genes with evolutionary and expression patterns similar to new genes in primates and rodents.
- New genes predominantly arise from gene duplication, show expression in testes and immune tissues, and are depleted in the adult brain.
- While most rumen-expressed genes are ancient (pre-split), some new genes contribute significantly to rumen development, particularly the PRD-SPRRII gene family, which is under positive selection.
Conclusions:
- The study provides novel ruminant genomes and insights into the evolution of new mammalian organs.
- Ruminant-specific genes, including those involved in rumen development, play a significant role in the evolution of this specialized digestive organ.
- The PRD-SPRRII gene family's dynamic expression during rumen development suggests a key role in forming the rumen's keratinized surface.
More Related Videos
Related Concept Videos
02:05Gene Evolution - Fast or Slow?
7.3K
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...
7.3K
03:21Genome Size and the Evolution of New Genes
8.1K
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
8.1K
00:43Bacterial RNA Polymerase
29.9K
Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
In most genes, the transcription site is a single base present upstream of the coding sequence. Though RNAP is a catalytically efficient enzyme, it does not recognize...
29.9K
01:53Bacterial Transcription
28.9K
RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
Transcription can be divided into three main stages, each involving distinct DNA sequences to guide the polymerase. These are:
28.9K
02:24Ribosome Profiling
3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
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