Related Experiment Video
Updated: Oct 16, 2025
06:34
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
8.5K
Data integration and evolutionary analysis of long non-coding RNAs in 25 flowering plants
Shiye Sang1,2, Wen Chen1, Di Zhang1,2
1CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, 666303, Yunnan, China.
BMC Genomics
|October 15, 2021
Summary
This study analyzed the evolutionary history of long non-coding RNAs (lncRNAs) in 25 flowering plants, revealing conserved lncRNAs have distinct characteristics and functions. These findings advance our understanding of plant lncRNA evolution and function.
Area of Science:
- Plant biology
- Genomics
- Evolutionary biology
Background:
- Long non-coding RNAs (lncRNAs) are crucial for plant biological processes.
- Current research primarily focuses on lncRNA identification and function, neglecting evolutionary history.
- Investigating lncRNA evolution requires integrating large plant lncRNA datasets.
Purpose of the Study:
- To conduct a large-scale evolutionary analysis of lncRNAs across 25 flowering plant species.
- To identify and categorize lncRNAs, focusing on orthologous relationships and conservation.
- To characterize conserved lncRNAs in Arabidopsis thaliana and infer their potential functions.
Main Methods:
- Integrated large-scale lncRNA data from 25 flowering plants.
- Identified 199,796 high-confidence lncRNAs and grouped them into 5,497 orthologous families.
- Analyzed sequence conservation, characteristics, and expression patterns of lncRNAs in Arabidopsis thaliana.
Main Results:
- Identified nearly 200,000 lncRNAs across 25 species, forming 5,497 orthologous families.
- Conserved lncRNAs in Arabidopsis thaliana exhibit more exons, longer sequences, higher expression, and lower tissue specificity than non-conserved ones.
- Functional annotation suggests conserved lncRNAs are involved in autophagy, locomotion, cell cycle, and tissue-specific growth and development.
Conclusions:
- A comprehensive evolutionary overview of plant lncRNAs, including origin, conservation, and orthology, was established.
- Conserved lncRNAs in Arabidopsis thaliana possess distinct characteristics and functions compared to non-conserved lncRNAs.
- This study provides a foundation for deeper investigations into plant lncRNA evolution and function.
Keywords:
Arabidopsis thalianaCo-expression networkConservationEvolutionary analysisFlowering plantslncRNAsMore 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
10.7K
07:09A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
Published on: May 28, 2021
9.9K
Related Concept Videos
02:39lncRNA - Long Non-coding RNAs
9.0K
In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
9.0K
02:54Evolutionary Relationships through Genome Comparisons
6.5K
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...
6.5K
03:21RNA-seq
10.5K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.5K
02:18Alternative RNA Splicing
22.0K
Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
22.0K
02:05Gene Evolution - Fast or Slow?
7.6K
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...
7.6K
02:02Cis-regulatory Sequences
10.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
10.9K