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RNA-seq

RNA-seq

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...

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Updated: May 25, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

Comprehensive analysis of Metacrinus rotundus full length transcriptome.

Zhong Li^1,2, Yue Dong^1,2, Xuebao He³

¹College of Environmental Science and Engineering, Ocean University of China, Qingdao, 266100, China.

Scientific Reports

|February 25, 2025

Summary

This study reveals the transcriptome of Metacrinus rotundus, a modern stalked crinoid. It identifies novel genes, long non-coding RNAs, and transposable elements, offering insights into crinoid evolution.

Keywords:

Single-molecule real-time Stalked crinoid Transposable elements

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Last Updated: May 25, 2025

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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Published on: June 24, 2021

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Marine Biology
Evolutionary Biology
Genomics

Background:

Modern stalked crinoids are ancestral echinoderms, crucial for understanding echinoderm evolution.
Metacrinus rotundus represents a key species for investigating crinoid evolutionary history.

Purpose of the Study:

To characterize the transcriptome of the modern stalked crinoid Metacrinus rotundus.
To provide a valuable genetic resource for studying crinoid adaptive evolution.

Main Methods:

Utilized Pacific Biosciences single-molecule real-time (SMRT) long-read sequencing (Iso-Seq) to generate full-length transcripts.
Analyzed 160,849 full-length transcripts, including annotation, identification of novel genes, long non-coding RNAs (LncRNAs), simple sequence repeats (SSRs), and transcription factors (TFs).

Main Results:

Generated a comprehensive M. rotundus transcriptome with 160,849 full-length transcripts, 110,859 annotated.
Identified 71,740 LncRNAs, 57,548 SSRs, and 3,486 TFs, noting higher proportions of zf-CCCH and TF_Otx TFs and trinucleotide SSRs compared to other echinoids.
Discovered that transposable elements (TEs), particularly RNA transposons, constitute a significant portion of the transcriptome.

Conclusions:

The study provides a detailed characterization of the M. rotundus transcriptome.
This research offers a significant genetic resource for future studies on adaptive evolution in crinoids and other echinoderms.