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Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

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...

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Updated: Aug 24, 2025

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

EchinoDB: an update to the web-based application for genomic and transcriptomic data on echinoderms.

Varnika Mittal¹, Robert W Reid², Denis Jacob Machado²

¹Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, Charlotte, NC, 28223, USA. vmittal@uncc.edu.

BMC Genomic Data

|October 24, 2022

Summary

This summary is machine-generated.

EchinoDB v2.0 offers updated genomic and transcriptomic data for echinoderms, enhancing research in phylogenetics and developmental biology. This new version includes new datasets and cloud-based accessibility for broader scientific discovery.

Keywords:

Database Echinoderms Echinoids Gene family Genome Mutable collagenous tissue Notch Ophiuroids Orthocluster Ortholog Paralog Spicule matrix proteins Tensilin Transcriptome Wnt

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Area of Science:

Genomics
Developmental Biology
Echinoderm Research

Background:

EchinoDB is a database for echinoderm genomic and transcriptomic data.
The initial version contained 749,397 orthologous and paralogous transcripts.
It was first released in 2016 and implemented in GO on a local server.

Purpose of the Study:

To release an updated version of EchinoDB (v2.0) with enhanced features and data.
To provide researchers with improved access to echinoderm genomic and transcriptomic information.
To facilitate research in areas such as phylogenetics, developmental biology, and regeneration.

Main Methods:

Incorporated new RNA-Seq data for Ophioderma brevispinum and genomic assembly data for Lytechinus variegatus.
Enabled keyword searches for annotated data and updated SequenceServer for Basic Local Alignment Search Tool (BLAST) searches.
Re-implemented the database using R Shiny and migrated to a cloud-based infrastructure for improved reliability and scalability.

Main Results:

EchinoDB v2.0 now includes comprehensive genomic and transcriptomic data for key echinoderm species.
Enhanced search functionalities (keyword and BLAST) and data download in FASTA format are available.
The database runs on a cloud platform, ensuring better accessibility and performance.

Conclusions:

EchinoDB v2.0 supports diverse research fields including phylogenetics, developmental biology, genomics, physiology, neurobiology, and regeneration.
The database aids in studying signaling pathways in tissue regeneration and the conservation of echinoderm-specific proteins.
It enables investigation into the presence of biomineralization proteins and tensilin across the echinoderm phylum.