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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish.

Chun-Hsi Tso¹, Jen-Leih Wu², Ming-Wei Lu³

¹Department of Aquaculture, National Taiwan Ocean University, No.2, Beining Rd., Zhongzheng Dist, Keelung City, 20224, Taiwan.

BMC Bioinformatics

|May 6, 2020

Summary

Blast2Fish offers a new way to annotate fish transcriptome data without needing pre-defined gene tags. This reference-based method improves functional enrichment analysis for non-model teleost fish studies.

Keywords:

Functional enrichment analysis Non-model organism RNA-Seq Transcriptome

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Area of Science:

Genomics
Bioinformatics

Background:

Next-generation sequencing and de novo assembly are valuable for non-model organism studies, particularly fish.
Functional annotation of assembled sequences is crucial but challenging due to limited genomic data and database limitations for non-model species.
Conventional annotation methods using Basic Local Alignment Search Tool (BLAST) and Gene Ontology (GO) analysis often lack sufficient pre-defined tags for non-model organisms.

Purpose of the Study:

To develop a novel approach for functional enrichment analysis of transcriptome data from non-model teleost fish.
To overcome the limitations of pre-defined gene tags in sequence annotation for non-model species.
To improve the accuracy and comprehensiveness of gene function annotation in fish genomics.

Main Methods:

Introduced Blast2Fish, a reference-based functional enrichment analysis pipeline.
Instead of relying on a single top BLAST hit and a pre-defined gene-to-tag database, Blast2Fish analyzes 500 BLAST hits.
Biological terms are extracted from related PubMed articles associated with these hits and used for annotation.

Main Results:

Blast2Fish successfully provided meaningful annotations for non-model fish transcriptome data.
The method demonstrated efficacy in identifying relevant biological terms, particularly for immunology-related topics.
The reference-based strategy proved effective in annotating sequences without requiring pre-existing gene-specific tags.

Conclusions:

Blast2Fish presents a novel and effective strategy for annotating sequences from non-model fish.
The reference-based approach facilitates gene functional enrichment analysis by circumventing the need for pre-defined tags.
This method significantly benefits research on non-model teleost fish, enhancing our understanding of their gene functions.