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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.

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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A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants

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Nanopore guided annotation of transcriptome architectures.

Jonathan S Abebe¹, Yasmine Alwie², Erik Fuhrmann²

¹Department of Microbiology, New York University School of Medicine, New York, New York, USA.

|July 2, 2024

Summary

We developed NAGATA, a new software tool that uses Nanopore direct RNA sequencing (DRS) data to accurately annotate viral transcriptomes. NAGATA improves the reconstruction of complex transcriptomes, outperforming existing methods for gene-dense viruses.

Keywords:

HAdV-F41 adenovirus annotation coronavirus direct RNA sequencing herpesvirus nanopore transcriptome

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Area of Science:

* Genomics
* Bioinformatics
* Molecular Biology

Background:

* Transcriptome annotation is crucial for understanding organismal biology and transcriptomic analyses.
* Existing annotation software struggles with small, gene-dense viral genomes due to overlapping RNAs and alternative splicing.
* Nanopore direct RNA sequencing (DRS) offers high-resolution, bias-free RNA analysis but requires sophisticated annotation tools.

Purpose of the Study:

* To develop a novel software package for high-resolution transcriptome annotation using DRS data.
* To address the limitations of current annotation tools in gene-dense viral genomes.
* To enable accurate reconstruction of complex transcriptomes, including overlapping and alternative transcripts.

Main Methods:

* Development of the Nanopore Guided Annotation of Transcriptome Architectures (NAGATA) software.
* Utilization of DRS datasets from diverse viruses (adenoviruses, herpesviruses, coronaviruses) and human cells.
* Comparative analysis of NAGATA against existing transcriptome annotation software using synthetic and real data.

Main Results:

* NAGATA demonstrated superior performance in reconstructing both gene-sparse and gene-dense transcriptomes.
* The software achieved high precision and recall across various viral and cellular datasets.
* Applied to human adenovirus type F41, NAGATA generated the first high-resolution annotation, identifying 77 transcripts and 23 proteins.

Conclusions:

* NAGATA is an effective tool for generating high-resolution transcriptome annotations from DRS data.
* The software overcomes challenges in annotating complex viral transcriptomes.
* This work provides a valuable resource for studying viruses like HAdV-41 and advancing transcriptomic research.