The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation

BMC Genomics, 2015 · DOI: 10.1186/s12864-015-1354-2 · Published: March 11, 2015

Simple Explanation

The brown ghost knifefish is a valuable model for neuroscience and biology research, particularly in areas like neural behavior, regeneration, and brain aging. However, there's a lack of genomic resources for this species. This study reports the assembly and annotation of the knifefish transcriptome, identifying protein-coding and non-coding RNA sequences. Proteomics confirmed the translation of numerous transcripts. This transcriptome assembly provides a comprehensive overview of RNA expressed in the central nervous system, which helps in understanding the unique traits of knifefish, like their regenerative capacity and negligible brain senescence.

Study Duration

Not specified

Participants

10 adult male and female knifefish for sequencing and 26 for proteomics

Evidence Level

Not specified

Key Findings

1
The de novo assembly uncovered 42,459 unique contigs containing at least a partial protein-coding sequence based on alignment to Actinopterygii sequences.
2
Many non-coding RNA sequences were identified and annotated, including lincRNA, miRNA, snRNA, and snoRNA.
3
Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants.

Research Summary

This study presents the first annotated de novo transcriptome assembly for Apteronotus leptorhynchus, offering a broad view of RNA expressed in the central nervous system. The assembly includes substantial coverage of protein-coding and non-coding transcripts, which will enable the development of better tools to understand the mechanisms underlying unique characteristics of the knifefish model system. The combination of transcriptomics and proteomics enhances shotgun proteomics identifications and confirms ORF assignment from transcriptome assembly experiments.

Practical Implications

Understanding Neurobiological Aspects

The availability of a targeted CNS reference transcriptome will provide novel molecular tools to explore the underlying cellular mechanisms of adult neurogenesis, neuronal regeneration, and the neural basis of behavior.

Phylogenetic Studies

The sequence information provided can be employed to study phylogenetic relationships and various aspects of CNS evolution in vertebrates.

Future Research

Future studies, using libraries from different tissues and developmental stages, will further improve the quality and applicability of the A. leptorhynchus assembly.

Study Limitations

1
Libraries were prepared from only the CNS of A. leptorhynchus, which may limit coverage compared to using other tissues.
2
The relatively low coverage of antisense transcripts from D. rerio may be due to lack of sufficient sequencing depth.
3
Some transcript reconstruction of low-expressed transcripts may be incomplete.

Your Feedback

Was this summary helpful?

Back to Neurology