Unveiling axolotl transcriptome for tissue regeneration with high-resolution annotation via long-read sequencing

Area of Science:

• Regenerative Biology
• Genomics
• Molecular Biology

Background:

• Axolotls exhibit remarkable regenerative capabilities, crucial for limb regrowth.
• Understanding the axolotl transcriptome is key to elucidating regenerative mechanisms.
• Current transcriptome annotations are limited, obscuring the function of unannotated transcripts in regeneration.

Purpose of the Study:

• To enhance axolotl transcriptome annotation using long-read sequencing.
• To identify novel transcripts and their potential roles in axolotl regeneration.
• To investigate alternative splicing events and their significance in regenerative pathways.

Main Methods:

• Employed long-read sequencing for full-length RNA transcript observation.
• Utilized short-read sequencing data for transcript quantification.
• Performed single-cell transcriptomic analysis to localize novel isoforms.

Main Results:

• Identified 222 novel gene loci and 4775 novel transcripts.
• Discovered novel homologs, potential functional proteins, noncoding RNAs, and alternative splicing events.
• Found novel transcripts implicated in cell cycle regulation, musculoskeletal development, and regeneration, predominantly in chondrocytes and mature tissue cells.

Conclusions:

• Novel transcripts and alternative splicing variants significantly advance understanding of the axolotl transcriptome.
• These findings provide new perspectives on the molecular underpinnings of axolotl regeneration.
• The identified transcripts likely play vital roles in the axolotl's robust regenerative capacities.