# The de novo transcriptome of the freshwater copepod Cyclops abyssorum tatricus reveals high-elevation adaptation

## TL;DR

This study creates a transcriptome for a copepod species that lives in alpine lakes, revealing genes linked to adaptation to cold environments.

## Contribution

The paper provides a new de novo transcriptome assembly for Cyclops abyssorum tatricus, enriched with cold acclimation genes.

## Key findings

- The transcriptome assembly includes 52,521 contigs with a BUSCO score of 80.7%.
- Gene ontology analysis showed enrichment in cellular processes and signaling annotations.
- The assembly is enriched for cold acclimation genes, indicating adaptation to high-elevation environments.

## Abstract

Copepods, small aquatic crustaceans, are one of the most abundant zooplankton in the world. These animals play a critical ecological role in aquatic ecosystems such as oceans, streams, or, as in this study, alpine lakes. In these ecosystems, copepods have adapted to stressful and dynamic environments, a process which can be investigated via comparative transcriptomics. An assembled transcriptome is a pre-requisite to applying transcriptomic tools in physiological research, but there are few transcriptome assemblies available for copepods. To address this gap, we assembled a de novo transcriptome of Cyclops abyssorum tatricus by merging Pacific Bioscience long reads from copepods collected in two lakes at two different time points. The final assembly consisted of 52,521 contigs with a BUSCO score of 80.7%. We annotated a total of 26,255 (49.99%) protein sequences using the eggNOG database. Gene ontology analyses revealed that most gene annotations were involved in cellular processes and signaling (34.61%). Comparisons with two other copepod species showed that the transcriptome assembly of C. abyssorum tatricus is enriched for cold acclimation genes, consistent with its long-term adaptation to cold water environments. This de novo transcriptome will enable comparative transcriptomic studies in this species, allowing us to investigate physiological adaptations to alpine environments.

The online version contains supplementary material available at 10.1038/s41598-026-46084-x.