Unlocking the Genetic Blueprint of the River Nerite Snail

Jim Crocker
9th March, 2024

Unlocking the Genetic Blueprint of the River Nerite Snail

Image Source: Natural Science News, 2024

Key Findings

  • Scientists assembled the first genome of the Baltic snail, Theodoxus fluviatilis, to study how it adapts to different salinities
  • The draft genome is fragmented but contains 74.3% of expected genes, aiding research into the snail's salinity tolerance
  • With 21,220 protein-coding genes identified, the genome provides a foundation for evolutionary studies in snails
Understanding how different species adapt to their environments is a key question in biology. The neritid snail Theodoxus fluviatilis, which lives in varying salinity conditions from the Baltic Sea to European lakes, provides a unique opportunity to study such adaptations. The University of Greifswald has taken a significant step in this research by presenting an annotated draft genome assembly for T. fluviatilis[1]. The genome of an organism is like its biological instruction manual. It contains all the genetic information necessary for the organism to develop, survive, and reproduce. Sequencing and assembling a genome is a complex process, typically involving reading small fragments of DNA and piecing them together to form a complete picture. This study's draft genome assembly is a critical resource for understanding the genetic basis of how T. fluviatilis tolerates different salinity levels, a trait that is not solely due to phenotypic plasticity, which is the ability of an organism to change its phenotype in response to environmental changes. The researchers used a combination of PacBio long reads and Illumina short reads, two different DNA sequencing technologies, to achieve a comprehensive view of the snail's genetic makeup. They also incorporated transcriptomic data, which are the RNA transcripts produced from the DNA, providing insight into which genes are active. Despite the challenges in isolating high-quality DNA from this species, the team managed to assemble a genome that is roughly 1045 kilobases in size. However, the genome remains highly fragmented, meaning there are many gaps where the exact sequence is unknown. To assess the quality of the genome assembly, the researchers used a tool called BUSCO[2], which checks for the presence of expected genes that are generally found in single copies in an organism's genome. The T. fluviatilis genome was found to be moderately high in complete gene content, with 74.3% of these 'benchmark' genes identified as complete and only a small portion duplicated or missing. This indicates that, despite the fragmentation, the assembly is still a valuable resource for genetic studies. The genome assembly revealed 21,220 protein-coding genes, which are genes that contain instructions for building proteins, the molecules that perform most life functions. This number is comparable to what is found in related species. The quality of these gene annotations was also validated using BUSCO, showing a majority of the genes as complete. This work builds on previous research[3] that sequenced and annotated the mitochondrial genomes of five brackish water neritids, including species from the same family as T. fluviatilis. The mitochondrial genome is the DNA located in the mitochondria, which are the energy-producing structures within cells, and is separate from the nuclear genome sequenced in this study. The earlier study provided insights into the evolutionary history of these snails and their differentiation during the Cenozoic period. The current genome assembly for T. fluviatilis will further enhance our understanding of the evolutionary position of Neritidae and the genetic underpinnings of their adaptation to different salinities. Additionally, this research complements tools such as BRAKER[4], which are used for annotating protein-coding genes in eukaryotic genomes. While BRAKER uses RNA-seq data or cross-species protein databases to predict protein-coding genes, the T. fluviatilis genome project incorporated both types of evidence to annotate genes. This approach likely contributed to the high completeness score of the gene annotations. The T. fluviatilis genome assembly is not only a step forward for the study of salinity tolerance in this species but also sets a foundation for comparative evolutionary studies across Gastropoda, as this is the first genome assembly for the basal snail family Neritidae. The work done by the University of Greifswald provides a valuable genetic resource that can be used to investigate the physiological mechanisms of osmoregulation—the process by which organisms maintain the proper balance of salts and water in their cells—across isolated populations with different salinity tolerances. In conclusion, the draft genome of Theodoxus fluviatilis represents a significant advancement in understanding the genetics behind environmental adaptation in snails. It paves the way for future research into the evolutionary biology of the Neritidae family and the mechanisms of osmoregulation in response to salinity changes.

GeneticsMarine BiologyEvolution

References

Main Study

1) A draft genome of the neritid snail Theodoxus fluviatilis.

Published 6th March, 2024

https://doi.org/10.1093/g3journal/jkad282

Related Studies

2) BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes.

https://doi.org/10.1093/molbev/msab199

3) Sequence comparison of the mitochondrial genomes of five brackish water species of the family Neritidae: Phylogenetic implications and divergence time estimation.

https://doi.org/10.1002/ece3.8984

4) TSEBRA: transcript selector for BRAKER.

https://doi.org/10.1186/s12859-021-04482-0


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