Evolution of SL-RNA Genes and Their Splicing Targets in Parasitic Flatworms

Area of Science:

• Molecular Biology
• Genomics
• Parasitology

Background:

• Spliced leader (SL) trans-splicing is crucial for mRNA processing in eukaryotes, particularly in parasitic flatworms.
• Previous characterization of SL trans-splicing in flatworms has been limited to single-species studies, lacking a broad phylogenetic perspective.

Purpose of the Study:

• To conduct a comprehensive analysis of SL trans-splicing across 24 cestode and trematode species.
• To identify SL-RNA sequences, splicing acceptor transcripts, and sites within these species.
• To explore the evolutionary patterns and usage of SL trans-splicing in flatworms.

Main Methods:

• Analysis of genomic and transcriptomic data from 24 flatworm species.
• Identification of SL-RNA sequences and their associated splicing sites.
• Comparative analysis of SL trans-splicing patterns across different species and with other organisms like nematodes.

Main Results:

• A conserved evolutionary pattern of SL-RNA loci was identified in most flatworms, with divergence in some species.
• No target specialization was observed even in species with divergent SL-RNAs.
• SL trans-splicing was detected in a limited proportion of mRNAs (<31%) across all species, with extensive use of cis-splicing acceptor sites.
• Ancestral SL trans-splicing sites were found in conserved genes and putative operons shared between cestodes and trematodes.

Conclusions:

• Flatworm SL trans-splicing exhibits a distinct pattern compared to nematodes, characterized by conserved evolution, limited usage, and lack of target specialization.
• The findings provide insights into the evolution and functional significance of SL trans-splicing in parasitic flatworms.
• Shared ancestral SL trans-splicing sites suggest conserved gene regulation mechanisms in early flatworm evolution.