Differences in non-LTR retrotransposons within C. elegans and C. briggsae genomes

Area of Science:

• Genomics
• Molecular Evolution
• Comparative Genomics

Background:

• Non-LTR retrotransposons are mobile genetic elements with significant roles in genome evolution.
• The Sam/Frodo family is a notable group of non-LTR retrotransposons found in nematodes.

Purpose of the Study:

• To conduct a comparative genomic analysis of the Sam/Frodo retrotransposon family in Caenorhabditis elegans and Caenorhabditis briggsae.
• To investigate the evolutionary dynamics and functional potential of these elements in two related nematode species.

Main Methods:

• Genome-wide analysis of non-LTR retrotransposon sequences.
• Comparative sequence analysis to identify subfamily divergence and functional elements.
• Phylogenetic analysis and assessment of selection pressures.

Main Results:

• C. briggsae possesses 60 Sam/Frodo elements, including a new 'Merry' subfamily, whereas C. elegans has over 1000 elements.
• C. briggsae elements are shorter and less complete, lacking functional ORF1 and having only one functional reverse transcriptase gene.
• Evidence of purifying selection on reverse transcriptase in master/leader elements was observed in both species, despite low copy numbers in C. briggsae.
• Sam elements in C. elegans are most abundant, possess functional ORF1, and exhibit higher GC content, suggesting increased transcription.

Conclusions:

• Significant differences exist in the abundance, completeness, and potential functionality of Sam/Frodo retrotransposons between C. elegans and C. briggsae.
• The lack of functional ORF1 and limited reverse transcriptase repertoire in C. briggsae likely contributes to the reduced size and integrity of its retrotransposon populations.
• Despite variations, conserved selection pressures on key retrotransposon genes highlight their evolutionary importance in both nematode genomes.