Evolution of transcript structure and base composition of rDNA expansion segment D3 in ticks

Area of Science:

• Molecular Biology
• Genetics
• Acarology

Background:

• The ribosomal DNA (rDNA) 28S gene's expansion segment D3 is a target for phylogenetic studies.
• Understanding sequence variation and structural constraints in tick rDNA can inform species identification and evolutionary analyses.

Purpose of the Study:

• To sequence and analyze the rDNA 28S gene expansion segment D3 and flanking H14 stem in six Ixodes tick species.
• To investigate sequence variation, length differences, and secondary structure evolution within this gene segment across different tick species.

Main Methods:

• DNA sequencing of the rDNA 28S gene expansion segment D3 and H14 stem in six Ixodes species.
• Sequence alignment and comparative analysis to determine sequence identity, length variation, and mutation patterns.
• Secondary structure prediction to assess the impact of sequence changes on RNA conformation.

Main Results:

• Sequence similarity among tick species ranged from 66% to 97%, with significant length variation (approx. 60 bases difference) attributed to deletions in I. persulcatus.
• Secondary structure analysis revealed conserved low-energy conformations, with variations primarily in loops and bulges, and compensatory base substitutions/indels maintaining structure.
• Sequence differences were equally contributed by insertion/deletion events (indels) and base substitutions, with transversions biased towards G/U gain and A/C loss.

Conclusions:

• The rDNA 28S D3 segment in Ixodes ticks exhibits length variation and conserved secondary structures, suggesting selective constraints on its evolution.
• Unequal exchange among subrepeats may explain the observed length reduction in I. persulcatus D3.
• Biased substitution patterns potentially facilitate the re-establishment of base pairing after disruptive indels, maintaining RNA secondary structure.