ITS2 Sequence-Structure Alignment for Haptophyte Phylogeny

A study by Louisa Ridder integrates ribosomal RNA secondary structure information into phylogenetic analysis of haptophytes. The dataset includes 396 representative 18S sequences and 224 ITS2 sequences, compiled from over 40,000 available sequences. The work was published on figshare in March 2026.

Use Cases

• Comparing phylogenetic resolution based on sequence-only versus sequence-structure alignments.
• Distinguishing closely related haptophyte species using ITS2 sequence-structure data.
• Analyzing conserved and variable features in 18S and ITS2 secondary structures.
• Evaluating the impact of taxon sampling and methodological choices on phylogenetic outcomes.

Strengths

• Includes 396 representative 18S sequences derived from over 40,000 available sequences.
• Compiles 224 ITS2 sequences for analysis.
• Integrates secondary structure information to improve alignment quality and reduce phylogenetic artifacts.
• The 18S sequence-structure ML tree is described as a reliable depiction of haptophyte phylogeny.

Limitations

• ITS2 data presented alignment challenges due to high sequence variability, length differences, and limited taxon representation.
• ITS2 remained unsuitable for resolving deep relationships among haptophytes.
• Some backbone relationships in the phylogeny remain weakly supported.
• Column-level documentation is absent; field semantics must be inferred after download.

Provenance

Source

figshare

Collection Method

Taxon sampling reduced over 40,000 available 18S sequences to 396 representatives, alongside a compilation of 224 ITS2 sequences. Comparative modeling and homology-based structure prediction were used.

Freshness

Last updated 2026-03-19 17:23:02