The shortest animal introns: insights from parasitic cnidarians

Spliceosomal introns are nearly ubiquitous across eukaryotes, yet constraints shaping their length remain poorly understood. Generally, introns shorter than ∼30 bp are considered absent from animals. Here, we show that such ultra-short introns evolved independently at least twice within Metazoa. Using long-read sequencing, we assembled and annotated the genome of the myxobolid myxozoan Henneguya salminicola and identified exceptionally short introns with a median length of 27 bp. Comparative analyses of 51 metazoan genomes revealed that extreme intron shortening characterizes myxobolids, with Thelohanellus kitauei and Myxobolus rasmusseni exhibiting the shortest median intron length (22 bp) among sequenced animals. Outside Myxozoa, similarly short introns were found only in the dicyemid Dicyema japonicum. Sequence-logo analyses showed reduced 5' and 3' splice-site motifs in myxobolids and D. japonicum relative to other animals. Together, these results demonstrate that introns shorter than 30 bp occur in animals, and that extreme intron shortening evolved convergently in at least two parasitic animal lineages.