A comparative transcriptomic analysis provides new insights into the ecological adaptations in Ichthyophis bannanicus

Banna caecilian (Ichthyophis bannanicus) was the first species of Gymnophiona to be discovered in China, with unique lifestyles and characteristics. Although there have been some studies on distribution and morphological characteristics in I. bannanicus, few have focused on the molecular level. A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions.

To provide new insights into molecular mechanisms of ecological adaptation in I. bannanicus, we generated a comprehensive and high-resolution transcriptomic atlas, which covers 19 major organs for I. bannanicus. We identified 5,092 housekeeping genes (HKGs), 2,169 tissue-specific genes (TSGs), and conducted weighted gene co-expression network analysis to determine the modules most relevant to each tissue. Functional enrichment indicated that HKGs support basic cellular activities, while TSGs and the module genes are associated with tissue differentiation and specific physiological processes. And the cross-species comparison of HKGs, TSGs, and co-expression modules highlighted an enhanced and unique immune capacity in I. bannanicus. Notably, the comparative genomic analysis between I. bannanicus and Xenopus tropicalis revealed genes potentially lost in I. bannanicus, including RCVRN.1, GNAT2, SAG, GRK7, SMURF1, NOG, and MAPK14, which may be associated with degeneration of its visual system and limb structures.

Our findings demonstrate that HKGs, TSGs, and co-expression module genes offer valuable perspectives on tissue specialization and evolutionary divergence. The comparative transcriptomic analysis across multiple species and diverse tissue types provides valuable clues into the molecular features that may contribute to ecological adaptation in I. bannanicus.