A Segregating Structural Variant Defines Novel Venom Phenotypes in the Eastern Diamondback Rattlesnake

Area of Science:

• Evolutionary Biology
• Genomics
• Biochemistry

Background:

• Structural variants are key drivers of phenotypic variation, yet challenging to identify.
• Snake venom composition exhibits significant intraspecific variation, with parallel evolution of neurotoxic venoms observed in rattlesnakes.
• This evolution involves deletion of snake venom metalloproteinase (SVMP) toxins and recruitment of phospholipase A2 (PLA2) toxins.

Purpose of the Study:

• To investigate the role of structural variation in shaping venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus).
• To identify specific genetic mechanisms, such as gene deletions, contributing to venom variation within this species.
• To understand the geographic distribution and evolutionary implications of identified structural variants.

Main Methods:

• Generation of a haplotype-resolved, chromosome-level genome assembly for Crotalus adamanteus.
• Population-genomic analysis to assess the frequency and distribution of structural variants across the species' range.
• Genotyping of SVMP and myotoxin (MYO) genes to correlate with venom phenotypes.

Main Results:

• Discovery of a large (∼225 Kb) deletion encompassing six SVMP genes in C. adamanteus, mirroring a key step in neurotoxic venom evolution.
• Identification of this SVMP deletion as the dominant homozygous genotype in the vulnerable northwestern periphery of the species' range.
• Demonstration that SVMP deletions and MYO copy number variation are genetically independent, leading to novel venom phenotypes across the geographic range.

Conclusions:

• Structural variation, specifically large gene deletions, is a primary determinant of geographic venom variation in C. adamanteus.
• C. adamanteus exhibits a unique evolutionary trajectory, deleting SVMP genes without concurrently recruiting neurotoxic PLA2s.
• The independent variation of SVMP and MYO genotypes results in a diverse array of venom phenotypes, highlighting the complex evolutionary pathways in rattlesnake venom.