Complete chloroplast genome of Euphorbia resinifera: overcoming biogeographical bias in phylogenetic inference and establishing a conservation genomics framework for threatened North-West African cactiform species

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Introduction Euphorbia resinifera O. Berg (1863) is an endemic cactiform species from Morocco's arid High Atlas Mountains, valued for its medicinal properties and melliferous importance. It faces conservation challenges from habitat degradation and phylogenetic incongruence between xeromorphic adaptations and current sectional classification. Methods We pioneered a non-destructive spine-DNA genome-skimming approach to generate the complete chloroplast genome, and applied a multi-pronged molecular strategy including cpSSR profiling, whole-plastome phylogenetics, and rpl22 gene analysis. Results The complete chloroplast genome (163,065 bp; 35.11% GC) contains 132 genes and 96 SSR loci, representing the first genomic resource for threatened North-West African cactiform Euphorbia . cpSSR profiles recovered relationships only within sect. Euphorbia , while whole-plastome analysis showed biogeographical clustering. The rpl22 gene precisely distinguished growth forms and revealed perfect sequence identity between morphologically similar pairs ( E. ampliphylla and E. resinifera, E. neospinescens and E. neoarborescens, E. micractina and E. pekinensis ), with E. royleana showing near-perfect identity to E. ampliphylla and E. resinifera (1 SNP difference). Notably, E. drupifera was excluded from the cactiform core within sect. Euphorbia through 10 diagnostic SNPs and a unique AGC deletion. Discussion This study establishes rpl22 as a powerful taxonomic discriminator for Euphorbia systematics, with future multi-gene approaches recommended for broader phylogenetic resolution.

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