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

<h4>Introduction</h4><i>Euphorbia resinifera</i> 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.<h4>Methods</h4>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 <i>rpl22</i> gene analysis.<h4>Results</h4>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 <i>Euphorbia</i>. cpSSR profiles recovered relationships only within sect. <i>Euphorbia</i>, while whole-plastome analysis showed biogeographical clustering. The <i>rpl22</i> gene precisely distinguished growth forms and revealed perfect sequence identity between morphologically similar pairs (<i>E. ampliphylla</i> and <i>E. resinifera, E. neospinescens</i> and <i>E. neoarborescens, E. micractina</i> and <i>E. pekinensis</i>), with <i>E. royleana</i> showing near-perfect identity to <i>E. ampliphylla</i> and <i>E. resinifera</i> (1 SNP difference). Notably, <i>E. drupifera</i> was excluded from the cactiform core within sect. <i>Euphorbia</i> through 10 diagnostic SNPs and a unique AGC deletion.<h4>Discussion</h4>This study establishes <i>rpl22</i> as a powerful taxonomic discriminator for <i>Euphorbia</i> systematics, with future multi-gene approaches recommended for broader phylogenetic resolution.