Mitochondrial Genomes Reveal Global Population Structure, Lineage Divergence, and Candidate Diagnostic Markers of Diaphorina citri

The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is the primary vector of Candidatus Liberibacter asiaticus, the causal agent of huanglongbing, the most devastating disease of citrus worldwide. Understanding its population structure and developing lineage-specific markers are important for surveillance, quarantine and pest management. Here, 133 complete mitochondrial genomes were analyzed, comprising 77 previously published sequences, 13 newly assembled genomes and 43 metagenome-assembled mitogenomes. Phylogenetic analysis revealed two highly differentiated mitochondrial lineages—an Asian lineage (n = 91, including the Uruguay sample) and an American lineage (n = 42, including the Pakistan sample) (FST = 0.560, p < 0.001)—separated by 32 fixed variants (132 genomes, excluding the reference sequence MF426268.1). Within the Asian lineage, the Yunnan–Guizhou Plateau population showed significant differentiation from lowland populations (FST = 0.130, p < 0.05), reduced nucleotide diversity and moderately supported monophyletic clustering consistent with long-term isolation, while demographic analyses suggested that Southeast China may have acted as a post-colonization expansion center. Candidate lineage-specific markers, including variants in trnG and rrn16, provide molecular resources for population-origin assignment, quarantine surveillance and pest monitoring; these candidates require validation across broader geographic sampling.