Large-scale organellar genomics reveals maternal evolutionary history and dynamism in the wolfberries

Introduction The organellar genomic diversity and maternal evolutionary history of the Lycium complex remain incompletely understood. Methods We compared organellar genomes from 201 accessions, with dense sampling of L. barbarum and L. ruthenicum plus representative relatives. A single L. ruthenicum mitogenome was assembled de novo and used as the reference for comparisons of 186 LR and LB-complex accessions. Results Plastome analyses resolved seven maternal genetic clusters and identified patterns consistent with complex maternal ancestry within the red wolfberry complex. However, plastid data alone cannot distinguish hybridization, introgression, and incomplete lineage sorting. All 201 plastomes retained a conserved quadripartite structure and 79 unique protein-coding genes. Illumina depth profiles identified a candidate 5.5-kb structural difference with strongly reduced coverage in the LB representative. The corresponding reference interval contains orf27, orf92 , and orf93 . This depth-supported interval defines a candidate mitochondrial region but does not establish its exact molecular configuration or biological function. Discussion This organellar resource provides a framework for testing evolutionary hypotheses and supporting wolfberry germplasm research.