Abstract
Mountain ecosystems of the Northern Tian Shan harbor rare endemic plant species that are increasingly vulnerable to environmental change. This study assessed the ontogenetic stage composition, selected anatomical characteristics, and chloroplast genome features of Malus sieversii, Ribes janczewskii, and Ikonnikovia kaufmanniana. Field surveys included five populations and 971 recorded individuals: two populations of M. sieversii, one population of R. janczewskii, and two populations of I. kaufmanniana. Individuals were assigned to juvenile, immature, vegetative adult, and generative stages. The proportion of juvenile and immature individuals varied from 23.78% to 41.89% among populations, indicating substantial differences in the representation of early ontogenetic stages. Comparative anatomical analysis identified structural traits associated with adaptation to local environmental conditions. Complete chloroplast genomes were assembled and annotated, with sizes of 160,192 bp (M. sieversii), 157,432 bp (R. janczewskii), and 162,624 bp (I. kaufmanniana). All plastomes exhibited a conserved quadripartite structure and contained 131–132 genes and SSR loci with species-specific composition. Phylogenomic analysis placed M. sieversii within a well-supported wild apple clade, confirmed the distinct lineage of R. janczewskii, and supported the separation of I. kaufmanniana from Limonium. These findings provide new data and lay a basis for further studies to better understand the evolutionary distinctiveness and conservation relevance of endemic plant species in the Northern Tian Shan.