Complete Chloroplast Genomes of Five Ulmus pumila Cultivars: Comparative Analysis, Evolutionary Dynamics, and Germplasm Authentication Implications

ABSTRACT

The complete chloroplast genomes of five Ulmus pumila cultivars (“Yangguang Nanhai,” “Yangguang Nühai,” “Xu Ri,” “Yang Gang,” and “Zhao Yang”) were sequenced and analyzed in this study, with publicly available Ulmus pumila accessions from NCBI included for intraspecific comparative analysis to elucidate cultivar‐level genomic variations, genetic diversity and phylogenetic placement. The chloroplast genomes showed typical circular quadripartite structures, ranging from 159,391 to 159,769 bp with GC contents of 35.47%–35.56%. Each genome encoded 131–133 genes, including 86–89 protein‐coding genes, 36–37 tRNAs, and 8 rRNAs, with minor intraspecific variations in gene content mainly attributed to tRNA pseudogenization. In total, 154–164 simple sequence repeats (SSRs) and 63–155 long repeats were identified, with SSRs predominantly comprising mononucleotide A/T repeats; cultivar‐specific repeat loci were detected that can serve as candidate markers for cultivar authentication. Nucleotide diversity analysis revealed hypervariable regions (e.g., trnH‐GUG_psbA , ndhF_rpl32 ) at the intraspecific level that could serve as complementary molecular markers for Ulmus pumila germplasm identification. IR boundary analysis revealed minor length fluctuations of boundary genes (e.g., rps19 , ycf1 ) among cultivars, representing intraspecific structural polymorphism rather than major evolutionary events. In phylogenetic analysis, the five cultivars were clustered into a single well‐supported clade together with other Ulmus pumila accessions, providing robust support for the monophyly of the genus Ulmus and confirming the close maternal genetic background of these cultivated materials. Overall, this study presents the first complete chloroplast genome resource for these five Ulmus pumila cultivars, fills the gap of intraspecific plastome variation for cultivated Ulmus pumila germplasm, and establishes a molecular foundation for germplasm identification, maternal lineage tracing and genetic breeding of Ulmus species.