Structural analysis of the chloroplast genome of the Kazakhstan endemic Kaufmann’s tulip (Tulipa kaufmanniana)

Abstract

Kaufmann’s tulip (Tulipa kaufmanniana) is an endemic species of Kazakhstan and an important ornamental plant. In this study, the complete chloroplast genome of this rare species was described for the first time using Illumina sequencing technology. The results revealed that the complete genome of T. kaufmanniana is highly conserved. The genome size was 152,374 bp, comprising a pair of inverted repeat (IR) regions of 26,371 bp each, a large single-copy (LSC) region of 82,369 bp, and a small single-copy (SSC) region of 17,260 bp. The overall GC content was 36.58%. A total of 130 genes were annotated, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. Analysis of simple sequence repeats (SSRs) identified 158 loci, predominantly distributed in the LSC region (63.3%), SSC region (19%), and IR regions (17.7%). Five categories of SSRs (mono-, di-, tri-, tetra-, and hexanucleotide) were detected. The most polymorphic protein-coding genes were ycf1, matK, rpoC2, rbcL, ndhF, cemA, rpl22, rps3, and psbH, showing high sequence variability (Pi = 2.570–6.085) and nucleotide diversity. Relative synonymous codon usage (RSCU) analysis revealed both overrepresented and underrepresented codons. Overall, the characterization of the chloroplast genome of T. kaufmanniana is essential for the conservation of genetic resources of this rare endemic species, as well as for gaining deeper insights into its evolutionary and phylogenetic features. These findings provide a foundation for developing effective molecular-level strategies for preserving the biological diversity of Kazakhstan’s flora.