Kazakhstan tulips: comparative analysis of complete chloroplast genomes of four local and endangered species of the genus Tulipa L

Abstract

Species of Tulipa are important ornamental plants used for horticultural purposes in various countries, across Asia, Europe, and North Africa. The present study is the first report on typical features of the complete chloroplast genome sequence of four local and endangered species including T. alberti, T. kaufmanniana, T. greigii, and T. dubia from Kazakhstan using Illumina sequencing technology. The comparative analyses revealed that the complete genomes of four species were highly conserved in terms of total genome size (152. 006 bp - 152. 382 bp), including a pair of inverted repeat regions (26. 330 bp - 26. 371 bp), separated by a large single copy region (82.169 bp - 82,378 bp) and a small copy region (17.172 bp -17.260 bp). Total GC content (36.58-36.62 %), gene number (131), and intron length (540 bp - 2620 bp) of 28 genes. The complete genomes of four species showed nucleotide diversity (π =0,003257). The total number of SSR loci was 159 in T. alberti, 158 in T. kaufmanniana, 174 in T. greigii, and 163 in T. dubia. The result indicated that ten CDS genes, namely rpoC2, cemA, rbcL, rpl36, psbH, rps3, rpl22, ndhF, ycf1, and matK, with effective polymorphic simple sequence repeats (SSRs), high sequence variability (SV) ranging from 2.581 to 6.102, and high nucleotide diversity (Pi) of these loci ranging from 0,004 to 0,010. For all intergenic regions longer than 150 bp, twenty one most variable regions were found with high sequence variability (SV) ranging from 4,848 to 11,862 and high nucleotide diversity (Pi) ranging from 0,01599 to 0,01839. Relative synonymous codon usage (RSCU) analysis was used to identify overrepresented and underrepresented codons for each amino acid. Based on the phylogenic analysis, the sequences clustered into four major groups, reflecting distinct evolutionary lineages corresponding to the subgenera Eriostemons, Tulipa, and Orithyia. Notably, T. greigii was distinctively grouped with species from Orithyia and Eriostemons rather than with other Tulipa species, suggesting a unique evolutionary history potentially shaped by geographical isolation or specific ecological pressures. The complete chloroplast genome of the four Tulipa species provides fundamental information for future research studies, even for designing the high number of available molecular markers.

Keywords: Tulipa L.; chloroplast genome; codon usage patterns; comparative analysis; phylogenetic analysis; simple sequence repeat (SSR).

Figure 1

Chloroplast genome maps of four Tulipa species in this study.

Figure 2

Comparison of SSC, IR, and LSC junction position among four Tulipa species. JSA, junction of SSC and IRA; JLA, junction of LSC and IRA; JLB, junction of LSC and IRB; JSB, junction of SSC and IRB.

Figure 3

Type and number of identified SSR motifs (mono, di, tri, tetra, penta and hexa) in the whole chloroplast genome of four Tulipa species. (A) frequency of different SSR motif types in the whole chloroplast genome; (B) frequency of Identified SSR motifs in the SSC, IRA, LSC, and IRB regions; (C) percentage of mono, di, tri, tetra, and penta SSR motifs in each chloroplast genomes; (D) type and number of identified SSR motifs (mono, di, tri, tetra, penta, and compound).

Figure 4

Sequence variability (SV) and nucleotide diversity (Pi) within each protein-coding sequences (CDS) and intergenic regions.

Figure 5

Codon content of 20 amino acids and stop codons in the CDS of four Tulipa species. The color of the histogram corresponds to the color of the codons.

Figure 6

Phylogenetic relationship for Tulipa L. species. Inferred from Maximum likelihood model.