Comparative Analysis of Plastome Sequences of Seven Tulipa L. (Liliaceae Juss.) Species from Section Kolpakowskianae Raamsd. Ex Zonn and Veldk

Abstract

Tulipa L. is a genus of significant economic, environmental, and cultural importance in several parts of the world. The exact number of species in the genus remains uncertain due to inherent taxonomic challenges. We utilized next-generation sequencing technology to sequence and assemble the plastid genomes of seven Tulipa species collected in Kazakhstan and conducted a comparative analysis. The total number of annotated genes was 136 in all seven studied Tulipa species, 114 of which were unique, including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Nine regions (petD, ndhH, ycf2-ycf3, ndhA, rpl16, clpP, ndhD-ndhF, rpoC2, and ycf1) demonstrated significant nucleotide variability, suggesting their potential as molecular markers. A total of 1388 SSRs were identified in the seven Tulipa plastomes, with mononucleotide repeats being the most abundant (60.09%), followed by dinucleotide (34.44%), tetranucleotide (3.90%), trinucleotide (1.08%), pentanucleotide (0.22%), and hexanucleotide (0.29%). The Ka/Ks values of the protein-coding genes ranged from 0 to 3.9286, with the majority showing values <1. Phylogenetic analysis based on a complete plastid genome and protein-coding gene sequences divided the species into three major clades corresponding to their subgenera. The results obtained in this study may contribute to understanding the phylogenetic relationships and molecular taxonomy of Tulipa species.

Keywords: Liliaceae; Tulipa; next-generation sequencing; phylogenetic relationships; plastid genome; variable regions.

Figure 1

Plastid genome map of T. behmiana, T. brachystemon, T. kolpakowskiana, T. lemmersii, T. ostrowskiana, T. tetraphylla, and T. zenaidae species from Kazakhstan. Within the circle, darker grey shades indicate GC content, whereas lighter grey shades indicate AT content. The plastid genome boundaries are divided into the LSC, SSC, IRA, and IRB regions. Genes from various functional groups are color-coded.

Figure 2

Number of forward, palindromic, reverse, and complementary repeats identified in plastid genomes of T. behmiana, T. brachystemon, T. kolpakowskiana, T. lemmersii, T. ostrowskiana, T. tetraphylla, and T. zenaidae.

Figure 3

The categorization of long repeats by their lengths in plastid genomes of T. behmiana, T. brachystemon, T. kolpakowskiana, T. lemmersii, T. ostrowskiana, T. tetraphylla, and T. zenaidae.

Figure 4

Nucleotide variability (Pi) analysis in 80 protein-coding genes of Tulipa plastid genomes using sliding window analysis (window length 600 bp and step size 200 bp). The vertical axis indicates the nucleotide diversity for each window, and the horizontal axis represents the midpoint position.

Figure 5

The Ka/Ks ratios of protein-coding genes from 17 Tulipa plastid genomes. The vertical axis indicates the Ka/Ks values (ratios), and the horizontal axis represents the protein-coding genes of the plastid genomes.

Figure 6

Comparisons of the borders of the LSC, IR, and SSC regions among Tulipa plastomes. JLB indicates the junction sites between the LSC and IRb regions, JSB indicates the junction sites between the IRb and SSC regions, JSA indicates the junction sites between the SSC and IRa regions, and JLA indicates the junction sites between the IRa and LSC regions.

Figure 7

The phylogenetic tree was reconstructed using complete plastid genome sequences from 17 Tulipa species and two outgroup species, employing both Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The numbers at the branch nodes represent ML bootstrap/BI posterior probability values. The species analyzed in this study are highlighted in blue.

Figure 8

Phylogenetic tree inferred from ycf1 gene nucleotide sequences for 17 Tulipa species and two outgroup species using Maximum Likelihood (ML) and Bayesian Inference (BI) methods. The numbers at the branch nodes represent ML bootstrap/BI posterior probability values. The species analyzed in this study are highlighted in blue.