Comparative chloroplast genome and phylogenetic analysis of Central Asian Tulips

Tulipa is a genus that comprises species highly valued as ornamentals
throughout the world. So far, only a few Tulipa plastid genomes have been
reported, and there are many taxonomically controversial species. In this
study, we sequenced the chloroplast genomes (CP) of nineteen species
collected from Uzbekistan and Kyrgyzstan and conducted comparative
analysis. In all CP, 136 genes were annotated, of which 114 were unique,
including 80 protein-coding, 30 tRNA, and 4 rRNA genes. Polymorphic SSRs
effective for discrimination between species and populations were
identified. Additionally, comparative Pi diversity analysis of both
protein coding genes and whole plastomes revealed that the ndhE, ndhF,
psaC, rpl32 and ycf1 genes and the regions rps16–trnQ-UUG, psbM–psbD,
trnT-UGU–trnL-UAA, petA–psbJ, rpl33–rps18, petD–rpoA, rpl36–rpl14,
rpl32–ccsA have higher variability than others. Further, phylogenetic
reconstruction including 37 species of Tulipa and 3 outgroups based on 76
shared coding sequences (CDS) and ycf1 genes were made. Both phylogenetic
trees divided the species into three major clades, and they had almost the
same topology, confirming that ycf1can be used as a marker for
phylogenetic relationships. However, the currently recognized sections
appear non-monophyletic. Insights into the taxonomic classification of
several species of Tulipa, based on several morphologic,
phytogeographic, and molecular data are discussed.