Comparative chloroplast genome and phylogenetic analysis of Central Asian tulips

Tulipa is a genus that comprises species highly valued as ornamentals throughout world. So far, only 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 ndh E, ndh F, psa C, rpl 32 and ycf 1 genes and the regions rps 16– trn Q‐UUG, psb M– psb D, trn T‐UGU– trn L‐UAA, pet A– psb J, rpl 33– rps 18, pet D– rpo A, rpl 36– rpl 14, rpl 32– ccs A have higher variability than others. Further, phylogenetic reconstruction including 37 species of Tulipa and 3 outgroups based on 76 shared coding sequences (CDS) and ycf 1 genes were made. Both phylogenetic trees divided the species into three major clades and they had almost the same topology, confirming that ycf 1can 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.