*Article* **Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers of** *Luculia yunnanensis***, an Endangered Species Endemic to Yunnan, Southwestern China**

**Yao Zhang 1,2, Xi Liu 3, Yuying Li 4, Xiongfang Liu 1,2, Hong Ma 1,5,\*, Suping Qu 6,\* and Zhenghong Li 1,\***


**Abstract:** *Luculia yunnanensis* (Rubiaceae), an evergreen shrub or small tree, is endemic to China and confined to Nujiang Prefecture, Yunnan Province. This plant is of high ornamental value owing to its attractive pink flowers, sweet fragrance, and long flowering period. Due to the influence of climate change and human factors, the distribution range of *L. yunnanensis* has exhibited a significant shrinking trend, and it has become a vulnerable species that is in urgent need of conservation and rational utilization research. In this study, the flower transcriptome sequencing of *L. yunnanensis* was conducted using an Illumina HiSeq platform. We designed and developed a series of EST-SSR primers based on the flower transcriptome data of *L. yunnanensis*. The results showed that 98,389 unigenes were obtained from the *L. yunnanensis* flower transcriptome, all of which were aligned with sequences in public databases. Nr, Nt, Pfam, KOG/COG, Swiss-Prot, KEGG, and GO annotated 31,859, 13,853, 22,684, 10,947, 21,416, 9722, and 23,390 unigenes, respectively. The MISA (Microsatellite) tool was used to identify SSR loci from all unigenes, and a total of 15,384 SSRs were identified. Repeat motifs were given priority with mononucleotides, dinucleotides, and trinucleotides. The 81 primer pairs were synthesized randomly, of which 44 pairs showed effective amplification. A total of 17 primers showed stable amplification, and rich polymorphism was observed in 6 populations. We concluded via genetic diversity analysis that the average effective number of alleles (Ne), Shannon's information index (I), and polymorphism information content (PIC) were 1.925, 0.837, and 0.403, respectively. In conclusion, 17 EST-SSR primers can be used for subsequent population genetic diversity analysis and molecular-marker-assisted breeding, which is of great significance for formulating resource conservation and utilization strategies for *L. yunnanensis*.

**Keywords:** *Luculia yunnanensis*; transcriptome; EST-SSR markers; polymorphism; conservation genetics
