**5. Conclusions**

We compared 24 plastomes, 20 newly sequenced and four other species sequences were collected from the NCBI GenBank, all representing 18 genera of the family Salicaceae *s.l.* The SSRs are considered effective molecular markers for plant species identification and population genetics. A total of 1798 SSRs were identified. Mono-nucleotide repeats were the most common with 1455 repeats accounting for about 80.92% of the total. Most of repeats were located in the non-coding region. We also identified five other types of repeats, including 1750 tandems, 434 forward, 407 palindromic, 86 reverse, and 30 complementary repeats. The species in Salicaceae *s.l*. have a conserved plastid genome. Each plastome presented a typical quadripartite structure and varied in size due to the expansion and contraction of the IR boundary, lacking major structural variations, but we identified six divergence hotspot regions (*matK-trnQ-UUG*, *trnS-GCU-trnG-UCC*, *psbZ-trnG-GCC*, *ndhF-trnL-UAG*, *psbE-petL*, and *ycf1*+*ndhF*). We obtained phylogenetic relationships in 18 genera of Salicaceae *s.l.* and the 26 species formed a highly supported lineage. *Casearia* was identified as the basal clade. The divergence time between Salicaceae *s.l.* and the outgroup was estimated as ~93 Mya, and *Salix* and *Populus* diverged around 34 Mya, consistent with previously reported times. This study demonstrates the potential of plastid genome to address the genus relationship of Salicaceae *s.l.* This data will contribute to further understanding of the phylogenetic relationships among Salicaceae *s.l.*

**Supplementary Materials:** Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/15/ 3788/s1.

**Author Contributions:** T.M. designed the research and revised the manuscript; M.-M.L., D.-Y.W., L.Z., and M.-H.K. performed the experiments and analyzed the data; M.-M.L. and D.-Y.W. wrote the paper; Z.-Q.L., R.-B.Z., X.-X.M., and Z.-X.X. contributed materials and revised the manuscript.

**Funding:** This research was funded by the National Key Research and Development Program of China (2016YFD0600101), the National Natural Science Foundation of China (41871044, 31561123001, 31500502), and the National Key Project for Basic Research (2012CB114504), and Fundamental Research Funds for the Central Universities (2018CDDY-S02-SCU, SCU2019D013).

**Conflicts of Interest:** The authors declare no conflicts of interest.
