Populus wulianensis is an endangered species endemic to Shandong Province, China. Despite the economic and ornamental value of this species, few genomics and genetic studies have been performed. In this study, we performed a relevant analysis of the full-length transcriptome sequencing data of P. wulianensis and obtained expressed sequence tag (EST)-simple sequence repeat (SSR) markers with polymorphisms that can be used for further genetic research. In total, 8.18 Gb (3,521,665) clean reads with an average GC content of 42.12% were obtained. From the corrected 64,737 high-quality isoforms, 42,323 transcript sequences were obtained after redundancy analysis with CD-HIT. Among these transcript sequences, 41,876 sequences were annotated successfully. A total of 23,539 potential EST-SSRs were identified from 16,057 sequences. Excluding mononucleotides, the most abundant motifs were trinucleotide SSRs (47.80%), followed by di- (46.80%), tetra- (2.98%), hexa- (1.58%) and pentanucleotide SSRs (0.84%). Among the 100 designed EST-SSRs, 18 were polymorphic with high PIC values (0.721 and 0.683) and could be used for analyses of the genetic diversity and population structure of P. wulianensis. These full-length transcriptome sequencing data will facilitate gene discovery and functional genomics research in P. wulianensis, and the novel EST-SSRs developed in our study will promote molecular-assisted breeding, genetic diversity and conservation biology research in this species.

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The genetic diversity and relationships among populations of Chinese-endemic rugged rose (Rosa rugosa) were studied at the molecular level, to provide theoretical guidance and technical support for the scientific evaluation, preservation and development of the germplasm resources of this endangered species. DNA samples of 120 specimens of R. rugosa, originating from six different Chinese source populations were amplified with CDDP (conserved DNA-derived polymorphism) primers. A total of 121 polymorphic loci out of the 128 total bands (94.53%) were recovered using 13 informative and reliable primers. The average number of amplified bands per primer was about 9.84. The number of specific bands was 8, accounting for 6.25%. Nei's gene diversity (H), Shannon's information index (I) and the effective number of alleles (Ne) were 0.3057, 0.4646 and 1.5131, respectively. A UPGMA (unweighted pair group method with arithmetic mean) cluster analysis suggested that these populations of rugged rose could be divided into six major groups, with a similarity coefficient of 0.81. Here we show that the CDDP marker technique can effectively reveal the genetic diversity among Chinese-endemic populations of the rugged rose. Based on the results from the cluster analysis, we suggest that although the population genetic structure mirrors the geographic structure to some extent, it is clear that other factors besides geographic distance contribute to the generation of genetic variation.

Rosa rugosa is an important shrub with economic, ecological, and pharmaceutical value. A high-quality chromosome-scale genome for R. rugosa sequences was assembled using PacBio and Hi-C technologies. The final assembly genome sequences size was about 407.1 Mb, the contig N50 size was 2.85 Mb, and the scaffold N50 size was 56.6 Mb. More than 98% of the assembled genome sequences were anchored to 7 pseudochromosomes (402.9 Mb). The genome contained 37,512 protein-coding genes, with 37,016 genes (98.68%) that were functionally annotated, and 206.67 Mb (50.76%) of the assembled sequences are repetitive sequences. Phylogenetic analyses indicated that R. rugosa diverged from Rosa chinensis approximately 6.6 million years ago, and no lineage-specific whole-genome duplication (WGD) event occurred after divergence from R. chinensis. Chromosome synteny analysis demonstrated highly conserved synteny between R. rugosa and R. chinensis, between R. rugosa and Prunus persica as well. Comparative genome and transcriptome analysis revealed genes related to color, scent, and environment adaptation. The chromosome-level reference genome provides important genomic resources for molecular-assisted breeding and horticultural comparative genomics research.