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Supplementary Table S1 (SuppFile1.xlsx) The RADseq data information for the 2 parents and 257 progeny in the F1 hybrid population of Populus deltoides and Populus simonii. Supplementary Appendix A (SuppFile2.pdf) Calculation of the coefficient of coincidence between the two adjacent SNP intervals for the female parent in an F1 population of Populus deltoides and Populus simonii

Cinnamomum camphora is a valuable broad-leaf tree indigenous to South China and East Asia and has been widely cultivated and utilized by humans since ancient times. However, owing to its overutilization for essential oil extraction, the Transplanting Big Trees into Cities Program, and over deforestation to make furniture, its wild populations have been detrimentally affected and are declining rapidly. In the present study, the genetic diversity and population structure of 180 trees sampled from 41 populations in South China were investigated with 22 expressed sequence tag-simple sequence repeat (EST-SSR) markers. In total, 61 alleles were harbored across 180 individuals, and medium genetic diversity level was inferred from the observed heterozygosity (Ho), expected heterozygosity (He), and Nei&rsquo, gene diversity (GD), which were 0.45, 0.44, and 0.44, respectively. Among the 41 wild populations, C. camphora had an average of 44 alleles, 2.02 effective alleles, and He ranging from 0.30 (SC) to 0.61 (HK). Analysis of molecular variance (AMOVA) showed that 17% of the variation among populations and the average pairwise genetic differentiation coefficient (FST) between populations was 0.162, indicating relatively low genetic population differentiations. Structure analysis suggested two groups for the 180 individuals, which was consistent with the principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA). Populations grouped to cluster I were nearly all distributed in Jiangxi Province (except population XS in Zhejiang Province), and cluster II mainly comprised populations from other regions, indicating a significant geographical distribution. Moreover, the Mantel test showed that this geographical distance was significantly correlated with genetic distance. The findings of this research will assist in future C. camphora conservation management and breeding programs.

Cinnamomum camphora (Lauraceae) is a well-known multipurpose tree with aromatic oils, insect-repellent effects and ornamental value. In this study, a total of 74,289 simple sequence repeats (SSRs) were found in 56,124 unigenes, of which 14,225 unigenes contained more than one SSR locus. Among these SSR loci, the mono-nucleotide repeats were the most frequent, with a frequency of 61.14%, followed by 24.87% di-nucleotide repeats and 12.87% tri-nucleotide repeats. Twenty-one polymorphic SSR markers were developed and validated in 45 camphor trees. The 21 loci were further examined for cross-species transferability in other six related species. The novel genic-SSR markers will not only benefit genetic diversity analysis and wild resources conservation of C. camphora, but also contribute to exploring the further evolutionary history and genetic differentiation pattern of Cinnamomum.

Transcriptome sequencing was performed using Illumina paired-end RNA sequencing technology, for facilitating gene discovery and SSR marker development in an endangered tree, Woonyoungia septentrionalis. A total of 41,578,222 high-quality reads were obtained, and 93,156 non-redundant unigenes were assembled and annotated by sequence similarity searching in diverse public databases. Analyses showed that 36,176 unigenes (38.83%) had at least blast hit against Nr, Nt, KO, SwissProt, PFAM, KO, or GO database; and 2945 unigenes (4.13%) were annotated in all seven databases. Totally, 17,719 genic-SSRs were identified in 14,629 (15.70%) out of 93,156 unigenes. Finally, 51 primers of the 64 designed SSR primers produced clear SSR bands, of which 20 SSR loci were polymorphic in 149 individuals representing four natural populations. Observed and expected heterozygosity varied from 0 to 0.846 and from 0 to 0.792, respectively. At the species level, the Ho and He of the four W. septentrionalis populations were 0.3325 and 0.3559, respectively. The average genetic diversity within populations, H and I were 0.3500 and 0.5937, respectively. Cross-species amplification of the 20 markers was tested in other related species. The transcriptomic resources and genic SSR markers are valuable tools not only for ecological conservation of this species, but also for phylogenetic studies.

EDITOR’S ABSTRACTSeeing New Qing History as a “malicious attack on a sovereign country” by “Western imperialists,” Li explicitly differentiates between a “wrong” and a “right” perspective on Qing history. In his view, the only legitimate standpoint is one that takes the People’s Republic of China’s territorial reach and “ethnic unity” as a necessary and natural result of history.

Background Cinnamomum camphora has been cultivated as an economically important tree for its medicinal and aromatic properties. Selective breeding has produced Cinnamomum plants for special uses, including spice strains with characteristic flavors and aromas and high-potency medicinal cultivars. The molecular biology underlying terpenoid biosynthesis is still unexplored. Results Gas chromatography-mass spectrometry was used to analyze the differences in contents and compositions of essential oil terpenoids in linalool- and borneol-type chemotypes of C. camphora. The data revealed that the essential oils consist primarily of monoterpenes with only very minor quantities of sesquiterpenes and diterpenes and that the essential oil differs in different chemotypes of C. camphora, with higher yields of (−)-borneol from the borneol-type than from the linalool-type. To study the terpenoid biosynthesis of signature compounds of the major monoterpenes, we performed RNA sequencing to profile the leaf transcriptomes of the two chemotypes of C. camphora. A total of 23.76 Gb clean data was generated from two chemotypes and assembled into 156,184 unigenes. The total length, average length, N50 and GC content of unigenes were 155,645,929 bp, 997 bp, 1430 bp, and 46.5%, respectively. Among them, 76,421 unigenes were annotated by publicly available databases, of which 67 candidate unigenes were identified to be involved in terpenoid biosynthesis in C. camphora. A total of 2863 unigenes were identified to be differentially expression between borneol-type and linalool-type, including 1714 up-regulated and 1149 down-regulated unigenes. Most genes encoding proteins involved in terpenoid precursor MVA and MEP pathways were expressed in similar levels in both chemotypes of C. camphora. In addition, 10 and 17 DEGs were significantly enriched in the terpene synthase activity and oxidoreductase activity terms of their directed acyclic graphs (DAG), respectively. Three monoterpene synthase genes, TPS14-like1, TPS14-like2 and TPS14-like3 were up-regulated in the borneol-type compared to the linalool-type, and their expression levels were further verified using quantitative real-time PCR. Conclusions This study provides a global overview of gene expression patterns related to terpenoid biosynthesis in C. camphora, and could contribute to a better understanding of the differential accumulation of terpenoids in different C. camphora chemotypes. Electronic supplementary material The online version of this article (10.1186/s12864-018-4941-1) contains supplementary material, which is available to authorized users.

The halophyte tamarisk (Tamarix) is extremely salt tolerant, making it an ideal material for salt tolerance-related studies. Although many salt-responsive genes of Tamarix were identified in previous studies, there are no reports on the role of post-transcriptional regulation in its salt tolerance. We constructed six small RNA libraries of Tamarix chinensis roots with NaCl treatments. High-throughput sequencing of the six libraries was performed and microRNA expression profiles were constructed. We investigated salt-responsive microRNAs to uncover the microRNA-mediated genes regulation. From these analyses, 251 conserved and 18 novel microRNA were identified from all small RNAs. From 191 differentially expressed microRNAs, 74 co-expressed microRNAs were identified as salt-responsive candidate microRNAs. The most enriched GO (gene ontology) terms for the 157 genes targeted by differentially expressed microRNAs suggested that transcriptions factors were highly active. Two hub microRNAs (miR414, miR5658), which connected by several target genes into an organic microRNA regulatory network, appeared to be the key regulators of post-transcriptional salt-stress responses. As the first survey on the tamarisk small RNAome, this study improves the understanding of tamarisk salt-tolerance mechanisms and will contribute to the molecular-assisted resistance breeding.