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Background: Long noncoding RNAs (lncRNAs) are functionally associated with cancer development and progression. Although gene copy number variation (CNV) is common in hepatocellular carcinoma (HCC), it is not known how CNV in lncRNAs affects HCC progression and recurrence. We aimed to identify a CNV-related lncRNA involved in HCC progression and recurrence and illustrate its underlying mechanisms and prognostic value., Methods: We analyzed the whole genome sequencing (WGS) data of matched cancerous and noncancerous liver samples from 49 patients with HCC to identify lncRNAs with CNV. The results were validated in another cohort of 238 paired HCC and nontumor samples by TaqMan copy number assay. We preformed Kaplan-Meier analysis and log-rank test to identify lncRNA CNV with prognostic value. We conducted loss- and gain-of-function studies to explore the biological functions of LINC01133 in vitro and in vivo. The competing endogenous RNAs (ceRNAs) mechanism was clarified by microRNA sequencing (miR-seq), quantitative real-time PCR (qRT-PCR), western blot, and dual-luciferase reporter assays. We confirmed the binding mechanism between lncRNA and protein by RNA pull-down, RNA immunoprecipitation, qRT-PCR, and western blot analyses., Results: Genomic copy numbers of LINC01133 were increased in HCC, which were positively related with the elevated expression of LINC01133. Increased copy number of LINC01133 predicted the poor prognosis in HCC patients. LINC01133 overexpression in HCC cells promoted proliferation and aggressive phenotypes in vitro, and facilitated tumor growth and lung metastasis in vivo, whereas LINC01133 knockdown had the opposite effects. LINC01133 sponged miR-199a-5p, resulting in enhanced expression of SNAI1, which induced epithelial-to-mesenchymal transition (EMT) in HCC cells. In addition, LINC01133 interacted with Annexin A2 (ANXA2) to activate the ANXA2/STAT3 signaling pathway., Conclusions: LINC01133 promotes HCC progression by sponging miR-199a-5p and interacting with ANXA2. LINC01133 CNV gain is predictive of poor prognosis in patients with HCC., (© 2021 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.)

Premise of the Study: To study population genetics, phylogeography, and hybridization of Nelumbo (Nelumbonaceae), chloroplast microsatellite markers were developed., Methods and Results: Seventeen microsatellite loci were identified from the chloroplast genomes of N. nucifera and N. lutea. Polymorphisms were assessed in three populations of N. nucifera and one population of N. lutea. Nine loci were found to be polymorphic in N. nucifera, and all 17 loci were found to be polymorphic in N. lutea. In N. nucifera, the number of alleles per locus ranged from two to six, and the unbiased haploid diversity per locus ranged from 0.198 to 0.790. In N. lutea, the number of alleles ranged from two to four, and the unbiased haploid diversity per locus ranged from 0.245 to 0.694., Conclusions: The identified chloroplast simple sequence repeat markers will be useful for the study of genetic diversity, phylogeography, and identification of Nelumbo cultivars.

Premise of the Study: Microsatellite primers were developed for Paeonia delavayi and P. ludlowii (Paeoniaceae) to study their population genetics and phytogeography., Methods and Results: Nine polymorphic nuclear microsatellite loci were isolated from an enriched library of P. delavayi and primers were designed. The number of alleles per locus ranged from two to 16; the observed and expected heterozygosities ranged from 0.014 to 0.687 and 0.042 to 0.875, respectively. Six polymorphic chloroplast microsatellite loci were identified in P. delavayi and primers were provided. The number of alleles per locus ranged from two to six and the polymorphic information content ranged from 0.08 to 0.716. Both nuclear and chloroplast primers were successfully applicable to P. ludlowii., Conclusions: The markers developed here will facilitate analyses of genetic diversity, population genetic structure, phytogeographical patterns, and conservation for P. delavayi and P. ludlowii.

Premise of the Study: Microsatellite primers were developed for a Chinese traditional herb, Panax notoginseng, to investigate its genetic diversity and cultivar breeding., Methods and Results: Twelve polymorphic microsatellite loci were isolated from the microsatellite-enriched genomic library of P. notoginseng. The polymorphisms were assessed in two populations and an assemblage containing individuals from the whole distribution area. The number of alleles per locus ranged from three to 12, with a mean of 5.8, and the observed and expected heterozygosity values ranged from 0.0411 to 0.8472 and from 0.0804 to 0.7653, respectively., Conclusions: These new microsatellite markers will be useful for investigation of the genetic diversity of cultivated P. notoginseng as well as assist in cultivar breeding.

Premise of the Study: Microsatellite primers were developed for a Chinese traditional herb, Panax notoginseng, to investigate its genetic diversity and cultivar breeding., Methods and Results: Twelve polymorphic microsatellite loci were isolated from the microsatellite-enriched genomic library of Panax notoginseng. The polymorphisms were assessed in two populations and an assemblage containing individuals from the entire distribution area. The number of alleles per locus ranged from 3 to 12, with a mean of 5.8; the observed and expected heterozygosity values ranged from 0.0411 to 0.8472 and from 0.0804 to 0.7653, respectively., Conclusions: These new microsatellite markers will be useful for investigating the genetic diversity of this cultivated Panax notoginseng as well as assist in cultivar breeding.

Premise of the Study: The development of compound microsatellite markers was conducted in Dysosma pleiantha to investigate genetic diversity and population genetic structure of this threatened medicinal plant., Methods and Results: Using the compound microsatellite marker technique, 14 microsatellite markers that were successfully amplified showed polymorphism when tested on 38 individuals from three populations in eastern China. Overall, the number of alleles per locus ranged from 2 to 14, with an average of 7.71 alleles per locus., Conclusions: These results indicate that these microsatellite markers are adequate for detecting and characterizing population genetic structure and genetic diversity in Dysosma pleiantha.

To evaluate the role of Quaternary refugial isolation in allopatric (incipient) speciation of East Asian temperate forest biotas, we analyzed amplified fragment length polymorphisms (AFLPs) and the breeding system in Dysosma versipellis. The study revealed that D. versipellis is mostly self-incompatible, genetically highly subdivided and depauperate at the population level (e.g., Φ(ST) = 0.572/H(E) = 0.083), and characterized by a low pollen-to-seed migration ratio (r ≈ 4.0). The latter outcome likely reflects limited pollen flow in a low-seed disperser whose hypothesized "sapromyophilous" flowers undergo scarce, inefficient, and likely specialized cross-pollination by small Anoplodera beetles, rather than carrion flies as assumed previously. In consequence, fruit set in D. versipellis was strongly pollen-limited. Our AFLP data support the hypothesis of a long-standing cessation of gene flow between western and central eastern populations, consistent with previous chloroplast DNA data. This phylogeographic pattern supports the role of the Sichuan Basin as a floristic boundary separating the Sino-Himalayan vs. Sino-Japanese Forest subkingdoms. Our genetic data of D. versipellis also imply that temperate deciduous forest elements to the west and the east of this basin responded differently to Quaternary climate change, which may have triggered or is leading to allopatric (incipient) speciation.

Sophora moorcroftiana is a perennial leguminous low shrub endemic to the middle reaches of Yarlung Zangbo River in Tibet. It is an important species to fix sand dunes and to avoid the formation of shifting sands; therefore, its progressive over-exploitation may enhance land desertification. The levels and distribution of genetic variability of this species were evaluated from 10 natural populations at 24 loci encoding 13 enzymes, using allozyme analysis by starch gel electrophoresis. Data obtained revealed moderate levels of genetic variation within populations (Pp=27.5%, Ap=1.5, Hep=0.122) and a considerable divergence among populations (FST=0.199). Significant positive correlations (r2=0.49, p<0.05; r2=0.46, p<0.05) were found between elevation and both mean number of alleles per locus (A) and gene diversity (He) in the studied populations of S. moorcroftiana. Lower genetic diversity in lower elevation populations might be due to the negative effects of human pressures and habitat fragmentation, to adaptation to high altitudes as a consequence of a peripatric speciation process, or to directional gene flow along the river basin from the source populations located in the west at higher altitudes. The evaluation of the degree of threat has led to the inclusion of this species in the category of EN ("endangered"), and conservation strategies for this endemic species are discussed on the basis of these findings.