Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution.

As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

TCP5 controls leaf margin development by regulating KNOX and BEL-like transcription factors in Arabidopsis.

Development of leaf margins is an important process in leaf morphogenesis. CIN-clade TCP (TEOSINTE BRANCHED1/CYCLOIDEA/PCF) transcription factors are known to have redundant roles in specifying leaf margins, but the specific mechanisms through which individual TCP genes function remain elusive. In this study, we report that the CIN-TCP gene TCP5 is involved in repressing the initiation and outgrowth of leaf serrations by activating two key regulators of margin development, the Class II KNOX factor KNAT3 and BEL-like SAW1. Specifically, TCP5 directly promotes the transcription of KNAT3 and indirectly activates the expression of SAW1. We also show that TCP5 regulates KNAT3 and SAW1 in a temporal- and spatial- specific manner that is largely in accordance with the progress of formation of serrations. This regulation might serve as a key mechanism in patterning margin morphogenesis and in sculpting the final form of the leaf.

RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis.

Plant organ growth requires the proper transition from cell proliferation to cell expansion and differentiation. The CIN-TCP transcription factor gene TCP4 and its post-transcriptional regulator microRNA319 play a pivotal role in this process. In this study, we identified a pathway in which the product of the C2H2 zinc finger gene RABBIT EARS (RBE) regulates the transcription of TCP4 during Arabidopsis (Arabidopsis thaliana) petal development. RBE directly represses TCP4 during the early stages of petal development; this contributes to the role of RBE in controlling the growth of petal primordia. We also found that the rbe-1 mutant strongly enhanced the petal phenotypes of tcp4soj6 and mir319a, two mutants with compromised miR319 regulation of TCP4 Our results show that transcriptional and post-transcriptional regulation function together to pattern the spatial and temporal expression of TCP4 This in turn controls petal size and shape in Arabidopsis.

Temporal Control of Plant Organ Growth by TCP Transcription Factors.

The Arabidopsis petal is a simple laminar organ whose development is largely impervious to environmental effects, making it an excellent model for dissecting the regulation of cell-cycle progression and post-mitotic cell expansion that together sculpt organ form. Arabidopsis petals grow via basipetal waves of cell division, followed by a phase of cell expansion. RABBIT EARS (RBE) encodes a C2H2 zinc finger transcriptional repressor and is required for petal development. During the early phase of petal initiation, RBE regulates a microRNA164-dependent pathway that controls cell proliferation at the petal primordium boundaries. The effects of rbe mutations on petal lamina growth suggest that RBE is also required to regulate later developmental events during petal organogenesis. Here, we demonstrate that, early in petal development, RBE represses the transcription of a suite of CIN-TCP genes that in turn act to inhibit the number and duration of cell divisions; the temporal alleviation of that repression results in the transition from cell division to post-mitotic cell expansion and concomitant petal maturation.

Fluctuations of epstein-barr virus serological antibodies and risk for nasopharyngeal carcinoma: a prospective screening study with a 20-year follow-up.

BACKGROUND: The impact of variation of Epstein-Barr virus (EBV) antibody titers before the development of nasopharyngeal carcinoma (NPC) is still unclear. We analyzed the fluctuations of antibodies against EBV before histopathological diagnosis to assess the risk of NPC and aimed to provide a reliable basis for screening in high risk populations. METHODS: This study was based on a population-based screening program in Sihui County in Guangdong Province of China. A total of 18,986 subjects were recruited in 1987 and 1992, respectively. Baseline and repeated serological tests were performed for IgA antibodies against EBV capsid antigen (VCA/IgA) and early antigen (EA/IgA). Follow-up until the end of 2007 was accomplished through linkage with population and health registers. Cox proportional hazards regression model was used to estimate the relative risk of NPC in association with EBV antibodies. Time-dependent receiver operating characteristic curve (ROC) analysis was used to further evaluate the predictive ability. RESULTS: A total of 125 NPCs occurred during an average of 16.9 years of follow-up. Using baseline information alone or together with repeated measurements, serological levels of VCA/IgA and EA/IgA were significantly associated with increased risks for NPC, with a striking dose-response relationship and most prominent during the first 5 years of follow-up. Considering the fluctuant types of serological titers observed during the first three tests, relative risk was highest among participants with ascending titers of EBV VCA/IgA antibodies with an adjusted hazard ratio (HR) of 21.3 (95% confidence interval [CI] 7.1 to 64.1), and lowest for those with decreasing titers (HR = 1.5, 95% CI 0.2 to 11.4), during the first 5 years of follow-up. Time-dependent ROC analysis showed that VCA/IgA had better predictive performance for NPC incidence than EA/IgA. CONCLUSION: Our study documents that elevated EBV antibodies, particularly with ascending titers, are strongly associated with an increased risk for NPC.

[Long-term efficacy of radiotherapy on children with nasopharyngeal carcinoma].

BACKGROUND & OBJECTIVE: Nasopharyngeal carcinoma (NPC) in children is a particular type of NPC with poor prognosis. This study was to analyze long-term treatment efficacy, and relevant factors influencing prognosis of NPC in children. METHODS: From Jan. 1975 to Dec. 1995, 47 children,7-14 years old, with NPC diagnosed by pathology received radiotherapy in our hospital. Radiation doses were 52-74 Gy/6-13 weeks [(64.68+/-5.68) Gy] in nasopharynx, and 46-73 Gy/5-13 weeks [(57.77+/-5.86) Gy] in neck; 21 received 1-3 cycles of chemotherapy (cisplatin, bleomycin, 5-fluoroucil, vincristine, and cyclophosphamide) before radiotherapy. Survival rate was calculated by Kaplan-Meier method, and analyzed by log-rank test with SPSS 10.0 software. RESULTS: The 1, 3, 5-year survival rates of 47 patients were 72.3%, 53.2%, and 40.4%, respectively. Clinical stage (P=0.046), mode of biopsy (P=0.024), radiation dose in nasopharynx (P=0.049), and short-term efficacy (P=0.005) correlated with prognosis of these patients. The average height of 15 male children with NPC who survived for more than 5 years was (161.5+/-1.23) cm. Among 3 female children with NPC who survived for more than 5 years, 2 had menstruation disturbance. CONCLUSIONS: Clinical stage, mode of biopsy, radiation dose in nasopharynx, short-term efficacy may influence prognosis of NPC in children. Radiation-induced long-term sequelae of NPC in children should not be overlooked.

Genome-wide scan for familial nasopharyngeal carcinoma reveals evidence of linkage to chromosome 4.

Nasopharyngeal carcinoma (NPC) occurs with high frequency in Asian populations, especially among people of Cantonese ancestry. In areas with high incidence, NPC clusters in families, which suggests that both geography and genetics may influence disease risk. Although the HLA-Bw46 locus is associated with increased risk of NPC, no predisposing genes have been identified so far. Here we report the results of a genome-wide search carried out in families at high risk of NPC from Guangdong Province, China. Parametric analyses provide evidence of linkage to the D4S405 marker on chromosome 4 with a logarithm of odds for linkage (lod) score of 3.06 and a heterogeneity-adjusted lod (hlod) score of 3.21. Fine mapping with additional markers flanking D4S405 resulted in a lod score of 3.54 and hlod score of 3.67 for the region 4p15.1-q12. Multipoint nonparametric linkage analysis gives lod scores of 3.54 at D4S405 (P = 5.4 x 10(-5)) and 4.2 at D4S3002 (P = 1.1 x 10(-5)), which is positioned 4.5 cM away from D4S405. When Epstein Barr virus antibody titer was included as a covariate, the lod scores reached 4.70 (P = 2.0 x 10(-5)) and 5.36 (P = 4.36 x 10(-6)) for D4S405 and D4S3002, respectively. Our findings provide evidence of a major susceptibility locus for NPC on chromosome 4 in a subset of families.

[Study on genetic epidemiology of nasopharyngeal carcinoma in Guangdong, China].

OBJECTIVE: To explore the characteristic of genetic epidemiology of nasopharyngeal carcinoma (NPC) in a high risk area Guangdong province, China. METHODS: Population investigation was made on the nuclear pedigrees of the first patient with NPC and his/her spouse, and then complex segregation analysis was performed using regressive Logistic model. RESULTS: The risk of suffering from NPC is 9.31 times higher in the first degree relatives of patient with NPC than in the first degree relatives of spouse. The separation ratio and heritability are 0.0588 (0.0182, 0.0994) and 68.08% respectively. The result of complex segregation analysis shows that model D is better than model A. CONCLUSION: The genetic trend and familial clustering of NPC are more significant and powerful in Guangdong. The risk of suffering from NPC is related with parent's state and senior sibling's state. Nasopharyngeal carcinoma is a multi-gene hereditary disease, but a single gene that decides the susceptibility to NPC may be present.