The Historical Demography and Genetic Variation of the Endangered Cycas multipinnata (Cycadaceae) in the Red River Region,Examined by Chloroplast DNA Sequences and Microsatellite Markers

Cycas multipinnata C.J. Chen & S.Y. Yang is a cycad endemic to the Red River drainage region that occurs under evergreen forest on steep limestone slopes in Southwest China and northern Vietnam. It is listed as endangered due to habitat loss and over-collecting for the ornamental plant trade, and only several populations remain. In this study, we assess the genetic variation, population structure, and phylogeography of C. multipinnata populations to help develop strategies for the conservation of the species. 60 individuals from six populations were used for chloroplast DNA (cpDNA) sequencing and 100 individuals from five populations were genotyped using 17 nuclear microsatellites. High genetic differentiation among populations was detected, suggesting that pollen or seed dispersal was restricted within populations. Two main genetic clusters were observed in both the cpDNA and microsatellite loci, corresponding to Yunnan China and northern Vietnam. These clusters indicated low levels of gene flow between the regions since their divergence in the late Pleistocene, which was inferred from both Bayesian and coalescent analysis. In addition, the result of a Bayesian skyline plot based on cpDNA portrayed a long history of constant population size followed by a decline in the last 50,000 years of C. multipinnata that was perhaps affected by the Quaternary glaciations, a finding that was also supported by the Garza-Williamson index calculated from the microsatellite data. The genetic consequences produced by climatic oscillations and anthropogenic disturbances are considered key pressures on C. multipinnata. To establish a conservation management plan, each population of C. multipinnata should be recognized as a Management Unit (MU). In situ and ex situ actions, such as controlling overexploitation and creating a germplasm bank with high genetic diversity, should be urgently implemented to preserve this species.     

Characterizing RNA–protein interaction using cross-linking and metabolite supplemented nuclear RNA-immunoprecipitation

RNA-immunoprecipitation (RNA-IP) is a method used to isolate and identify RNA molecules specifically associated with an RNA-binding protein. Non-coding RNAs are emerging as key regulators of many biological and developmental pathways and RNA-IP has become an important tool in studying their function(s). While RNA-IP is successfully used to determine protein-RNA interaction, specific details regarding the level of this association and the metabolic requirement of this interaction which can influence the success of RNA-IP remain unclear. Here, we investigate the conditions required for efficient nuclear RNA-IP using Arabidopsis AGO4 (Argonaute 4) and siRNA binding as the study model. We showed that formaldehyde cross-linking, but not UV cross-linking, allowed for efficient pull-down of 24-nt siRNAs, suggesting that AGO4–siRNA interaction involves other protein(s). We also showed that, while formaldehyde cross-linking could also be performed on purified nuclei, ATP supplementation to the nuclei isolation buffer was needed to efficiently pull down 24-nt siRNAs. This result indicates that ATP is required for efficient siRNA loading onto AGO4. As most of the known RNA-mediated regulatory processes occur in the nucleus, our findings on cross-linking conditions and metabolite requirement for successful AGO4 nuclear RNA-IP provide a valuable insight and future consideration when studying the function of protein–RNA interactions in plants.     

Analyse des pedigrees et calcul des coefficients d'identité par les arbres géniques

Two genes in a pedigree are identical by descent if they are two copies of a common ancestor gene. To obtain an unambiguous definition of the set of genes, at some autosomal locus, any gene is defined as an ordered pair of zygotes: the zygote who carries the gene, and the parent who transmitted it. The natural ordered structure on the set of zygotes yields an ordered structure upon the set of genes. Any event of the mendelian segregation splits down the set of genes into non-overlaping classes of identical genes: when considered as an ordered sub-set of genes, each class is shown to have the algebraic properties of a tree. Given a sub-set ?? of genes, a family of exclusive events ensuring identity between all genes of ?? is identified as a family of genic trees with some property. This relationship between segregational events and genic trees is extended to the case where two sub-sets ?? and ??′ of genes are considered together. As a consequence, a general method is obtained to compute either identity coefficients involving any number of genes splitted into one or two identity classes, or the fifteen coefficients defined among four genes, whichever the relationships between zygotes and genes might be. Using this approach to deal with the allelic structure in a set of genes carried by related zygotes is suggested.