A Connectivity-Based Eco-Regionalization Method of the Mediterranean Sea

Ecoregionalization of the ocean is a necessary step for spatial management of marine resources. Previous ecoregionalization efforts were based either on the distribution of species or on the distribution of physical and biogeochemical properties. These approaches ignore the dispersal of species by oceanic circulation that can connect regions and isolates others. This dispersal effect can be quantified through connectivity that is the probability, or time of transport between distinct regions. Here a new regionalization method based on a connectivity approach is described and applied to the Mediterranean Sea. This method is based on an ensemble of Lagrangian particle numerical simulations using ocean model outputs at 1/12° resolution. The domain is divided into square subregions of 50 km size. Then particle trajectories are used to quantify the oceanographic distance between each subregions, here defined as the mean connection time. Finally the oceanographic distance matrix is used as a basis for a hierarchical clustering. 22 regions are retained and discussed together with a quantification of the stability of boundaries between regions. Identified regions are generally consistent with the general circulation with boundaries located along current jets or surrounding gyres patterns. Regions are discussed in the light of existing ecoregionalizations and available knowledge on plankton distributions. This objective method complements static regionalization approaches based on the environmental niche concept and can be applied to any oceanic region at any scale.     

Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg

Key message

A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping.

Abstract

Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.

     

Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker

Background

Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in Brassica napus, a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions.

Results

Genome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of B. napus. Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the B. napus genome. Overall, these six ancestral blocks have 34 duplicated copies in the B.napus genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in B. napus.

Conclusions

Our study provides information on the involvement of duplicated loci in the control of stem canker resistance in B. napus. Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-498) contains supplementary material, which is available to authorized users.     

Epstein-Barr virus infection of polarized tongue and nasopharyngeal epithelial cells

Epstein-Barr virus (EBV) initially enters the body through the oropharyngeal mucosa and subsequently infects B lymphocytes through their CD21 (CR2) complement receptor. Mechanisms of EBV entry into and release from epithelial cells are poorly understood. To study EBV infection in mucosal oropharyngeal epithelial cells, we established human polarized tongue and pharyngeal epithelial cells in culture. We show that EBV enters these cells through three CD21-independent pathways: (i) by direct cell-to-cell contact of apical cell membranes with EBV-infected lymphocytes; (ii) by entry of cell-free virions through basolateral membranes, mediated in part through an interaction between beta1 or alpha5beta1 integrins and the EBV BMRF-2 protein; and (iii) after initial infection, by virus spread directly across lateral membranes to adjacent epithelial cells. Release of progeny virions from polarized cells occurs from both their apical and basolateral membranes. These data indicate that multiple approaches to prevention of epithelial infection with EBV will be necessary.     

Inhibition of human papillomavirus type 16 E7 phosphorylation by the S100 MRP-8/14 protein complex

The human papillomavirus type 16 (HPV16) E7 is a major viral oncoprotein that is phosphorylated by casein kinase II (CKII). Two S100 family calcium-binding proteins, macrophage inhibitory-related factor protein 8 (MRP-8) and MRP-14, form a protein complex, MRP-8/14, that inactivates CKII. The MRP-8/14 protein complex may inhibit CKII-mediated E7 phosphorylation and therefore may alter its interaction with cellular ligands and reduce E7 oncogenic activity. We examined the inhibitory effect of the MRP-8/14 complex on CKII activity and HPV16 E7 phosphorylation. We have shown that CKII activity and HPV16 E7 phosphorylation were inhibited by uptake of exogenous MRP-8/14 and activation of endogenous MRP-8/14. MRP-8/14-mediated inhibition of E7 phosphorylation occurred at the G1 phase of the cell cycle. Analysis of MRP expression in primary keratinocytes and in HPV16- and 18-transformed cervical and foreskin epithelial cell lines showed that expression of MRP-8, MRP-14, and the MRP-8/14 complex was detected only in primary untransformed keratinocytes and not in the HPV-infected immortalized epithelial cells. CKII activity in HPV-immortalized keratinocytes was approximately fourfold higher than in HPV-negative primary keratinocytes. Treatment of HPV-positive immortalized epithelial cells with exogenous MRP-8/14 resulted in E7 hypophosphorylation and complete inhibition of cell growth within 2 weeks, compared with HPV-negative primary and immortalized HPV-negative cervical epithelial cells, which showed 25 and 40% growth inhibition, respectively. Together these results suggests that the MRP-8/14 protein complex in HPV-infected epithelial cells may play an important role in regulation of CKII-mediated E7 phosphorylation and inhibition of its oncogenic activity.     

New insights into global biogeography,population structure and natural selection from the genome of the epipelagic copepod Oithona

In the epipelagic ocean, the genus Oithona is considered as one of the most abundant and widespread copepods and plays an important role in the trophic food web. Despite its ecological importance, little is known about Oithona and cyclopoid copepods genomics. Therefore, we sequenced, assembled and annotated the genome of Oithona nana. The comparative genomic analysis integrating available copepod genomes highlighted the expansions of genes related to stress response, cell differentiation and development, including genes coding Lin12‐Notch‐repeat (LNR) domain proteins. The Oithona biogeography based on 28S sequences and metagenomic reads from the Tara Oceans expedition showed the presence of O. nana mostly in the Mediterranean Sea (MS) and confirmed the amphitropical distribution of Oithona similis. The population genomics analyses of O. nana in the Northern MS, integrating the Tara Oceans metagenomic data and the O. nana genome, led to the identification of genetic structure between populations from the MS basins. Furthermore, 20 loci were found to be under positive selection including four missense and eight synonymous variants, harbouring soft or hard selective sweep patterns. One of the missense variants was localized in the LNR domain of the coding region of a male‐specific gene. The variation in the B‐allele frequency with respect to the MS circulation pattern showed the presence of genomic clines between O. nana and another undefined Oithona species possibly imported through Atlantic waters. This study provides new approaches and results in zooplankton population genomics through the integration of metagenomic and oceanographic data.