Comparative pan-genome analysis of Piscirickettsia salmonis reveals genomic divergences within genogroups

Indexación: Scopus.Piscirickettsia salmonis is the etiological agent of salmonid rickettsial septicemia, a disease that seriously affects the salmonid industry. Despite efforts to genomically characterize P. salmonis, functional information on the life cycle, pathogenesis mechanisms, diagnosis, treatment, and control of this fish pathogen remain lacking. To address this knowledge gap, the present study conducted an in silico pan-genome analysis of 19 P. salmonis strains from distinct geographic locations and genogroups. Results revealed an expected open pan-genome of 3,463 genes and a core-genome of 1,732 genes. Two marked genogroups were identified, as confirmed by phylogenetic and phylogenomic relationships to the LF-89 and EM-90 reference strains, as well as by assessments of genomic structures. Different structural configurations were found for the six identified copies of the ribosomal operon in the P. salmonis genome, indicating translocation throughout the genetic material. Chromosomal divergences in genomic localization and quantity of genetic cassettes were also found for the Dot/Icm type IVB secretion system. To determine divergences between core-genomes, additional pan-genome descriptions were compiled for the so-termed LF and EM genogroups. Open pan-genomes composed of 2,924 and 2,778 genes and core-genomes composed of 2,170 and 2,228 genes were respectively found for the LF and EM genogroups. The core-genomes were functionally annotated using the Gene Ontology, KEGG, and Virulence Factor databases, revealing the presence of several shared groups of genes related to basic function of intracellular survival and bacterial pathogenesis. Additionally, the specific pan-genomes for the LF and EM genogroups were defined, resulting in the identification of 148 and 273 exclusive proteins, respectively. Notably, specific virulence factors linked to adherence, colonization, invasion factors, and endotoxins were established. The obtained data suggest that these genes could be directly associated with inter-genogroup differences in pathogenesis and host-pathogen interactions, information that could be useful in designing novel strategies for diagnosing and controlling P. salmonis infection. © 2017 Nourdin-Galindo, Sánchez, Molina, Espinoza-Rojas, Oliver, Ruiz, Vargas-Chacoff, Cárcamo, Figueroa, Mancilla, Maracaja-Coutinho and Yañez.https://www.frontiersin.org/articles/10.3389/fcimb.2017.00459/ful

Tectonic Processes Along the Chile Convergent Margin

The Chile subduction zone, spanning more than 3500 km, provides a unique setting for studying, along a single plate boundary, the factors that govern tectonic processes at convergent margins. At large scale, the Chile trench is segmented by the subduction of the Chile Rise, an active spreading center, and by the Juan Fernández hot spot ridge. In addition, the extreme climatic change from the Atacama Desert in the north to the glacially influenced southern latitudes produces a dramatic variability in the volume of sediment supplied to the trench. The distribution of sediment along the trench is further influenced by the high relief gradients of the segmented oceanic lithosphere. We interpret new and reprocessed multichannel seismic reflection profiles, and multibeam bathymetric data, to study the variability in tectonic processes along the entire convergent margin. In central and south Chile, where the trench contains thick turbidite infill, accretionary prisms, some 50–60 km wide, have developed. These prisms, however, are ephemeral and can be rapidly removed by high-relief, morphological features on the incoming oceanic plate. Where topographic barriers inhibit the transport of turbidites along the trench, sediment infill abruptly decreases to less than 1 km thick and is confined to a narrow zone at the trench axis. There, all sediment is subducted; the margin is extending by normal faulting and collapsing due to basal tectonic erosion. The transition from accretion to tectonic erosion occurs over short distances (a few tens of km) along the trench. In the turbidite-starved northern Chile trench, ~1 km of slope debris reaches the trench and is subsequently subducted. There, tectonic erosion is causing pronounced steepening of the margin, associated pervasive extension across the slope and into the emerged coastal area, and consequent collapse of the overriding plate. The volume of subducting material varies little along much of the margin. However, the composition of the material varies from slope debris of upper-plate fragments and material removed from the upper plate by basal erosion, to turbidites derived from the Andes