Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme—GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species

Molecular characterization of Moenkhausia (Pisces: Characiformes) populations with different lateral line developmental levels

ABSTRACT The genera Hemigrammus and Moenkhausia have been traditionally diagnosed mainly by the former having lateral line completely pored whereas the latter having a lateral line with a few pored scales. Those features have been used to diagnose species of both genera in the upper Paraná River floodplain. Specimens with the diagnostic features of Moenkhausia bonita, collected in the upper Paraná River floodplain, exhibited different developmental levels of the lateral line, making it difficult to distinguish them from specimens of Hemigrammus sp. We analyzed the gene encoding cytochrome C oxidase I (COI) and intron 1 of the nuclear gene S7 to investigate the genetic similarities between the called Hemigrammus marginatus and M. bonita and to confirm their identities. Molecular sequences of other Moenkhausia species were analyzed for genus delimitation tests. The results reveal genetic similarities of M. bonita specimens with different developmental levels of the lateral line, and also distinguish between M. bonita and Hemigrammus sp. Species delimitation tests revealed that specimens from the upper Paraná River floodplain were M. bonita and were distinct from other Moenkhausia species. The developmental level of the lateral line is not a consistent characteristic that distinguishes between Moenkhausia and Hemigrammus species

Topological congruence between phylogenies of Anacanthorus spp. (Monogenea: Dactylogyridae) and their Characiformes (Actinopterygii) hosts: A case of host-parasite cospeciation.

Cophylogenetic studies aim at testing specific hypotheses to understand the nature of coevolving associations between sets of organisms, such as host and parasites. Monogeneans and their hosts provide and interesting platform for these studies due to their high host specificity. In this context, the objective of the present study was to establish whether the relationship between Anacanthorus spp. with their hosts from the upper Paraná River and its tributaries can be explained by means of cospeciation processes. Nine fish species and 14 monogenean species, most of them host specific, were studied. Partial DNA sequences of the genes RAG1, 16S and COI of the fish hosts and of the genes ITS2, COI and 5.8S of the parasite species were used for phylogenetic reconstruction. Maximum likelihood phylogenetic trees of the host and parasite species were built and used for analyses of topological congruence with PACo and ParaFit. The program Jane was used to estimate the nature of cospeciation events. The comparison of the two phylogenies revealed high topological congruence between them. Both PACo and ParaFit supported the hypothesis of global cospeciation. Results from Jane pointed to duplications as the most frequent coevolutionary event, followed by cospeciation, whereas duplications followed by host-switching were the least common event in Anacanthorus spp. studied. Host-sharing (spreading) was also identified but only between congeneric host species

Procrustean superimposition plot which minimizes the differences between the principal coordinates of patristic distances of <i>Anacanthorus</i> spp. and their Characiformes hosts.

<p>For each vector, the starting point (triangles) represent the configuration of <i>Anacanthorus</i> spp. and the arrowhead (points) the configuration of the corresponding hosts. The vector length represents the global fit (residual sum of squares) which is inversely proportional to the topological congruence. Host associations were grouped according to host families. Abbreviations of species names are the same as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0193408#pone.0193408.g003" target="_blank">Fig 3</a>.</p

GenBank accession numbers of the DNA sequences of genes RAG1, COI and 16S of fish hosts and associated species of <i>Anacanthorus</i> detected in the present effort on each fish species.

<p>GenBank accession numbers of the DNA sequences of genes RAG1, COI and 16S of fish hosts and associated species of <i>Anacanthorus</i> detected in the present effort on each fish species.</p

Sampling sites of fish in the Paraná River and its tributaries between 2012 and 2015.

<p>A) Project PELD area with rivers Ivinheima (22°47’S—53°32’W), Baia (22°43’S—53°17’W) and Paraná (22°45’S—53°15’W) in the flood plain of the upper Paraná River. B) Sampling sites of <i>Salminus hilarii</i> in the Taquari River: Site 1 (23°17’48. 23” S; 49°11’56.74” W); Site 2 (23°39’42.12” S; 49°08'08.42" W); Site 3 (23°31'28.82" S; 49°09'37.04" W).</p

Molecular mechanisms probably involved in plant colonization and plant growth promotion identified in the <i>H. seropedicae</i> SmR1 genome.

<p>Plant signals can modulate the expression of bacterial genes coding for adhesins, type IV <i>pili</i> and enzymes of lipopolysaccharide (LPS) synthesis, triggering bacterial attachment to root surfaces. The molecular communication involves bacterial protein secretion and phytohormones to stimulate plant growth and modulate plant defense response. In addition, modulation of plant ethylene levels by ACC deaminase may contribute to plant growth promotion. The success of the endophytic association depends on a compatible genetic background that leads to benefits for both organisms.</p

Proposed pathways for aromatic compounds metabolism in <i>H. seropedicae</i> SmR1.

<p>Proposed pathways for aromatic compounds metabolism in <i>H. seropedicae</i> SmR1.</p

The genome of <i>Herbaspirillum seropedicae</i> SmR1.

<p>From inside to outside 1) G+C content; 2) GC skew; 3) genes color-coded according the COG functional categories; genes in the + strand and − strand are represented in the inside and outside circles respectively; 4) rRNAS operons; 5) putative horizontally transferred regions identified using IVOM: light red indicates low score and dark red indicates high score; 6) regions of <i>H. seropedicae</i> genome identical to castor bean (<i>Ricinus communis</i>) sequences (minimum of 200 bp in length and higher than 90% in identity).</p