Genetic Diversity of \u3cem\u3eColletotrichum Sublineola\u3c/em\u3e on Sweet Sorghum and Wild Sorghum Relatives in Kentucky and the Southeastern U.S.

Anthracnose, caused by the fungus Colletotrichum sublineola, is one of the most important diseases on sorghum (Sorghum bicolor) in the United States (U.S.) and worldwide. The production of sweet sorghum for feedstock has been increasing in the Southeastern U.S. (SE), and anthracnose has emerged as a significant production constraint. Anthracnose is also common on the ubiquitous wild sorghum relative, johnsongrass (Sorghum halepense). The degree to which the pathogen population on johnsongrass contributes to disease epidemics on cultivated sorghum (S. bicolor) in the SE is unknown. Genetic and pathological diversity was characterized among a collection of Colletotrichum strains recovered from S. bicolor and S. halepense in Kentucky, Alabama, Georgia, and Florida. The pathogenicity of five C. sublineola isolates from sweet and grain sorghum and from johnsongrass was measured on the susceptible sweet sorghum inbred Sugar Drip in the field. Isolates from cultivated sorghum were more aggressive than isolates from S. halepense, which generally caused little or no disease. The disease levels observed in the field had no effect on the yields of sorghum biomass, grain, or juice, or on Brix levels. Removal of sorghum seed heads increased sugar levels in the plants, but this had no effect on susceptibility to anthracnose. Greenhouse and laboratory assays were developed that gave rankings of relative strain aggressiveness that were consistent with the field results. Marker analyses with repetitive fingerprinting probes were used to evaluate several hundred Colletotrichum strains isolated from S. bicolor and S. halepense across the SE. Results revealed that, with a few exceptions, isolates from cultivated sorghum were genetically distinct from isolates from S. halepense. A restriction fragment length polymorphism (RFLP) analysis based on probes against individual sequences presumed to encode effectors and secondary metabolism enzymes confirmed that most isolates from johnsongrass grouped separately from most isolates from cultivated sorghum. The RFLP analysis revealed the presence of three distinct groups within the population that were distinguished by fixed allelic variations, or by presence-absence polymorphisms, of some of these putative pathogenicity genes. Phylogenetic trees were inferred based on a sampling of isolates from both host species and representing each of the three groups by using the internal transcribed spacer (ITS) sequence of the ribosomal DNA; portions of the DNA lyase gene (Apn2) and the manganese superoxide dismutase gene (Sod2); and a region between the Mat1 and the Apn2 genes (Mat1/Apn2). The trees were found to be congruent, and to identify three distinct species, including C. sublineola and two previously undescribed species. One of these novel species was found associated only with S. halepense throughout the SE. This new species was named Colletotrichum halepense (Xavier & Vaillancourt). There was evidence for cross-infection of S. bicolor and S. halepense by C. sublineola and the second new species, which was named C. caselae (Xavier & Vaillancourt). These findings have significant implications for the development and deployment of resistant sweet sorghum varieties in areas where johnsongrass is common. This information will help to evaluate the potential for Colletotrichum spp. to cause epidemics in sweet sorghum if acreages continue to expand in the SE in the future

A Comparative Genomic Analysis of Putative Pathogenicity Genes in the Host-Specific Sibling Species \u3cem\u3eColletotrichum graminicola\u3c/em\u3e and \u3cem\u3eColletotrichum sublineola\u3c/em\u3e

Background: Colletotrichum graminicola and C. sublineola cause anthracnose leaf and stalk diseases of maize and sorghum, respectively. In spite of their close evolutionary relationship, the two species are completely host-specific. Host specificity is often attributed to pathogen virulence factors, including specialized secondary metabolites (SSM), and small-secreted protein (SSP) effectors. Genes relevant to these categories were manually annotated in two co-occurring, contemporaneous strains of C. graminicola and C. sublineola. A comparative genomic and phylogenetic analysis was performed to address the evolutionary relationships among these and other divergent gene families in the two strains. Results: Inoculation of maize with C. sublineola, or of sorghum with C. graminicola, resulted in rapid plant cell death at, or just after, the point of penetration. The two fungal genomes were very similar. More than 50% of the assemblies could be directly aligned, and more than 80% of the gene models were syntenous. More than 90% of the predicted proteins had orthologs in both species. Genes lacking orthologs in the other species (non-conserved genes) included many predicted to encode SSM-associated proteins and SSPs. Other common groups of non-conserved proteins included transporters, transcription factors, and CAZymes. Only 32 SSP genes appeared to be specific to C. graminicola, and 21 to C. sublineola. None of the SSM-associated genes were lineage-specific. Two different strains of C. graminicola, and three strains of C. sublineola, differed in no more than 1% percent of gene sequences from one another. Conclusions: Efficient non-host recognition of C. sublineola by maize, and of C. graminicola by sorghum, was observed in epidermal cells as a rapid deployment of visible resistance responses and plant cell death. Numerous non-conserved SSP and SSM-associated predicted proteins that could play a role in this non-host recognition were identified. Additional categories of genes that were also highly divergent suggested an important role for co-evolutionary adaptation to specific host environmental factors, in addition to aspects of initial recognition, in host specificity. This work provides a foundation for future functional studies aimed at clarifying the roles of these proteins, and the possibility of manipulating them to improve management of these two economically important diseases

NEOTROPICAL CARNIVORES: a data set on carnivore distribution in the Neotropics

Mammalian carnivores are considered a key group in maintaining ecological health and can indicate potential ecological integrity in landscapes where they occur. Carnivores also hold high conservation value and their habitat requirements can guide management and conservation plans. The order Carnivora has 84 species from 8 families in the Neotropical region: Canidae; Felidae; Mephitidae; Mustelidae; Otariidae; Phocidae; Procyonidae; and Ursidae. Herein, we include published and unpublished data on native terrestrial Neotropical carnivores (Canidae; Felidae; Mephitidae; Mustelidae; Procyonidae; and Ursidae). NEOTROPICAL CARNIVORES is a publicly available data set that includes 99,605 data entries from 35,511 unique georeferenced coordinates. Detection/non-detection and quantitative data were obtained from 1818 to 2018 by researchers, governmental agencies, non-governmental organizations, and private consultants. Data were collected using several methods including camera trapping, museum collections, roadkill, line transect, and opportunistic records. Literature (peer-reviewed and grey literature) from Portuguese, Spanish and English were incorporated in this compilation. Most of the data set consists of detection data entries (n = 79,343; 79.7%) but also includes non-detection data (n = 20,262; 20.3%). Of those, 43.3% also include count data (n = 43,151). The information available in NEOTROPICAL CARNIVORES will contribute to macroecological, ecological, and conservation questions in multiple spatio-temporal perspectives. As carnivores play key roles in trophic interactions, a better understanding of their distribution and habitat requirements are essential to establish conservation management plans and safeguard the future ecological health of Neotropical ecosystems. Our data paper, combined with other large-scale data sets, has great potential to clarify species distribution and related ecological processes within the Neotropics. There are no copyright restrictions and no restriction for using data from this data paper, as long as the data paper is cited as the source of the information used. We also request that users inform us of how they intend to use the data