Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits. We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar (“Pawnee”) and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives. Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

Rhodococcus fascians , a phytopathogen that alters plant development, inflicts significant losses in plant production around the world. We report here the complete genome sequence of R. fascians D188, a well-characterized model isolate, and Rhodococcus species PBTS (pistachio bushy top syndrome) 1 and 2, which were shown to be responsible for a disease outbreak in pistachios.

Pistachio Bushy Top Syndrome (PBTS) is a recently emerged disease that has strongly impacted the pistachio industry in California, Arizona, and New Mexico. The disease is caused by two bacteria, designated PBTS1 that is related to Rhodococcus corynebacterioides and PBTS2 that belongs to the species R. fascians. Here, we assessed the pathogenic character of the causative agents and examined their chromosomal sequences to predict the presence of particular functions that might contribute to the observed co-occurrence and their effect on plant hosts. In diverse assays, we confirmed the pathogenicity of the strains on “UCB-1” pistachio rootstock and showed that they can also impact the development of tobacco species, but concurrently inconsistencies in the ability to induce symptoms were revealed. We additionally evidence that fas genes are present only in a subpopulation of pure PBTS1 and PBTS2 cultures after growth on synthetic media, that these genes are easily lost upon cultivation in rich media, and that they are enriched for in an in planta environment. Analysis of the chromosomal sequences indicated that PBTS1 and PBTS2 might have complementary activities that would support niche partitioning. Growth experiments showed that the nutrient utilization pattern of both PBTS bacteria was not identical, thus avoiding co-inhabitant competition. PBTS2 appeared to have the potential to positively affect the habitat fitness of PBTS1 by improving its resistance against increased concentrations of copper and penicillins. Finally, mining the chromosomes of PBTS1 and PBTS2 suggested that the bacteria could produce cytokinins, auxins, and plant growth-stimulating volatiles and that PBTS2 might interfere with ethylene levels, in support of their impact on plant development. Subsequent experimentation supported these in silico predictions. Altogether, our data provide an explanation for the observed pathogenic behavior and unveil part of the strategies used by PBTS1 and PBTS2 to interact with plants.

Phytophthora species were isolated from rivers and streams in the southwestern United States by leaf baiting and identified by sequence analysis of internal transcribed spacer (ITS) ribosomal DNA (rDNA). The major waterways examined included the Rio Grande River, Gila River, Colorado River, and San Juan River. The most prevalent species identified in rivers and streams were Phytophthora lacustris and P. riparia , both members of Phytophthora ITS clade 6. P. gonapodyides , P. cinnamomi , and an uncharacterized Phytophthora species in clade 9 were also recovered. In addition, six isolates recovered from the Rio Grande River were shown to be hybrids of P. lacustris × P. riparia . Pathogenicity assays using P. riparia and P. lacustris failed to produce any disease symptoms on commonly grown crops in the southwestern United States. Inoculation of Capsicum annuum with P. riparia was shown to inhibit disease symptom development when subsequently challenged with P. capsici , a pathogenic Phytophthora species. IMPORTANCE Many Phytophthora species are significant plant pathogens causing disease on a large variety of crops worldwide. Closer examinations of streams, rivers, and forest soils have also identified numerous Phytophthora species that do not appear to be phytopathogens and likely act as early saprophytes in aquatic and saturated environments. To date, the Phytophthora species composition in rivers and streams of the southwestern United States has not been evaluated. This article details a study to determine the identity and prevalence of Phytophthora species in rivers and streams located in New Mexico, Arizona, Colorado, Utah, and Texas. Isolated species were evaluated for pathogenicity on crop plants and for their potential to act as biological control agents.

Carya illinoinensis (pecan) produce a high valued and desired nut crop; with production expanding worldwide. Important attributes of pecans and their ability to adapt to different environments aside from their native regions are currently being investigated. Microbial communities are known to play an important role in crop productivity and overall plant health. Studies in other plant species have shown that the plant microbiome may be influenced by both the environmental conditions and genetics of the plant. Microbiota research in pecan is in its early stages and here we report insights into the core microbiome of seedlings derived from five pecan cultivars located in an orchard from Las Cruces, New Mexico. Seeds from open-pollinated pecan cultivars (‘Burkett’, ‘Mandan’, ‘Pawnee’, ‘Western’, and ‘Wichita’) were collected and grown in a quarantine greenhouse under highly regulated conditions. DNA from the resulting seedlings were used for next generation sequencing (MiSeq) for 16S and ITS and microbiome analyses revealed significant differences in microbial composition and relative abundance (bacterial and fungal) between seedling organs, with roots having the highest alpha diversity followed by stems and leaves. Bacterial family Chitinophagaceae was identified to be most relatively abundant in the roots of seedlings compared to the bacterial families Rhizobiaceae and Moraxellaceae, which were found to be most relatively abundant in the stems and leaves, respectively. Analyses also indicated that there were several families (bacterial families: Rhizobiaceae, Enterobacteriaceae, Chitinophagaceae, Burkholderiaceae, Sphingomonadaceae, Pseudomonadaceae, Moraxellaceae, Microscillaceae, Rubritaleaceae, Caulobacteraceae; fungal families: Serendipitaceae, Nectriaceae, Ophiostomataceae, Hypocreaceae, Aspergillaceae, and Cephalothecaceae) that were found in all seedlings and these constitute a core microbiome for pecan. There were also differences in microbial composition (bacterial and fungal) between seedlings from different maternal pecan cultivars and these differences are proposed to constitute a signature microbiome for the maternal cultivar. As pecan trees continues to extend to other growing regions it is important to understand the role that these microbes play in pecan. By establishing the core microbiome of pecans, the selection of microbes for breeding and improving pecan production will become a possibility.