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Ostertagia ostertagi is a cattle stomach nematode that causes significant disease; however, little is known about host responses to infection. Due to the emergence of drug resistance in these parasites, there is a need for alternative treatments. To understand host responses to O. ostertagi infection in the gastric mucosa, gene expression in fundic and pyloric mucosa was compared between infected and uninfected calves for 21 d post-infection. The number of differentially expressed genes (DEGs) increased over time with more upregulated than downregulated DEGs at each time point. Fundic mucosa had more DEGs than pyloric mucosa across all time points. The largest changes occurred between d 7 to 9 and 10 post-infection. Most DEGs are associated with immunity, cellular reorganization, cell migration, and proliferation. Tuft/epithelial cell response to the infection was atypical, lacking key cytokines. Numerous genes associated with T cell exhaustion were upregulated. The data collectively indicate that O. ostertagi infection elicited host immune responses, yet also suggest parasite-induced immunosuppression is present. This may explain why cattle are slow in developing protective immunity to O. ostertagi. Understanding mechanisms of parasite evasion will facilitate the rational design of protective vaccines against complex nematode parasites. [ABSTRACT FROM AUTHOR]

Plants and arbuscular mycorrhizal fungi (AMF) engage in mutually beneficial symbioses based on a reciprocal exchange of nutrients. The beneficial character of the symbiosis is maintained through a mechanism called autoregulation of mycorrhization (AOM). AOM includes root-to-shoot-to-root signaling; however, the molecular details of AOM are poorly understood. AOM shares many features of autoregulation of nodulation (AON) where several genes are known, including the receptor-like kinase SUPER NUMERIC NODULES (SUNN), root-to-shoot mobile CLAVATA3/ENDOSPERM SURROUNDING REGION (ESR)-RELATED (CLE) peptides, and the hydroxyproline O -arabinosyltransferase ROOT DETERMINED NODULATION1 (RDN1) required for post-translational peptide modification. In this work, CLE53 was identified to negatively regulate AMF symbiosis in a SUNN- and RDN1-dependent manner. CLE53 expression was repressed at low phosphorus, while it was induced by AMF colonization and high phosphorus. CLE53 overexpression reduced AMF colonization in a SUNN- and RDN1 dependent manner, while cle53 , rdn1 , and sunn mutants were more colonized than the wild type. RNA-sequencing identified 700 genes with SUNN-dependent regulation in AMF-colonized plants, providing a resource for future identification of additional AOM genes. Disruption of AOM genes in crops potentially constitutes a novel route for improving AMF-derived phosphorus uptake in agricultural systems with high phosphorus levels. [ABSTRACT FROM AUTHOR]

A growing number of small secreted peptides (SSPs) in plants are recognized as important regulatory molecules with roles in processes such as growth, development, reproduction, stress tolerance, and pathogen defense. Recent discoveries further implicate SSPs in regulating root nodule development, which is of particular significance for legumes. SSP-coding genes are frequently overlooked, because genome annotation pipelines generally ignore small open reading frames, which are those most likely to encode SSPs. Also, SSP-coding small open reading frames are often expressed at low levels or only under specific conditions, and thus are underrepresented in non-tissue-targeted or non-condition-optimized RNA-sequencing projects. We previously identified 4,439 SSP-encoding genes in the model legume Medicago truncatula. To support systematic characterization and annotation of these putative SSP-encoding genes, we developed the M. truncatula Small Secreted Peptide Database (MtSSPdb; https://mtsspdb.noble.org/). MtSSPdb currently hosts (1) a compendium of M. truncatula SSP candidates with putative function and family annotations; (2) a large-scale M. truncatula RNA-sequencing-based gene expression atlas integrated with various analytical tools, including differential expression, coexpression, and pathway enrichment analyses; (3) an online plant SSP prediction tool capable of analyzing protein sequences at the genome scale using the same protocol as for the identification of SSP genes; and (4) information about a library of synthetic peptides and root and nodule phenotyping data from synthetic peptide screens in planta. These datasets and analytical tools make MtSSPdb a unique and valuable resource for the plant research community. MtSSPdb also has the potential to become the most complete database of SSPs in plants. [ABSTRACT FROM AUTHOR]

Weaning in ruminants is characterized by the transition from a milk-based diet to a solid diet which drives a critical gastrointestinal tract transformation. Identifying regulatory control of this transformation during weaning can help identify strategies to improve rumen health. This study aimed to identify regions of accessible chromatin in rumen epithelial tissue in preand post-weaning calves and investigate differentially accessible regions (DARs) to uncover regulatory elements in cattle rumen development using the ATAC-seq approach. A total of 126,071 peaks were identified, covering 1.15% of the cattle genome. From these accessible regions, 2,766 DARs were discovered. Gene ontology enrichment resulted in GO terms related to cell adhesion, anchoring junction, growth, cell migration, motility, and morphogenesis. In addition, putative regulatory canonical pathways were identified (TGFß, Integrin-linked kinase, Integrin signaling, and regulation of the epithelial-mesenchymal transition). Canonical pathways integrated with co-expression results showed that TGFß and ILK signaling pathways play essential roles in rumen development through the regulation of cellular adhesions. In this study, DARs during weaning have been identified, revealing enhancers, transcription factors, and candidate target genes that represent potential biomarkers for the bovine rumen development which will serve as a molecular tool for rumen development studies. [ABSTRACT FROM AUTHOR]

Next-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonym-ous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding. [ABSTRACT FROM AUTHOR]

Red alder (Alnus rubra Bong.) is an ecologically significant and important fast-growing commercial tree species native to western coastal and riparian regions of North America, having highly desirable wood, pigment, and medicinal properties. We have sequenced the genome of a rapidly growing clone. The assembly is nearly complete, containing the full complement of expected genes. This supports our objectives of identifying and studying genes and pathways involved in nitrogen-fixing symbiosis and those related to secondary metabolites that underlie red alder's many interesting defense, pigmentation, and wood quality traits. We established that this clone is most likely diploid and identified a set of SNPs that will have utility in future breeding and selection endeavors, as well as in ongoing population studies. We have added a well-characterized genome to others from the order Fagales. In particular, it improves significantly upon the only other published alder genome sequence, that of Alnus glutinosa. Our work initiated a detailed comparative analysis of members of the order Fagales and established some similarities with previous reports in this clade, suggesting a biased retention of certain gene functions in the vestiges of an ancient genome duplication when compared with more recent tandem duplications. [ABSTRACT FROM AUTHOR]