Transcriptional Profiling of Early Defense Response to White Pine Blister Rust Infection in Pinus albicaulis (Whitebark Pine).

Pathogen perception generates the activation of signal transduction cascades to host defense. White pine blister rust (WPBR) is caused by Cronartium ribicola J.C. Fisch and affects a number of species of Pinus. One of the most severely affected species is Pinus albicaulis Engelm (whitebark pine). WPBR resistance in the species is a polygenic and complex trait that requires an optimized immune response. We identified early responses in 2-year-old seedlings after four days of fungal inoculation and compared the underlying transcriptomic response with that of healthy non-inoculated individuals. A de novo transcriptome assembly was constructed with 56,796 high quality-annotations derived from the needles of susceptible and resistant individuals in a resistant half-sib family. Differential expression analysis identified 599 differentially expressed transcripts, from which 375 were upregulated and 224 were downregulated in the inoculated seedlings. These included components of the initial phase of active responses to abiotic factors and stress regulators, such as those involved in the first steps of flavonoid biosynthesis. Four days after the inoculation, infected individuals showed an overexpression of chitinases, reactive oxygen species (ROS) regulation signaling, and flavonoid intermediates. Our research sheds light on the first stage of infection and emergence of disease symptoms among whitebark pine seedlings. RNA sequencing (RNA-seq) data encoding hypersensitive response, cell wall modification, oxidative regulation signaling, programmed cell death, and plant innate immunity were differentially expressed during the defense response against C. ribicola.

A genome sequence for the threatened whitebark pine.

Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from the introduced fungal pathogen white pine blister rust (WPBR, Cronartium ribicola) and additional threats from mountain pine beetle (Dendroctonus ponderosae), wildfire, and maladaptation due to changing climate. Vast acreages of WBP have suffered nearly complete mortality. Genomic technologies can contribute to a faster, more cost-effective approach to the traditional practices of identifying disease-resistant, climate-adapted seed sources for restoration. With deep-coverage Illumina short reads of haploid megagametophyte tissue and Oxford Nanopore long reads of diploid needle tissue, followed by a hybrid, multistep assembly approach, we produced a final assembly containing 27.6 Gb of sequence in 92,740 contigs (N50 537,007 bp) and 34,716 scaffolds (N50 2.0 Gb). Approximately 87.2% (24.0 Gb) of total sequence was placed on the 12 WBP chromosomes. Annotation yielded 25,362 protein-coding genes, and over 77% of the genome was characterized as repeats. WBP has demonstrated the greatest variation in resistance to WPBR among the North American white pines. Candidate genes for quantitative resistance include disease resistance genes known as nucleotide-binding leucine-rich repeat receptors (NLRs). A combination of protein domain alignments and direct genome scanning was employed to fully describe the 3 subclasses of NLRs. Our high-quality reference sequence and annotation provide a marked improvement in NLR identification compared to previous assessments that leveraged de novo-assembled transcriptomes.

Measuring Developmental Delays: Comparison of Parent Report and Direct Testing.

PURPOSE: Developmental assessment is part of a comprehensive autism evaluation. During in-person evaluations, developmental assessment is completed via direct testing by an examiner. In telehealth evaluations, developmental assessment relies on caregiver-report instruments. This study examined correspondence between caregiver report and direct testing of developmental skills. METHODS: Participants were 93 children, aged 18-42 months, undergoing evaluation for possible autism spectrum disorder (ASD). Caregivers were interviewed with the Developmental Profile, 4th edition (DP-4) via telehealth platform and children were tested in person 2-4 weeks later using the Mullen Scales of Early Learning (MSEL). RESULTS: Correlations between the DP-4 and MSEL were high (ranging from 0.50 to 0.82) across standard scores, age equivalents, and functional categories, as well as across individual subtests and overall composite scores. CONCLUSION: The high convergent validity found in this study suggests that the DP-4 provides a suitable proxy for direct developmental testing using the MSEL in the context of telehealth evaluations for ASD in young children, delivering a good estimate of both developmental functioning and presence of delays. TRIAL REGISTRATION: Data were obtained from registered clinical trial NCT05047224, date of registration 2021-09-07.