@article{katherine m. d'amico-willman_niederhuth_sovic_anderson_gradziel_fresnedo-ramirez_2024, title={Hypermethylation and small RNA expression are associated with increased age in almond<i> (Prunus</i><i> dulcis</i> [Mill.] DA Webb) accessions}, volume={338}, ISSN={["1873-2259"]}, DOI={10.1016/j.plantsci.2023.111918}, abstractNote={The focus of this study is to profile changes in DNA methylation and small RNA expression occurring with increased age in almond breeding germplasm to identify possible biomarkers of age that can be used to assess the potential of individuals to develop aging-related disorders. To profile DNA methylation in almond germplasm, 70 methylomes were generated from almond individuals representing three age cohorts (11, 7, and 2 years old) using an enzymatic methyl-seq approach followed by analysis to call differentially methylated regions (DMRs) within these cohorts. Small RNA (sRNA) expression was profiled in three breeding selections, each from two age cohorts (1 and 6 years old), using sRNA-Seq followed by differential expression analysis. Weighted chromosome-level methylation analysis reveals hypermethylation in 11-year-old almond breeding selections when compared to 2-year-old selections in the CG and CHH contexts. Seventeen consensus DMRs were identified in all age contrasts. sRNA expression differed significantly between the two age cohorts tested, with significantly decreased expression in sRNAs in the 6-year-old selections compared to the 1-year-old. Almond shows a pattern of hypermethylation and decreased sRNA expression with increased age. Identified DMRs and differentially expressed sRNAs could function as putative biomarkers of age following validation in additional age groups.}, journal={PLANT SCIENCE}, author={Katherine M. D'Amico-Willman and Niederhuth, Chad E. and Sovic, Michael G. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramirez, Jonathan}, year={2024}, month={Jan} }
 @article{fresnedo-ramirez_anderson_d'amico-willman_gradziel_2023, title={A review of plant epigenetics through the lens of almond}, ISSN={["1940-3372"]}, DOI={10.1002/tpg2.20367}, abstractNote={Abstract}, journal={PLANT GENOME}, author={Fresnedo-Ramirez, Jonathan and Anderson, Elizabeth S. and D'Amico-Willman, Katherine and Gradziel, Thomas M.}, year={2023}, month={Jul} }
 @article{katherine m. d'amico-willman_joglekar_luna_ritchie_fagen_huerta_2022, title={Complete Genome Sequence of Xanthomonas arboricola pv. pruni Strain Xcp1 Isolated in 1984 from a Bacterial Spot Spring Canker on Prunus persica var. nucipersica cv. "Redgold"}, volume={11}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00209-22}, abstractNote={
            Xanthomonas arboricola
            pv.
            pruni
            is an important plant pathogen and the causal agent of bacterial spot of stone fruits (
            Prunus
            spp). Here, we report a complete genome of
            X. arboricola
            pv.
            pruni
            strain Xcp1 generated from hybrid PacBio Sequel and Illumina NextSeq2000 sequencing.
          }, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Katherine M. D'Amico-Willman and Joglekar, Prasanna and Luna, Emily K. and Ritchie, David F. and Fagen, Jennie and Huerta, Alejandra I.}, year={2022}, month={Nov} }
 @article{katherine m. d'amico-willman_sideli_allen_anderson_gradziel_fresnedo-ramirez_2022, title={Identification of Putative Markers of Non-infectious Bud Failure in Almond [Prunus dulcis (Mill.) DA Webb] Through Genome Wide DNA Methylation Profiling and Gene Expression Analysis in an Almond x Peach Hybrid Population}, volume={13}, ISSN={["1664-462X"]}, DOI={10.3389/fpls.2022.804145}, abstractNote={Almond [Prunus dulcis(Mill.) D.A. Webb] is an economically important nut crop susceptible to the genetic disorder, Non-infectious Bud Failure (NBF). Despite the severity of exhibition in several prominent almond cultivars, no causal mechanism has been identified underlying NBF development. The disorder is hypothesized to be associated with differential DNA methylation patterns based on patterns of inheritance (i.e., via sexual reproduction and clonal propagation) and previous work profiling methylation in affected trees. Peach (Prunus persicaL. Batsch) is a closely related species that readily hybridizes with almond; however, peach is not known to exhibit NBF. A cross between an NBF-exhibiting ‘Carmel’ cultivar and early flowering peach (‘40A17’) produced an F1where ∼50% of progeny showed signs of NBF, including canopy die-back, erratic branching patterns (known as “crazy-top”), and rough bark. In this study, whole-genome DNA methylation profiles were generated for three F1progenies exhibiting NBF and three progenies considered NBF-free. Subsequent alignment to both the almond and peach reference genomes showed an increase in genome-wide methylation levels in NBF hybrids in CG and CHG contexts compared to no-NBF hybrids when aligned to the almond genome but no difference in methylation levels when aligned to the peach genome. Significantly differentially methylated regions (DMRs) were identified by comparing methylation levels across the genome between NBF- and no-NBF hybrids in each methylation context. In total, 115,635 DMRs were identified based on alignment to the almond reference genome, and 126,800 DMRs were identified based on alignment to the peach reference genome. Nearby genes were identified as associated with the 39 most significant DMRs occurring either in the almond or peach alignments alone or occurring in both the almond and peach alignments. These DMR-associated genes include several uncharacterized proteins and transposable elements. Quantitative PCR was also performed to analyze the gene expression patterns of these identified gene targets to determine patterns of differential expression associated with differential DNA methylation. These DMR-associated genes, particularly those showing corresponding patterns of differential gene expression, represent key targets for almond breeding for future cultivars and mitigating the effects of NBF-exhibition in currently affected cultivars.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Katherine M. D'Amico-Willman and Sideli, Gina M. and Allen, Brian J. and Anderson, Elizabeth S. and Gradziel, Thomas M. and Fresnedo-Ramirez, Jonathan}, year={2022}, month={Feb} }