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Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Transcriptome profiling of postharvest strawberry fruit in response to exogenous auxin and abscisic acid

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Juglanthraquinone C, a novel natural compound derived from Juglans mandshurica Maxim, induces S phase arrest and apoptosis in HepG2 cells

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Targeted spatio-temporal expression based characterization of state of infection and time-point of maximum defense in wheat NILs during leaf rust infection

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Knockdown of berberine bridge enzyme by RNAi accumulates (S)-reticuline and activates a silent pathway in cultured California poppy cells

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Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)

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Predicting breeding values and genetic components using generalized linear mixed models for categorical and continuous traits in walnut (Juglans regia)

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Walnut: past and future of genetic improvement

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Genome-wide identification and expression analysis of GRF genes regulating apple tree architecture

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Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L.

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The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

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Juglone, isolated from Juglans mandshurica Maxim, induces apoptosis via down-regulation of AR expression in human prostate cancer LNCaP cells

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FERONIA Receptor Kinase Contributes to Plant Immunity by Suppressing Jasmonic Acid Signaling in Arabidopsis thaliana

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Identification and quantification of phytosterols in black walnut kernels

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Defining the sources of Paradox: DNA sequence markers for North American walnut (Juglans L.) species and hybrids

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Identification and Characterization of Phenolic Compounds in Black Walnut Kernels

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Cytotoxic Compounds from the Roots of Juglans mandshurica

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Gene Ontology: tool for the unification of biology

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The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

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A fungal pathogen secretes plant alkalinizing peptides to increase infection

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S-nitrosylation of the zinc finger protein SRG1 regulates plant immunity

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Multiplex mutagenesis of four clustered CrRLK1L with CRISPR/Cas9 exposes their growth regulatory roles in response to metal ions

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A domain swap approach reveals a role of the plant wall-associated kinase 1 (WAK1) as a receptor of oligogalacturonides

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Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.

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Requirement for Pectin Methyl Esterase and Preference for Fragmented over Native Pectins for Wall-associated Kinase-activated, EDS1/PAD4-dependent Stress Response in Arabidopsis

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Oxidation of Monolignols by Members of the Berberine Bridge Enzyme Family Suggests a Role in Plant Cell Wall Metabolism

inferredcites →https://doi.org/10.1080/11263504.2016.1271054openalex-snapshot

Analyses of abiotic stress and brassinosteroid-related some genes in barley roots grown under salinity stress and HBR treatments: Expression profiles and phylogeny

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DAGchainer: a tool for mining segmental genome duplications and synteny

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CAFE: a computational tool for the study of gene family evolution

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Using native and syntenically mapped cDNA alignments to improve de novo gene finding

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BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

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BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS

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PAML 4: Phylogenetic Analysis by Maximum Likelihood

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eggNOG: automated construction and annotation of orthologous groups of genes

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Pfam: the protein families database

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Comparative Evolutionary Analysis of Chalcone Synthase and Alcohol Dehydrogenase Loci in Arabidopsis, Arabis, and Related Genera (Brassicaceae)

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Associations Between Armillaria Species and Host Plants in U.K. Gardens

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Characterization and Pathogenicity ofBotryosphaeriaceaeSpecies Collected from Olive and Other Hosts in Spain and California

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Loss-of-Function Mutation of REDUCED WALL ACETYLATION2 in Arabidopsis Leads to Reduced Cell Wall Acetylation and Increased Resistance to Botrytis cinerea

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Novel Molecular Markers for Late Phases of the Growth Cycle of Arabidopsis thaliana Cell-Suspension Cultures Are Expressed during Organ Senescence

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Wall-Associated Kinases Are Expressed throughout Plant Development and Are Required for Cell Expansion

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EnTAP : Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes

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Detecting nonlinear response of spring phenology to climate change by B ayesian analysis

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New insights into adaptation and population structure of cork oak using genotyping by sequencing

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Pectin activation of MAP kinase and gene expression is WAK2 dependent

inferredcites →https://doi.org/10.1111/j.1469-8137.2007.02202.xopenalex-snapshot

Mating patterns and pollen dispersal in a heterodichogamous tree, Juglans mandshurica (Juglandaceae)

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A metacalibrated time‐tree documents the early rise of flowering plant phylogenetic diversity

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A new genomic tool for walnut ( Juglans regia L.): development and validation of the high‐density Axiom™ J. regia 700K SNP genotyping array

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Araport11: a complete reannotation of the Arabidopsis thaliana reference genome

inferredcites →https://doi.org/10.1111/tpj.13852openalex-snapshot

Four Arabidopsis berberine bridge enzyme‐like proteins are specific oxidases that inactivate the elicitor‐active oligogalacturonides

inferredcites →https://doi.org/10.1126/science.1128691openalex-snapshot

The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

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Conserved Molecular Components for Pollen Tube Reception and Fungal Invasion

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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12864-015-1906-5openalex-snapshot

Synteny analysis in Rosids with a walnut physical map reveals slow genome evolution in long-lived woody perennials

inferredcites →https://doi.org/10.1186/s12870-016-0959-1openalex-snapshot

Short oligogalacturonides induce pathogen resistance-associated gene expression in Arabidopsis thaliana

inferredcites →https://doi.org/10.1186/s13059-015-0721-2openalex-snapshot

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy

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YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut

inferredcites →https://doi.org/10.1371/journal.pcbi.1003998openalex-snapshot

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

inferredcites →https://doi.org/10.1534/g3.118.200030openalex-snapshot

Genomic Variation Among and Within SixJuglansSpecies

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Walnuts among the Shuhi in Shuiluo, eastern Himalayas

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Resistance to Phytophthora and Graft Compatibility with Persian Walnut among Selections of Chinese Wingnut

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Effects of Hormone Treatments on Cut Flower Opening and Senescence in Wintersweet (Chimonanthus praecox)

inferredcites →https://doi.org/10.3389/fpls.2017.01148openalex-snapshot

Phylogenetic Resolution in Juglans Based on Complete Chloroplast Genomes and Nuclear DNA Sequences

inferredcites →https://doi.org/10.3389/fpls.2017.01554openalex-snapshot

Role of CrRLK1L Cell Wall Sensors HERCULES1 and 2, THESEUS1, and FERONIA in Growth Adaptation Triggered by Heavy Metals and Trace Elements

inferredcites →https://doi.org/10.3389/fpls.2018.01799openalex-snapshot

Hardwood Tree Genomics: Unlocking Woody Plant Biology

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3390/biology9050104openalex-snapshot

The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

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