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1. An updated gene atlas for maize reveals organ‐specific and stress‐induced genes

   https://doi.org/10.1111/tpj.14184  

   Hoopes, Genevieve M. ; Hamilton, John P. ; Wood, Joshua C. ; Esteban, Eddi ; Pasha, Asher ; Vaillancourt, Brieanne ; Provart, Nicholas J. ; Buell, C. Robin ( January 2019 , The Plant Journal)

   Maize (Zea maysL.), a model species for genetic studies, is one of the two most important crop species worldwide. The genome sequence of the reference genotype, B73, representative of the stiff stalk heterotic group was recently updated (AGPv4) using long‐read sequencing and optical mapping technology. To facilitate the use ofAGPv4 and to enable functional genomic studies and association of genotype with phenotype, we determined expression abundances for replicatedmRNA‐sequencing datasets from 79 tissues and five abiotic/biotic stress treatments revealing 36 207 expressed genes. Characterization of the B73 transcriptome across six organs revealed 4154 organ‐specific and 7704 differentially expressed (DE) genes following stress treatment. Gene co‐expression network analyses revealed 12 modules associated with distinct biological processes containing 13 590 genes providing a resource for further association of gene function based on co‐expression patterns. Presence−absence variants (PAVs) previously identified using whole genome resequencing data from 61 additional inbred lines were enriched in organ‐specific and stress‐induced DE genes suggesting thatPAVs may function in phenological variation and adaptation to environment. Relative to core genes conserved across the 62 profiled inbreds,PAVs have lower expression abundances which are correlated with their frequency of dispersion across inbreds and on average have significantly fewer co‐expression network connections suggesting that a subset ofPAVs may be on an evolutionary path to pseudogenization. To facilitate use by the community, we developed the Maize Genomics Resource website (maize.plantbiology.msu.edu) for viewing and data‐mining these resources and deployed two new views on the maize electronic Fluorescent Pictograph Browser (bar.utoronto.ca/efp_maize).

    

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2. Gene expression profiling of soaked dry beans ( Phaseolus vulgaris L.) reveals cell wall modification plays a role in cooking time

   https://doi.org/10.1002/tpg2.20364  

   Jeffery, Hannah R. ; Mudukuti, Nyasha ; Buell, Carol Robin ; Childs, Kevin L. ; Cichy, Karen ( July 2023 , The Plant Genome)

   Dry beans (Phaseolus vulgarisL.) are a nutritious food, but their lengthy cooking requirements are barriers to consumption. Presoaking is one strategy to reduce cooking time. Soaking allows hydration to occur prior to cooking, and enzymatic changes to pectic polysaccharides also occur during soaking that shorten the cooking time of beans. Little is known about how gene expression during soaking influences cooking times. The objectives of this study were to (1) identify gene expression patterns that are altered by soaking and (2) compare gene expression in fast‐cooking and slow‐cooking bean genotypes. RNA was extracted from four bean genotypes at five soaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detected using Quant‐seq. Differential gene expression analysis and weighted gene coexpression network analysis were used to identify candidate genes within quantitative trait loci for water uptake and cooking time. Genes related to cell wall growth and development as well as hypoxic stress were differentially expressed between the fast‐ and slow‐cooking beans due to soaking. Candidate genes identified in the slow‐cooking beans included enzymes that increase intracellular calcium concentrations and cell wall modification enzymes. The expression of cell wall‐strengthening enzymes in the slow‐cooking beans may increase their cooking time and ability to resist osmotic stress by preventing cell separation and water uptake in the cotyledon.

    

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3. Identification and Expression Analyses of the Nitrate Transporter Gene ( NRT2 ) Family Among Skeletonema species (Bacillariophyceae)

   https://doi.org/10.1111/jpy.12896  

   Kang, Lee‐Kuo ; Rynearson, Tatiana A. ; Kroth, ed., P. ( August 2019 , Journal of Phycology)

   High‐affinity nitrate transporters are considered to be the major transporter system for nitrate uptake in diatoms. In the diatom genusSkeletonema, three forms of genes encoding high‐affinity nitrate transporters (NRT2) were newly identified from transcriptomes generated as part of the marine microbial eukaryote transcriptome sequencing project. To examine the expression of each form ofNRT2under different nitrogen environments, laboratory experiments were conducted under nitrate‐sufficient, ammonium‐sufficient, and nitrate‐limited conditions using three ecologically importantSkeletonemaspecies:S. dohrnii,S. menzelii,andS. marinoi. Primers were developed for eachNRT2form and species and Q‐RT‐PCRwas performed. For eachNRT2form, the threeSkeletonemaspecies had similar transcriptional patterns. The transcript levels ofNRT2:1were significantly elevated under nitrogen‐limited conditions, but strongly repressed in the presence of ammonium. The transcript levels ofNRT2:2were also repressed by ammonium, but increased 5‐ to 10‐fold under nitrate‐sufficient and nitrogen‐limited conditions. Finally, the transcript levels ofNRT2:3did not vary significantly under various nitrogen conditions, and behaved more like a constitutively expressed gene. Based on the observed transcript variation amongNRT2forms, we propose a revised model describing nitrate uptake kinetics regulated by multiple forms of nitrate transporter genes in response to various nitrogen conditions inSkeletonema. The differentialNRT2transcriptional responses among species suggest that species‐specific adaptive strategies exist within this genus to cope with environmental changes.

    

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4. Extensive loss of Wnt genes in Tardigrada

   https://doi.org/10.1186/s12862-021-01954-y  

   Chavarria, Raul A. ; Game, Mandy ; Arbelaez, Briana ; Ramnarine, Chloe ; Snow, Zachary K. ; Smith, Frank W. ( December 2021 , BMC Ecology and Evolution)

   Wnt genes code for ligands that activate signaling pathways during development in Metazoa. Through the canonical Wnt (cWnt) signaling pathway, these genes regulate important processes in bilaterian development, such as establishing the anteroposterior axis and posterior growth. In Arthropoda, Wnt ligands also regulate segment polarity, and outgrowth and patterning of developing appendages. Arthropods are part of a lineage called Panarthropoda that includes Onychophora and Tardigrada. Previous studies revealed potential roles of Wnt genes in regulating posterior growth, segment polarity, and growth and patterning of legs in Onychophora. Unlike most other panarthropods, tardigrades lack posterior growth, but retain segmentation and appendages. Here, we investigated Wnt genes in tardigrades to gain insight into potential roles that these genes play during development of the highly compact and miniaturized tardigrade body plan.

   We analyzed published genomes for two representatives of Tardigrada,Hypsibius exemplarisandRamazzottius varieornatus. We identified single orthologs ofWnt4,Wnt5,Wnt9,Wnt11, andWntA, as well as twoWnt16paralogs in both tardigrade genomes. We only found aWnt2ortholog inH. exemplaris. We could not identify orthologs ofWnt1,Wnt6,Wnt7,Wnt8, orWnt10. We identified most other components of cWnt signaling in both tardigrade genomes. However, we were unable to identify an ortholog ofarrow/Lrp5/6, a gene that codes for a Frizzled co-receptor of Wnt ligands. Additionally, we found that some other animals that have lost several Wnt genes and are secondarily miniaturized, like tardigrades, are also missing an ortholog ofarrow/Lrp5/6. We analyzed the embryonic expression patterns of Wnt genes inH. exemplarisduring developmental stages that span the establishment of the AP axis through segmentation and leg development. We detected expression of all Wnt genes inH. exemplarisbesides one of theWnt16paralogs. During embryo elongation, expression of several Wnt genes was restricted to the posterior pole or a region between the anterior and posterior poles. Wnt genes were expressed in distinct patterns during segmentation and development of legs inH. exemplaris, rather than in broadly overlapping patterns.

   Our results indicate that Wnt signaling has been highly modified in Tardigrada. While most components of cWnt signaling are conserved in tardigrades, we conclude that tardigrades have lostWnt1,Wnt6,Wnt7,Wnt8, andWnt10, along witharrow/Lrp5/6. Our expression data may indicate a conserved role of Wnt genes in specifying posterior identities during establishment of the AP axis. However, the loss of several Wnt genes and the distinct expression patterns of Wnt genes during segmentation and leg development may indicate that combinatorial interactions among Wnt genes are less important during tardigrade development compared to many other animals. Based on our results, and comparisons to previous studies, we speculate that the loss of several Wnt genes in Tardigrada may be related to a reduced number of cells and simplified development that accompanied miniaturization and anatomical simplification in this lineage.

    

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5. Differential gene expression associated with fungal trophic shifts along the senescence gradient of the moss Dicranum scoparium

   https://doi.org/10.1111/1462-2920.14605  

   Chen, Ko‐Hsuan ; Liao, Hui‐Ling ; Bellenger, Jean‐Philippe ; Lutzoni, François ( April 2019 , Environmental Microbiology)

   Bryophytes harbour microbiomes, including diverse communities of fungi. The molecular mechanisms by which perennial mosses interact with these fungal partners along their senescence gradients are unknown, yet this is an ideal system to study variation in gene expression associated with trophic state transitions. We investigated differentially expressed genes of fungal communities and their hostDicranum scopariumacross its naturally occurring senescence gradient using a metatranscriptomic approach. Higher activity of fungal nutrient‐related (carbon, nitrogen, phosphorus and sulfur) transporters and Carbohydrate‐Active enZyme (CAZy) genes was detected toward the bottom, partially decomposed, layer of the moss. The most prominent variation in the expression levels of fungal nutrient transporters was from inorganic nitrogen‐related transporters, whereas the breakdown of organonitrogens was detected as the most enriched gene ontology term for the hostD. scoparium, for those transcripts having higher expression in the partially decomposed layer. The abundance of bacterial rRNA transcripts suggested that more living members ofCyanobacteriaare associated with the photosynthetic layer ofD. scoparium, while members ofRhizobialesare detected throughout the gametophytes. Plant genes for specific fungal–plant communication, including defense responses, were differentially expressed, suggesting that different genetic pathways are involved in plant‐microbe crosstalk in photosynthetic tissues compared to partially decomposed tissues.

    

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