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1. How does genome size affect the evolution of pollen tube growth rate, a haploid performance trait?

   https://doi.org/10.1002/ajb2.1326  

   Reese, John B. ; Williams, Joseph H. ( July 2019 , American Journal of Botany)

   Male gametophytes of most seed plants deliver sperm to eggs via a pollen tube. Pollen tube growth rates (PTGRs) of angiosperms are exceptionally rapid, a pattern attributed to more effective haploid selection under stronger pollen competition. Paradoxically, whole genome duplication (WGD) has been common in angiosperms but rare in gymnosperms. Pollen tube polyploidy should initially acceleratePTGRbecause increased heterozygosity and gene dosage should increase metabolic rates. However, polyploidy should also independently increase tube cell size, causing more work which should decelerate growth. We asked how genome size changes have affected the evolution of seed plantPTGRs.

   We assembled a phylogenetic tree of 451 species with knownPTGRs. We then used comparative phylogenetic methods to detect effects of neo‐polyploidy (within‐genus origins),DNAcontent, andWGDhistory onPTGR, and correlated evolution ofPTGRandDNAcontent.

   Gymnosperms had significantly higherDNAcontent and slowerPTGRoptima than angiosperms, and theirPTGRandDNAcontent were negatively correlated. For angiosperms, 89% of model weight favored Ornstein‐Uhlenbeck models with a fasterPTGRoptimum for neo‐polyploids, whereasPTGRandDNAcontent were not correlated. For within‐genus and intraspecific‐cytotype pairs,PTGRs of neo‐polyploids < paleo‐polyploids.

   Genome size increases should negatively affectPTGRwhen genetic consequences ofWGDs are minimized, as found in intra‐specific autopolyploids (low heterosis) and gymnosperms (fewWGDs). But in angiosperms, the higherPTGRoptimum of neo‐polyploids and non‐negativePTGR‐DNAcontent correlation suggest that recurrentWGDs have caused substantialPTGRevolution in a non‐haploid state.

    

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2. H v 1 Proton Channels in Dinoflagellates: Not Just for Bioluminescence?

   https://doi.org/10.1111/jeu.12627  

   Kigundu, Gabriel ; Cooper, Jennifer L. ; Smith, Susan M. E. ( May 2018 , Journal of Eukaryotic Microbiology)

   Bioluminescence in dinoflagellates is controlled byH_V1 proton channels. Database searches of dinoflagellate transcriptomes and genomes yielded hits with sequence features diagnostic of all confirmedH_V1, and show thatH_V1 is widely distributed in the dinoflagellate phylogeny including the basal speciesOxyrrhis marina. Multiple sequence alignments followed by phylogenetic analysis revealed three major subfamilies ofH_V1 that do not correlate with presence of theca, autotrophy, geographic location, or bioluminescence. These data suggest that most dinoflagellates express aH_V1 which has a function separate from bioluminescence. Sequence evidence also suggests that dinoflagellates can contain more than oneH_V1 gene.

    

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3. Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: Birth, death and adaptation

   https://doi.org/10.1111/mec.14348  

   Calla, Bernarda ; Noble, Katherine ; Johnson, Reed M. ; Walden, Kimberly K. O. ; Schuler, Mary A. ; Robertson, Hugh M. ; Berenbaum, May R. ( October 2017 , Molecular Ecology)

   Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely.CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by co‐evolution between herbivores and their chemically defended hostplants. Alternatively, variation inCYPome size may be due to random “birth‐and‐death” processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examinedCYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella).CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, familiesCYP6,CYP9 andCYP321 are most diverse andCYP6AB,CYP6AE,CYP6B,CYP9A andCYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization (“P450 blooms”), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm,Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defences, consistent with an adaptive, nonrandom process driven by ecological interactions.

    

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4. Engineering the future of Physalis grisea : A focus on agricultural challenges, model species status, and applied improvements

   https://doi.org/10.1002/ppp3.10536  

   Dale, Savanah Marie ; Tomaszewski, Elise ; Lippman, Zachary ; Van_Eck, Joyce ( July 2024 , PLANTS, PEOPLE, PLANET)

   Groundcherry (Physalis grisea) is a plant species grown for its flavorful fruit. The fruit drops from the plant, hence the common name groundcherry. This makes harvest cumbersome and puts the fruit at risk for carrying soil‐borne pathogens, therefore making them unsellable. Furthermore, insects often damage the plants, reducing yield. Advances in gene editing offer promise for addressing these issues and aiding home gardeners and farmers. Improvement will expand access to this nutritious fruit, rich in potassium, vitamin C, and antioxidants. Additionally, studies of its biology could serve as a model for improving other fruiting plants, particularly underutilized species.

   P. griseais an underutilized, semidomesticated fruit crop with rising agronomic value. Several resources have been developed for its use in fundamental biological research, including a plant transformation system and a high‐quality reference genome. Already,P. griseahas been used as a model to investigate biological phenomena including inflated calyx syndrome and gene compensation.P. griseahas also been used to demonstrate the potential of fast‐tracking domestication trait improvement through approaches such as CRISPR/Cas9 gene editing. This work has led to thePhysalisImprovement Project, which relies on reverse genetics to understand the mechanisms that underlie fruit abscission and plant–herbivore interactions to guide approaches for improvement of undesirable characteristics. CRISPR/Cas9 gene editing has been used to targetP. griseagenes that are suspected to act in fruit abscission, particularly orthologs of those that are reported in tomato abscission zone development. A similar approach is being taken to targetP. griseagenes involved in the withanolide biosynthetic pathway to determine the impact of withanolides on plant–herbivore interactions. Results from these research projects will lead to a greater understanding of important biological processes and will also generate knowledge needed to develop cultivars with reduced fruit drop and increased resistance to insect herbivory.

    

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5. Beyond Autoantibodies: Biologic Roles of Human Autoreactive B Cells in Rheumatoid Arthritis Revealed by RNA‐Sequencing

   https://doi.org/10.1002/art.40772  

   Mahendra, Ankit ; Yang, Xingyu ; Abnouf, Shaza ; Adolacion, Jay R. T. ; Park, Daechan ; Soomro, Sanam ; Roszik, Jason ; Coarfa, Cristian ; Romain, Gabrielle ; Wanzeck, Keith ; et al ( February 2019 , Arthritis & Rheumatology)

   To obtain the comprehensive transcriptome profile of human citrulline‐specific B cells from patients with rheumatoid arthritis (RA).

   Citrulline‐ and hemagglutinin‐specific B cells were sorted by flow cytometry using peptide–streptavidin conjugates from the peripheral blood ofRApatients and healthy individuals. The transcriptome profile of the sorted cells was obtained byRNA‐sequencing, and expression of key protein molecules was evaluated by aptamer‐basedSOMAscan assay and flow cytometry. The ability of these proteins to effect differentiation of osteoclasts and proliferation and migration of synoviocytes was examined by in vitro functional assays.

   Citrulline‐specific B cells, in comparison to citrulline‐negative B cells, from patients withRAdifferentially expressed the interleukin‐15 receptor α (IL‐15Rα) gene as well as genes related to protein citrullination and cyclicAMPsignaling. In analyses of an independent cohort of cyclic citrullinated peptide–seropositiveRApatients, the expression ofIL‐15Rα protein was enriched in citrulline‐specific B cells from the patients’ peripheral blood, and surprisingly, all B cells fromRApatients were capable of producing the epidermal growth factor ligand amphiregulin (AREG). Production ofAREGdirectly led to increased migration and proliferation of fibroblast‐like synoviocytes, and, in combination with anti–citrullinated protein antibodies, led to the increased differentiation of osteoclasts.

   To the best of our knowledge, this is the first study to document the whole transcriptome profile of autoreactive B cells in any autoimmune disease. These data identify several genes and pathways that may be targeted by repurposing severalUSFood and Drug Administration–approved drugs, and could serve as the foundation for the comparative assessment of B cell profiles in other autoimmune diseases.

    

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