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Abstract Key MessageTheC. roseus ZCTsare jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the terpenoid indole alkaloid pathway when highly expressed. AbstractCatharanthus roseusis the sole known producer of the anti-cancer terpenoid indole alkaloids (TIAs), vinblastine and vincristine. While the enzymatic steps of the pathway have been elucidated, an understanding of its regulation is still emerging. The present study characterizes an important subgroup of Cys2-His2 zinc finger transcription factors known asZinc fingerCatharanthusTranscription factors (ZCTs).We identified three new ZCT members (named ZCT4, ZCT5, and ZCT6) that clustered with the putative repressors of the TIA pathway, ZCT1, ZCT2, and ZCT3. We characterized the role of these six ZCTs as potential redundant regulators of the TIA pathway, and their tissue-specific and jasmonate-responsive expression. These ZCTs share high sequence conservation in their two Cys2-His2 zinc finger domains but differ in the spacer length and sequence between these zinc fingers. The transient overexpression ofZCTsin seedlings significantly repressed the promoters of the terpenoid (pLAMT) and condensation branch (pSTR1) of the TIA pathway, consistent with that previously reported for ZCT1, ZCT2, and ZCT3. In addition, ZCTs significantly repressed and indirectly activated several promoters of the vindoline pathway (not previously studied). TheZCTsdiffered in their tissue-specific expression but similarly increased with jasmonate in a dosage-dependent manner (except forZCT5). We showed significant activation of thepZCT1andpZCT3promoters by the de-repressed CrMYC2a, suggesting that the jasmonate-responsive expression of theZCTscan be mediated by CrMYC2a. In summary, theC. roseus ZCTsare jasmonate-responsive, can be induced by CrMYC2a, and can act as significant regulators of the TIA pathway when highly expressed. 

Dry beans (Phaseolus vulgarisL.) are a nutritious food, but their lengthy cookingrequirements are barriers to consumption. Presoaking is one strategy to reduce cook-ing time. Soaking allows hydration to occur prior to cooking, and enzymatic changesto pectic polysaccharides also occur during soaking that shorten the cooking time ofbeans. Little is known about how gene expression during soaking influences cook-ing times. The objectives of this study were to (1) identify gene expression patternsthat are altered by soaking and (2) compare gene expression in fast-cooking andslow-cooking bean genotypes. RNA was extracted from four bean genotypes at fivesoaking time points (0, 3, 6, 12, and 18 h) and expression abundances were detectedusing Quant-seq. Differential gene expression analysis and weighted gene coexpres-sion network analysis were used to identify candidate genes within quantitative traitloci for water uptake and cooking time. Genes related to cell wall growth and devel-opment as well as hypoxic stress were differentially expressed between the fast- andslow-cooking beans due to soaking. Candidate genes identified in the slow-cookingbeans included enzymes that increase intracellular calcium concentrations and cellwall modification enzymes. The expression of cell wall-strengthening enzymes inthe slow-cooking beans may increase their cooking time and ability to resist osmoticstress by preventing cell separation and water uptake in the cotyledon. 

Abstract The majority of sequenced genomes in the monocots are from species belonging to Poaceae, which include many commercially important crops. Here, we expand the number of sequenced genomes from the monocots to include the genomes of 4 related cyperids: Carex cristatella and Carex scoparia from Cyperaceae and Juncus effusus and Juncus inflexus from Juncaceae. The high-quality, chromosome-scale genome sequences from these 4 cyperids were assembled by combining whole-genome shotgun sequencing of Nanopore long reads, Illumina short reads, and Hi-C sequencing data. Some members of the Cyperaceae and Juncaceae are known to possess holocentric chromosomes. We examined the repeat landscapes in our sequenced genomes to search for potential repeats associated with centromeres. Several large satellite repeat families, comprising 3.2–9.5% of our sequenced genomes, showed dispersed distribution of large satellite repeat clusters across all Carex chromosomes, with few instances of these repeats clustering in the same chromosomal regions. In contrast, most large Juncus satellite repeats were clustered in a single location on each chromosome, with sporadic instances of large satellite repeats throughout the Juncus genomes. Recognizable transposable elements account for about 20% of each of the 4 genome assemblies, with the Carex genomes containing more DNA transposons than retrotransposons while the converse is true for the Juncus genomes. These genome sequences and annotations will facilitate better comparative analysis within monocots. 

Abstract The bowfin ( Amia calva ) is a ray-finned fish that possesses a unique suite of ancestral and derived phenotypes, which are key to understanding vertebrate evolution. The phylogenetic position of bowfin as a representative of neopterygian fishes, its archetypical body plan and its unduplicated and slowly evolving genome make bowfin a central species for the genomic exploration of ray-finned fishes. Here we present a chromosome-level genome assembly for bowfin that enables gene-order analyses, settling long-debated neopterygian phylogenetic relationships. We examine chromatin accessibility and gene expression through bowfin development to investigate the evolution of immune, scale, respiratory and fin skeletal systems and identify hundreds of gene-regulatory loci conserved across vertebrates. These resources connect developmental evolution among bony fishes, further highlighting the bowfin’s importance for illuminating vertebrate biology and diversity in the genomic era.