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  1. Abstract

    Protein translation is tightly and precisely controlled by multiple mechanisms including upstream open reading frames (uORFs), but the origins of uORFs and their role in maize are largely unexplored. In this study, an active transposition event was identified during the propagation of maize inbred line B73. The transposon, which was named BTA for ‘B73 active transposable element hAT’, creates a novel dosage-dependent hypomorphic allele of the hexose transporter gene ZmSWEET4c through insertion within the coding sequence in the first exon, and results in reduced kernel size. The BTA insertion does not affect transcript abundance but reduces protein abundance of ZmSWEET4c, probably through the introduction of a uORF. Furthermore, the introduction of BTA sequence in the exon of other genes can regulate translation efficiency without affecting their mRNA levels. A transposon capture assay revealed 79 novel insertions for BTA and BTA-like elements. These insertion sites have typical euchromatin features, including low levels of DNA methylation and high levels of H3K27ac. A putative autonomous element that mobilizes BTA and BTA-like elements was identified. Together, our results suggest a transposon-based origin of uORFs and document a new role for transposable elements to influence protein abundance and phenotypic diversity by affecting the translation rate.

  2. During meiosis, crossovers (COs) are typically required to ensure faithful chromosomal segregation. Despite the requirement for at least one CO between each pair of chromosomes, closely spaced double COs are usually underrepresented due to a phenomenon called CO interference. LikeMus musculusandSaccharomyces cerevisiae,Arabidopsis thalianahas both interference-sensitive (Class I) and interference-insensitive (Class II) COs. However, the underlying mechanism controlling CO distribution remains largely elusive. Both AtMUS81 and AtFANCD2 promote the formation of Class II CO. Using both AtHEI10 and AtMLH1 immunostaining, two markers of Class I COs, we show that AtFANCD2 but not AtMUS81 is required for normal Class I CO distribution among chromosomes. DepletingAtFANCD2leads to a CO distribution pattern that is intermediate between that of wild-type and a Poisson distribution. Moreover, inAtfancm,Atfigl1, andAtrmi1mutants where increased Class II CO frequency has been reported previously, we observe Class I CO distribution patterns that are strikingly similar toAtfancd2.Surprisingly, we found that AtFANCD2 plays opposite roles in regulating CO frequency inAtfancmcompared with either inAtfigl1orAtrmi1.Together, these results reveal that although AtFANCD2, AtFANCM, AtFIGL1, and AtRMI1 regulate Class II CO frequency by distinct mechanisms, they have similar roles in controlling the distribution of Class I COs among chromosomes.

  3. INTRODUCTION During the independent process of cereal evolution, many trait shifts appear to have been under convergent selection to meet the specific needs of humans. Identification of convergently selected genes across cereals could help to clarify the evolution of crop species and to accelerate breeding programs. In the past several decades, researchers have debated whether convergent phenotypic selection in distinct lineages is driven by conserved molecular changes or by diverse molecular pathways. Two of the most economically important crops, maize and rice, display some conserved phenotypic shifts—including loss of seed dispersal, decreased seed dormancy, and increased grain number during evolution—even though they experienced independent selection. Hence, maize and rice can serve as an excellent system for understanding the extent of convergent selection among cereals. RATIONALE Despite the identification of a few convergently selected genes, our understanding of the extent of molecular convergence on a genome-wide scale between maize and rice is very limited. To learn how often selection acts on orthologous genes, we investigated the functions and molecular evolution of the grain yield quantitative trait locus KRN2 in maize and its rice ortholog OsKRN2 . We also identified convergently selected genes on a genome-wide scale in maize and rice, usingmore »two large datasets. RESULTS We identified a selected gene, KRN2 ( kernel row number2 ), that differs between domesticated maize and its wild ancestor, teosinte. This gene underlies a major quantitative trait locus for kernel row number in maize. Selection in the noncoding upstream regions resulted in a reduction of KRN2 expression and an increased grain number through an increase in kernel rows. The rice ortholog, OsKRN2 , also underwent selection and negatively regulates grain number via control of secondary panicle branches. These orthologs encode WD40 proteins and function synergistically with a gene of unknown function, DUF1644, which suggests that a conserved protein interaction controls grain number in maize and rice. Field tests show that knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by ~10% and ~8%, respectively, with no apparent trade-off in other agronomic traits. This suggests potential applications of KRN2 and its orthologs for crop improvement. On a genome-wide scale, we identified a set of 490 orthologous genes that underwent convergent selection during maize and rice evolution, including KRN2/OsKRN2 . We found that the convergently selected orthologous genes appear to be significantly enriched in two specific pathways in both maize and rice: starch and sucrose metabolism, and biosynthesis of cofactors. A deep analysis of convergently selected genes in the starch metabolic pathway indicates that the degree of genetic convergence via convergent selection is related to the conservation and complexity of the gene network for a given selection. CONCLUSION Our findings show that common phenotypic shifts during maize and rice evolution acting on conserved genes are driven at least in part by convergent selection, which in maize and rice likely occurred both during and after domestication. We provide evolutionary and functional evidence on the convergent selection of KRN2/OsKRN2 for grain number between maize and rice. We further found that a complete loss-of-function allele of KRN2/OsKRN2 increased grain yield without an apparent negative impact on other agronomic traits. Exploring the role of KRN2/OsKRN2 and other convergently selected genes across the cereals could provide new opportunities to enhance the production of other global crops. Shared selected orthologous genes in maize and rice for convergent phenotypic shifts during domestication and improvement. By comparing 3163 selected genes in maize and 18,755 selected genes in rice, we identified 490 orthologous gene pairs, including KRN2 and its rice ortholog OsKRN2 , as having been convergently selected. Knockout of KRN2 in maize or OsKRN2 in rice increased grain yield by increasing kernel rows and secondary panicle branches, respectively.« less
    Free, publicly-accessible full text available March 25, 2023
  4. Abstract In this study, a simple energetically based dynamical system model of tropical cyclone (TC) intensification is modified to account for the observed dependence of the intensification rate (IR) on the storm intensity. According to the modified dynamical system model, the TC IR is controlled by the intensification potential (IP) and the weakening rate due to surface friction beneath the eyewall. The IP is determined primarily by the rate of change in the potential energy available for a TC to develop, which is a function of the thermodynamic conditions of the atmosphere and the underlying ocean, and the dynamical efficiency of the TC system. The latter depends strongly on the degree of convective organization within the eyewall and the inner-core inertial stability of the storm. At a relatively low TC intensity, the IP of the intensifying storm is larger than the frictional weakening rate, leading to an increase in the TC IR with TC intensity in this stage. As the storm reaches an intermediate intensity of 30-40 m s -1 , the difference between IP and frictional weakening rate reaches its maximum, concurrent with the maximum IR. Later on, the IR decreases as the TC intensifies further because the frictionalmore »dissipation increases with TC intensity at a faster rate than the IP. Finally, the storm approaches its maximum potential intensity (MPI) and the IR becomes zero. The modified dynamical system model is validated with results from idealized simulations with an axisymmetric nonhydrostatic, cloud-resolving model.« less
  5. Abstract In this study, based on the 6-hourly tropical cyclone (TC) best track data and the ERA-Interim reanalysis data, statistical analyses as well as a machine learning approach, XGBoost, are used to identify and quantify factors that affect the overwater weakening rate (WR) of TCs over the western North Pacific (WNP) during 1980–2017. Statistical analyses show that the TC rapid weakening events usually occur when intense TCs cross regions with a sharp decrease in sea surface temperature (DSST) with relatively faster eastward or northward translational speeds, and move into regions with large environmental vertical wind shear (VWS) and dry conditions in the upshear-left quadrant. Results from XGBoost indicate that the relative intensity of TC (TC intensity normalized by its maximum potential intensity), DSST, and VWS are dominant factors determining TC WR, contributing 26.0%, 18.3%, and 14.9% to TC WR, and 9, 5, and 5 m s−1 day−1 to the variability of TC WR, respectively. Relative humidity in the upshear-left quadrant of VWS, zonal translational speed, divergence at 200 hPa, and meridional translational speed contribute 12.1%, 11.8%, 8.8%, and 8.1% to TC WR, respectively, but only contribute 2–3 m s−1 day−1 to the variability of TC WR individually. These findings suggestmore »that the improved accurate analysis and prediction of the dominant factors may lead to substantial improvements in the prediction of TC WR.« less
  6. Abstract Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1—another PcG protein interacting with the EZL1 complex—reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome.