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18 páginas.- 6 figuras.- 4 tablas.- 92 referencias.-Supplementary Materials, ydroxystilbenes are a class of polyphenolic compounds that behave as lignin monomers participating in radical coupling reactions during the lignification. Here, we report the synthesis and characterization of various artificial copolymers of monolignols and hydroxystilbenes, as well as low-molecular-mass compounds, to obtain the mechanistic insights into their incorporation into the lignin polymer. Integrating the hydroxystilbenes, resveratrol and piceatannol, into monolignol polymerization in vitro, using horseradish peroxidase to generate phenolic radicals, produced synthetic lignins [dehydrogenation polymers (DHPs)]. Copolymerization of hydroxystilbenes with monolignols, especially sinapyl alcohol, by in vitro peroxidases notably improved the reactivity of monolignols and resulted in substantial yields of synthetic lignin polymers. The resulting DHPs were analyzed using two-dimensional NMR and 19 synthesized model compounds to confirm the presence of hydroxystilbene structures in the lignin polymer. The cross-coupled DHPs confirmed both resveratrol and piceatannol as authentic monomers participating in the oxidative radical coupling reactions during polymerization., This work was supported by grants from the DOE Great Lakes Bioenergy Research Center, and H.K. and J.Ra. were funded by the DOE BER Office of Science (DE- SC0018409). J.Re. and J.C.d.R. were supported by the projects AGL2017-83036-R and PID2020-118968RB-I00 (funded by MCIN/AEI/10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”) and by the Andalusian Regional Government (project P20-00017). T.J.E. was funded by the Extreme Science and Engineering Discovery Environment (XSEDE), supported by the National Science Foundation grant number ACI-1548562. This work was made possible in part by a grant for high-performance computing resources and technical support from the Alabama Supercomputer Authority. This research was supported in part by the U.S. Department of Agriculture, U.S. Forest Service.

8 figuras.- refefencias.- Versión aceptada del artículo.- Supplementary data kiab469_Suppl. https://academic.oup.com/plphys/advance-article/doi/10.1093/plphys/kiab469/6400262#supplementary-data, Recent studies demonstrate that several polyphenolic compounds produced from beyond the canonical monolignol biosynthetic pathways can behave as lignin monomers, participating in radical coupling reactions and being incorporated into lignin polymers. Here, we show various classes of flavonoids, the chalconoid naringenin chalcone, the flavanones naringenin and dihydrotricin, and the flavone tricin, incorporate into the lignin polymer of papyrus (Cyperus papyrus L.) rind. These flavonoids were released from the rind lignin by DFRC, a chemical degradative method that cleaves the β-ether linkages, indicating that at least a fraction of each was integrated into the lignin as β-ether linked structures. Due to the particular structure of tricin and dihydrotricin, whose C-3ʹ and C-5ʹ positions at their B-rings are occupied by methoxy groups, these compounds can only be incorporated into the lignin through 4ʹ–O–β bonds. However, naringenin chalcone and naringenin have no substituents at these positions and can therefore form additional carbon-carbon linkages, including 3ʹ– or 5ʹ–β linkages that form phenylcoumaran structures not susceptible to cleavage by DFRC. Furthermore, NMR analysis indicated that naringenin chalcone can also form additional linkages through its conjugated double bond. The discovery expands the range of flavonoids incorporated into natural lignins, further broadens the traditional definition of lignin, and enhances the premise that any phenolic compound present at the cell wall during lignification could be oxidized and potentially integrated into the lignin structure, depending only on its chemical compatibility. This study indicates that papyrus lignin has a unique structure as it is the only lignin known to date that integrates such a diversity of phenolic compounds from different classes of flavonoids. This discovery will open up new ways to engineer and design lignins with specific properties and for enhanced value., This work was funded by the Spanish State Research Agency and the European Regional 51 Development Fund (project AGL2017-83036-R), the Consejería de Transformación 52 Económica, Industria, Conocimiento y Universidades, Junta de Andalucía (project P20-53 00017), the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE54 SC0018409), and the Austrian Biorefinery Center Tulln (ABCT). MJR thanks the Spanish 55 Ministry of Science, Innovation and Universities for a FPI fellowship (PRE2018-083267).

4 páginas.- 3 figuras. 17 referencias.- Comunicación oral presentada en el 16th European Workshop on Lignocellulosics and Pulp (EWLP) Gothenburg, Sweden, June 28 – July 1, 2022, As ever more component monomers are discovered, lignin can no longer be regarded as deriving from just the three canonical monolignols. Pathway intermediates and additional products of truncated biosynthesis are now established lignin monomers. The array of acylated monolignols continues to expand. Game-changing findings have demonstrated that phenolics from alternative pathways, including flavonoids and hydroxystilbenes, are also involved in lignification, expanding the traditional concept. Beyond the basic science intrigue, these findings propound exciting new avenues for valorizing lignins, or for producing more readily extractable or depolymerizable lignins, in crop and bioenergy plants., We further acknowledge lots of colleagues and collaborators, and funding from the Swiss National Science Foundation (Synergia) grant # CRS115_180258, and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409).

16 Pág. Instituto de Ciencias Forestales (ICIFOR), Fine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems., This research was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research through the Center for Bioenergy Innovation (CBI), and a DOE Bioenergy Research Center. The publisher, by accepting the article for publication, acknowledges that the U.S. Government retains a nonexclusive, paid-up, irrevocable, worldwide license to publish, or reproduce the published form of this work, or allow others to do so, for U.S. Government purposes. The views expressed in the article do not necessarily represent the views of the U.S. Department of Energy or the United States Government. Work on heterochiasmy was supported by the National Science Foundation (award 1542509 to SD). The breeding of the 7×7 population was initially funded by an award under the Western Sun Grant program to Washington State University (Subgrant T-0013A). Dr Macaya-Sanz was partially supported by “Atracción de Talento Investigador” of the Community of Madrid (ref. 2019-T2/BIO-12780). The project “Conservación y promoción de recursos genéticos forestales contempladas en el programa nacional de desarrollo rural” (ref. IMP2018-002), funded by the Spanish Ministry of Ecological Transition, also covered some expenses of this study.

Este registro contiene el PDF editorial, el manuscrito aceptado y la información suplementaria (Supplementary text: 2 notas; Suplementary figures: 9 figuras; Referencias bibliográficas.), Allopolyploidy generates diversity by increasing the number of copies and sources of chromosomes. Many of the best-known evolutionary radiations, crops, and industrial organisms are ancient or recent allopolyploids. Allopolyploidy promotes differentiation and facilitates adaptation to new environments, but the tools to test its limits are lacking. Here we develop an iterative method of Hybrid Production (iHyPr) to combine the genomes of multiple budding yeast species, generating Saccharomyces allopolyploids of at least six species. When making synthetic hybrids, chromosomal instability and cell size increase dramatically as additional copies of the genome are added. The six-species hybrids initially grow slowly, but they rapidly regain fitness and adapt, even as they retain traits from multiple species. These new synthetic yeast hybrids and the iHyPr method have potential applications for the study of polyploidy, genome stability, chromosome segregation, and bioenergy., This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Number DEB-1253634; the USDA National Institute of Food and Agriculture Hatch Project Number 1020204; and the Robert Draper Technology Innovation Fund from the Wisconsin Alumni Research Foundation (WARF). D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme, grant agreement No. 747775. K.J.F. is a Morgridge Metabolism Interdisciplinary Fellow of the Morgridge Institute for Research. C.T.H. is a Pew Scholar in the Biomedical Sciences, a Vilas Early Career Investigator, and a H. I. Romnes Faculty Fellow, supported by the Pew Charitable Trusts, Vilas Trust Estate, and Office of the Vice Chancellor for Research and Graduate Education with funding from WARF, respectively. The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported under Contract No. DE-AC02-05CH11231.

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes., Some computations were performed on Tirant III of the Spanish Supercomputing Network (“Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin–Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation program Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. D.P. is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. Q.K.L. was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB−1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. C.R.L. holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by an NSERC Discovery Grant.

39 páginas.- 14 figuras.- 134 referencias, Lignin is largely produced by the oxidative radical coupling of the three monolignols, p-coumaryl, coniferyl, and sinapyl alcohols, which form the p-hydroxyphenyl, guaiacyl, and syringyl lignin units in the lignin polymer. However, it is increasingly appreciated that other “unconventional” phenolic compounds can also behave as lignin monomers participating in oxidative radical reactions during the lignification process and becoming integrated into the lignin polymer in some plants. Various phenolic compounds have been found incorporated into the lignin, including phenolic compounds derived from the monolignol biosynthetic pathway (e.g., monolignol ester conjugates, caffeyl and 5-hydroxyconiferyl alcohols, hydroxycinnamaldehydes, among others). More fascinating still was the discovery in some plants of a series of phenolic compounds arising from other polyphenolic biosynthetic pathways, including flavonoids (tricin, dihydrotricin, naringenin, naringenin chalcone), hydroxystilbenes (resveratrol, piceatannol, and isorhapontigenin, and their O-glucosylated counterparts piceid, astringin, and isorhapontin), and ferulic acid amides (feruloyltyramine, and diferuloylputrescine), that are integrated into the lignin polymer. All of these discoveries indicate that the lignin structure is far more complex than previously thought, that the definition of lignin should not be restricted to a polymer derived solely from the three traditional monolignols, and that other unconventional lignin monomers must be considered, thus expanding the established definition of lignin. The overriding factor remains, however, that lignification, the process of polymerization to the lignin polymer, allows this compositional flexibility because it is a simple chemical process. © 2022 Elsevier Ltd, JCdR, JRe and AG were funded by the Spanish Project AGL2017-83036-R and PID2020-118968RB-100 (financed by Ministerio de Ciencia e Innovación, MCIN, Agencia Estatal de Investigación, AEI, and European Regional Development Fund, ERDF, "A way of making Europe"), the Regional Andalusian Government (Consejerı ́a de Transformación Económica, Industria, Conocimiento y Universidades, Junta de Andalucıía, project P20-00017), and CSIC (project PIE 202040E185). JRa and HK were funded by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science DE-SC0018409

13 pág.- 9 figuras.- 1 tabla.- 38 referencias.- The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fpls.2021.642848/full#supplementary-material, he monolignols, p-coumaryl, coniferyl, and sinapyl alcohol, arise from the general phenylpropanoid biosynthetic pathway. Increasingly, however, authentic lignin monomers derived from outside this process are being identified and found to be fully incorporated into the lignin polymer. Among them, hydroxystilbene glucosides, which are produced through a hybrid process that combines the phenylpropanoid and acetate/malonate pathways, have been experimentally detected in the bark lignin of Norway spruce (Picea abies). Several interunit linkages have been identified and proposed to occur through homo-coupling of the hydroxystilbene glucosides and their cross-coupling with coniferyl alcohol. In the current work, the thermodynamics of these coupling modes and subsequent rearomatization reactions have been evaluated by the application of density functional theory (DFT) calculations. The objective of this paper is to determine favorable coupling and cross-coupling modes to help explain the experimental observations and attempt to predict other favorable pathways that might be further elucidated via in vitro polymerization aided by synthetic models and detailed structural studies., JRa and HK were funded by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science BER DE-SC0018409). JRe and JCR were funded by the Spanish Projects CTQ2014-60764-JIN and AGL2017-83036-R (financed by Agencia Estatal de Investigación, AEI and Fondo Europeo de Desarrollo Regional, FEDER).

16 páginas.- 6 figuras.- 131 referencias, Lignin is conventionally defined as being formed by the oxidative polymerization of three main monolignols, p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, that are derived from the general phenylpropanoid biosynthetic pathway. Many other phenolic compounds that are also derived from the phenylpropanoid pathway are also known to perform as genuine lignin monomers in many plants, as is the case of the monolignol ester conjugates, phenolic compounds arising from the truncated biosynthesis of monolignols, or ferulate esters. Recent investigations, however, have indicated that phenolic compounds arising from beyond the canonical phenylpropanoid pathway, namely flavonoids, hydroxystilbenes, and hydroxycinnamic amides, may also behave as authentic lignin monomers and are incorporated into the lignin in some plants, further challenging the traditional definition of lignin. This is the case of the flavone tricin that is incorporated into the lignin of grasses and other monocots, the hydroxystilbene piceatannol (together with resveratrol and isorhapontigenin, at lower levels) that has been found in the lignins of palm fruit shells, their respective O-glucosides (astringin, piceid, and isorhapontin) that are present in the lignin of Norway spruce bark, or the ferulic amides feruloyltyramine, incorporated into the lignin of tobacco and potato tubers, and diferuloylputrescine, which appears to be incorporated into maize kernel lignin. These valuable compounds are potentially available in high amounts and at low cost and may be obtained from the waste products from the processing of agricultural or forest biomass., J. C. del Rıo, J. Rencoret, and A. Gutiérrez were funded by the Spanish Project AGL2017-83036-R (financed by Agencia Estatal de Investigacion, AEI, and Fondo Europeo de Desarrollo ́ Regional, FEDER). J. Ralph and H. Kim were funded by the DOE Great Lakes Bioenergy Research Center (DOE Office of Science DE-SC0018409). T. Elder was funded by the National Science Foundation (grant number ACI-1548562).

Genetic analysis of phenotypic differences between species is typically limited to interfertile species. Here, we conducted a genome-wide noncomplementation screen to identify genes that contribute to a major difference in thermal growth profile between two reproductively isolated yeast species, Saccharomyces cerevisiae and Saccharomyces uvarum. The screen identified only a single nuclear-encoded gene with a moderate effect on heat tolerance, but, in contrast, revealed a large effect of mitochondrial DNA (mitotype) on both heat and cold tolerance. Recombinant mitotypes indicate that multiple genes contribute to thermal divergence, and we show that protein divergence in COX1 affects both heat and cold tolerance. Our results point to the yeast mitochondrial genome as an evolutionary hotspot for thermal divergence., This work was supported by the NIH (grant GM080669) to J.C.F. Additional support to C.T.H. was provided by the USDA National Institute of Food and Agriculture (Hatch project 1003258), the National Science Foundation (DEB-1253634), and the DOE Great Lakes Bioenergy Research Center (DOE BER Office of Science DE-SC0018409 and DE-FC02-07ER64494 to T. J. Donohue). C.T.H. is a Pew Scholar in the Biomedical Sciences and a Vilas Faculty Early Career Investigator, supported by the Pew Charitable Trusts and the Vilas Trust Estate, respectively. D.P. is a Marie Sklodowska-Curie fellow of the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 747775).