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Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N6-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement., Sequencing and genomic diversification of five allopolyploid cotton species provide insights into polyploid genome evolution and epigenetic landscapes for cotton improvement.

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops., Pecan is an important specialty crop that has experienced extensive interspecific hybridization and nearly-obligate outcrossing. Here, the authors assemble diploid genomes of four outbred genotypes, identify interspecific introgressions through comparative genomics analyses, and map QTLs associated with pest resistance.

Background Plants can transmit somatic mutations and epimutations to offspring, which in turn can affect fitness. Knowledge of the rate at which these variations arise is necessary to understand how plant development contributes to local adaption in an ecoevolutionary context, particularly in long-lived perennials. Results Here, we generate a new high-quality reference genome from the oldest branch of a wild Populus trichocarpa tree with two dominant stems which have been evolving independently for 330 years. By sampling multiple, age-estimated branches of this tree, we use a multi-omics approach to quantify age-related somatic changes at the genetic, epigenetic, and transcriptional level. We show that the per-year somatic mutation and epimutation rates are lower than in annuals and that transcriptional variation is mainly independent of age divergence and cytosine methylation. Furthermore, a detailed analysis of the somatic epimutation spectrum indicates that transgenerationally heritable epimutations originate mainly from DNA methylation maintenance errors during mitotic rather than during meiotic cell divisions. Conclusion Taken together, our study provides unprecedented insights into the origin of nucleotide and functional variation in a long-lived perennial plant.

BackgroundSex chromosomes in a wide variety of species share common characteristics, including the presence of suppressed recombination surrounding sex determination loci. They have arisen independently in numerous lineages, providing a conclusive example of convergent evolution. Mammalian sex chromosomes contain multiple palindromic repeats across the non-recombining region that facilitate sequence conservation through gene conversion, and contain genes that are crucial for sexual reproduction. Plant sex chromosomes are less well understood, and in particular it is not clear how coding sequence conservation is maintained in the absence of homologous recombination.ResultsHere we present the first evidence of large palindromic structures in a plant sex chromosome, based on a highly contiguous assembly of the W chromosome of the dioecious shrubSalix purpurea. Two consecutive palindromes span over a region of 200 kb, with conspicuous 20 kb stretches of highly conserved sequences among the four arms. The closely-related speciesS. suchowensisalso has two copies of a portion of the palindrome arm and provides strong evidence for gene conversion. Four genes in the palindrome are homologous to genes in the SDR of the closely-related genusPopulus, which is located on a different chromosome. These genes show distinct, floral-biased expression patterns compared to paralogous copies on autosomes.ConclusionThe presence of palindromic structures in sex chromosomes of mammals and plants highlights the intrinsic importance of these features in adaptive evolution in the absence of recombination. Convergent evolution is driving both the independent establishment of sex chromosomes as well as their fine-scale sequence structure.

13 Pags.- 6 Figs. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder, While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in any individual genome. Genes present in all lines are enriched for essential biological functions, while genes present in only some lines are enriched for conditionally beneficial functions (e.g., defense and development), display faster evolutionary rates, lie closer to transposable elements and are less likely to be syntenic with orthologous genes in other grasses. Our data suggest that differentially present genes contribute substantially to phenotypic variation within a eukaryote species, these genes have a major influence in population genetics, and transposable elements play a key role in pan-genome evolution., The work conducted by the US DOE Joint Genome Institute is supported by the Office of Science of the US Department of Energy under Contract no. DE-AC02-05CH11231. D.P. W. and R.A. were funded in part by the National Science Foundation (grant no. IOS–1258126), and the Great Lakes Bioenergy Research Center (Department of Energy Biological and Environmental Research Office of Science grant no. DE– FCO2–07ER64494). TEJ and DLDM were supported by NSF PGRP grant IOS-0922457. P.C. and B.C.M. were funded by Spanish MINECO (CGL2012-39953-C02-01 and CGL2016-79790-P). B.C.M. was partially funded by DGA—Obra Social La Caixa (grant number GA-LC-059-2011) and Spanish MINECO (AGL2013-48756-R, CSIC13-4E-2490). PC was partially funded by Spanish Aragon Government-European Social Fund (Bioflora).

Sex pheromone produced by Callosobruchus subinnotatus females stimulates conspecific males to walk upwind toward the source. Gas chromatographic and mass spectrometric analyses of sex pheromone components and their hydrogenated derivatives suggested that the sex pheromone consisted of two short-chain fatty acids, (E)-3-methyl-2-heptenoic acid (E32C7) and (Z)-3-methyl-2-heptenoic acid (Z32C7). The composition of the sex pheromone was confirmed by electrophysiological and behavioral bioassays with synthetic compounds. A mixture of 5 ng E32C7 and 5 ng Z32C7 elicited a 2.1-mV male EAG response, whereas the solvent control elicited 0.1 mV. Mixtures of the two compounds at various ratios were attractive to males in Y-tube bioassays. A pitfall-type trap equipped with a lure impregnated with 1 ng E32C7 and 1 ng Z32C7 was effective in trapping males. Traps baited with the lure caught 80% of males in a glass aquarium during nighttime and 50% during daytime, whereas control traps (solvent treated) in a separate aquarium caught 20% and 10%, respectively.

Mating and oviposition behaviors were studied inCallosobruchus subinnotatus. Copulation was most frequent during the late scotophase, 2–3 h before onset of photophase. The females were less willing to mate during photophase, which increased the time to initiate mating while decreasing the duration of mating. Females exhibited increased movement prior to mating, resting immediately after mating, and remained stationary for 6 h when oviposition commenced. Multiple mating by both males and females affected the number of eggs laid, duration of mating, and uncoupling time at the end of mating. Females that mated two or three times laid more eggs than females that mated once or more than three times. Females that remainedin copula for less than 18 min showed greater readiness to remate than those that remainedin copula longer. There was a gradual decrease in the number of eggs females could lay with an increase in the number of previous matings by males.

Sex pheromone activity ofEriborus terebrans (Gravenhorst) (Hymenoptera: Ichneumonidae) was recovered from acetone rinses of flasks that previously contained females. The acetone flask rinses elicited the following male responses: upwind anemotaxis, casting, hovering, landing, wingfanning, and mating attempts with other nearby males. Activity of the acetone flask rinse lasted up to four days on a glass substrate. Polar component and nonpolar components were demonstrated in the acetone flask rinse. The polar component elicited male behavioral responses similar to those by the acetone flask rinse, although retention of males at the pheromone source and the period of wing-fanning were of shorter duration. Chromatography data and chemical derivatization indicated that the polar component had the properties of a carboxylic acid with an additional oxygen-containing functional group. The non-polar component acted as a synergist since it was inactive alone but increased male behavioral responses when added to the polar component. Florisil open column chromatography suggested that the nonpolar component was a hydrocarbon(s).

A kairomone that effects host-seeking behavior inTrichogramma nubilale Ertle and Davis, an egg parasitoid of the European corn borer,Ostrinia nubilalis (Hübner), was isolated from moth scales of the European corn borer. The kairomone was identified as a mixture of 11,15-, 13,17-, and 15,19-dimethylnonatriacontanes. The three dimethylnonatriacontanes were synthesized, and bioassays showed that the 13,17 isomer was the most active in terms of klinokinetic and retention effects. The 11,15 isomer and the 15,19 isomer had some effect on klinokinesis, but they failed to effect retention of the wasps. The 13,17-dimethylnonatriacontane is considered to be the most important component of the kairomone.

Nature 463, 178–183 (2010) During resubmission of this work, a paper was published1 that used a comparative genomics approach between soybean and maize to show that a single-base mutation in chromosome 19 accounts for the duplicate recessive epistasis needed to greatly reduce phytate production in soybean seed.

Background: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. Results: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. Conclusions: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.

Background: Cell-fate specification and tissue differentiation during development are largely achieved by the regulation of gene transcription. Results: As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, we examined 2,179 genes by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos. The photomicrographs were annotated using controlled vocabularies for anatomical structures that are organized into a developmental hierarchy. We also generated a detailed time course of gene expression during embryogenesis using microarrays to provide an independent corroboration of the in situ hybridization results. All image, annotation and microarray data are stored in publicly available database. We found that the RNA transcripts of about 1% of genes show clear subcellular localization. Nearly all the annotated expression patterns are distinct. We present an approach for organizing the data by hierarchical clustering of annotation terms that allows us to group tissues that express similar sets of genes as well as genes displaying similar expression patterns. Conclusions: Analyzing gene-expression patterns by in situ hybridization to whole-mount embryos provides an extremely rich dataset that can be used to identify genes involved in developmental processes that have been missed by traditional genetic analysis. Systematic analysis of rigorously annotated patterns of gene expression will complement and extend the types of analyses carried out using expression microarrays.

Role des composants chimiques de l'hote de T.n. dans son comportement de recherche de son hote