Here, we present the sequence data and scripts utilized for dating angiosperms, as described in our publication titled "Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits". A comprehensive step-by-step guide on analyzing these data along with corresponding results can be accessed within the folder labeled 'Dating'. In addition, the final version of the dated tree is available in a separate folder named 'Drawing'.
As a new branch of genomics, plant paleogenomics reconstructs ancestral genomes from actual modern species and infers palaeohistory, evolutionary and/or speciation events that have shaped the modern species. Advances in high-throughput sequencing technologies yield accurate long reads, promote the progress of plant genome sequence assembly, and thereby offer paleogenomics a large collection of valuable reference genomes from modern species. Whole-genome duplication (WGD) and polyploidization cause rapid genomic reorganization, massive gene losses and structural variations. WGD events are therefore central to plant evolution. In this review, we summarize recent progress in sequencing and assembly of plant genomes, principles of plant paleogenomics, WGD events in plant genomes, and the most likely evolutionary scenario in plants. Furthermore, we highlight some of the challenges as well as future directions.
Adaptation to cool climates has occurred several times in different angiosperm groups. Among them, Pooideae, the largest grass subfamily with ∼3,900 species including wheat and barley, have successfully occupied many temperate regions and play a prominent role in temperate ecosystems. To investigate possible factors contributing to Pooideae adaptive evolution to cooling climates, we performed phylogenetic reconstruction using five gene sets (with 1,234 nuclear genes and their subsets) from 157 transcriptomes/genomes representing all 15 tribes and 24 of 26 subtribes. Our phylogeny supports the monophyly of all tribes (except Diarrheneae) and all subtribes with at least two species, with strongly supported resolution of their relationships. Molecular dating suggests that Pooideae originated in the late Cretaceous, with subsequent divergences under cooling conditions first among many tribes from the early middle to late Eocene and again among genera in the middle Miocene and later periods. We identified a cluster of gene duplications (CGD5) shared by the core Pooideae (with 80% Pooideae species) near the Eocene-Oligocene transition, coinciding with the transition from closed to open habitat and an upshift of diversification rate. Molecular evolutionary analyses homologs of CBF for cold resistance uncovered tandem duplications during the core Pooideae history, dramatically increasing their copy number and possibly promoting adaptation to cold habitats. Moreover, duplication of AP1/FUL-like genes before the Pooideae origin might have facilitated the regulation of the vernalization pathway under cold environments. These and other results provide new insights into factors that likely have contributed to the successful adaptation of Pooideae members to temperate regions.
Pomegranate (Punica granatum L.) has an ancient cultivation history and has become an emerging profitable fruit crop due to its attractive features such as the bright red appearance and the high abundance of medicinally valuable ellagitannin-based compounds in its peel and aril. However, the limited genomic resources have restricted further elucidation of genetics and evolution of these interesting traits. Here, we report a 274-Mb high-quality draft pomegranate genome sequence, which covers approximately 81.5% of the estimated 336-Mb genome, consists of 2177 scaffolds with an N50 size of 1.7 Mb and contains 30 903 genes. Phylogenomic analysis supported that pomegranate belongs to the Lythraceae family rather than the monogeneric Punicaceae family, and comparative analyses showed that pomegranate and Eucalyptus grandis share the paleotetraploidy event. Integrated genomic and transcriptomic analyses provided insights into the molecular mechanisms underlying the biosynthesis of ellagitannin-based compounds, the colour formation in both peels and arils during pomegranate fruit development, and the unique ovule development processes that are characteristic of pomegranate. This genome sequence provides an important resource to expand our understanding of some unique biological processes and to facilitate both comparative biology studies and crop breeding.
Abstract Sulfite is an important food preservative that is widely used in wine brewing, and the mechanism of sulfite metabolism in some strains of Saccharomyces cerevisiae has been reported. However, there is still something unclear in the sulfite metabolism, because there are different mechanisms in the different strains. To study the sulfite metabolism in the transcriptional network and gene expression of S. cerevisiae strains, SSU1 , and FZF1 genes were identified from genome sequences of yeast strains, and the transcriptional profile was mined from cDNA microarray. The fifth zinc finger of FZF1 protein was found to be another vital region for regulation, just as the first and fourth fingers previously reported. The functional difference of SSU1 protein in all surveyed strains might be related to the variation sites at 19, 52, 164, 291 and 344, and that of FZF1 protein might be related to the variation sites at 100, 107, 115, 120 and 258. The sulfur-tolerant capability of EC1118, UWOPS03-461-4, UWOPS05-217-3, UWOPS05-227-2, YPS128 and YPS606 strains was higher than the other strains surveyed, according to the CAI value of SSU1 and FZF1 genes. The evolutions of SSU1 and FZF1 genes were pushed by the mutation pressures. The expression levels of SSU1 and FZF1 genes might be enhanced by ROX1, ADR1, YPR015C, HAP4 and GIS1 genes. In addition, the function of YPR015C was validated, and the YPR015C gene was firstly found to play an important role in regulating sulfite metabolism.
Abstract Unraveling evolutionary history and genomic basis of heterosis is fundamental for advancing rice productivity. We developed a genome-scale phylogeny of Oryzeae by coalescing 39,984 gene trees. Our analysis supports parallel, independent origins and nearly synchronous evolutionary trajectories leading to the subsequent domestication of indica and japonica , evidenced by molecular dating and synonymous substitution rates for syntenic and domestication-associated genes. Our survey of 1,383 gene duplications in ancestor of O. sativa uncovers their roles in vital biological processes, highlighting the significance in environmental adaptability. Additionally, we confirm the lack of hybridization event among subspecies ancestors through gene tree topology and D-statistical analyses. We generated 71.67 GB whole-genome sequencing data for five super-hybrid rice varieties and their progenitors, revealing differential positive selection and genetic exchanges between subspecies, essential for heterosis formation. Crucially, our study underscores the role of non-additive gene expression in heterosis, particularly in genes associated with DNA repair and recombination, which may confer resistance traits. Furthermore, eQTL and de novo mutation analyses identify key developmental and stress response genes, offering targets for enhancing heterosis in rice. Overall, our research reveals crucial insights into the genetics of rice domestication and heterosis, offering a genomic resource to improve rice’s agricultural productivity.
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine–cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
An experiment was conducted from 2016 to 2017 to assess the effect of kernel metabolism in development stages after organic mulching compared to control. Organic mulching significantly increased crop yields (higher 128% in 2016, higher 60% in 2017), oil content (the highest oil content was 27.6% higher than that of the control), and improved soil properties (SOC, SAN, AP, and AK). In this study, soil pH, SOC, AN, AP, and AK in 0-30 cm soil depth were measured. Results showed that the effect of mulching on soil pH was not significant at the harvesting stage. The greatest metabolic differences occurred during the period of high oil conversion (S2-S4), primarily involving 11 relevant metabolic pathways. This further verified that
ABSTRACT Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary‐fruit “modules” each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single‐seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole‐genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
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