The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

AbstractThe fruits of Physalis (Solanaceae) have a unique structure, a lantern-like fruiting calyx known as inflated calyx syndrome (ICS) or the Chinese lantern, and are rich in steroid-related compounds. However, the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown. Here, we present a high-quality chromosome-level reference genome assembly of Physalis floridana (~1.40 Gb in size) with a contig N50 of ~4.87 Mb. Through evolutionary genomics and experimental approaches, we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that, together with the previously revealed mutation affecting floral MPF2 expression, might have contributed to the origination of ICS in Physaleae, suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation. Moreover, the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits. The results reveal the importance of gene gains (duplication) and/or subsequent losses as genetic bases of the evolution of distinct fruit traits, and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

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Classification and Phylogeny of the MADS-Box Multigene Family Suggest Defined Roles of MADS-Box Gene Subfamilies in the Morphological Evolution of Eukaryotes

Journal of Molecular Evolution ◽

10.1007/pl00006110 ◽

1996 ◽

Vol 43 (5) ◽

pp. 484-516 ◽

Cited By ~ 3

Author(s):

Günter Theißen ◽

Jan T. Kim ◽

Heinz Saedler

Keyword(s):

Multigene Family ◽

Morphological Evolution ◽

Mads Box ◽

Mads Box Gene

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Molecular Evolution of Genes Controlling Petal and Stamen Development: Duplication and Divergence Within the APETALA3 and PISTILLATA MADS-Box Gene Lineages

Genetics ◽

10.1093/genetics/149.2.765 ◽

1998 ◽

Vol 149 (2) ◽

pp. 765-783 ◽

Cited By ~ 4

Author(s):

Elena M Kramer ◽

Robert L Dorit ◽

Vivian F Irish

Keyword(s):

Morphological Evolution ◽

Floral Organ ◽

Duplication Event ◽

Homeotic Genes ◽

Mads Box ◽

Floral Organ Identity ◽

Organ Identity ◽

Duplication Events ◽

Mads Box Gene ◽

Dicot Species

Abstract The specification of floral organ identity in the higher dicots depends on the function of a limited set of homeotic genes, many of them members of the MADS-box gene family. Two such genes, APETALA3 (AP3) and PISTILLATA (PI), are required for petal and stamen identity in Arabidopsis; their orthologs in Antirrhinum exhibit similar functions. To understand how changes in these genes may have influenced the morphological evolution of petals and stamens, we have cloned twenty-six homologs of the AP3 and PI genes from two higher eudicot and eleven lower eudicot and magnolid dicot species. The sequences of these genes reveal the presence of characteristic PI- and AP3-specific motifs. While the PI-specific motif is found in all of the PI genes characterized to date, the lower eudicot and magnolid dicot AP3 homologs contain distinctly different motifs from those seen in the higher eudicots. An analysis of all the available AP3 and PI sequences uncovers multiple duplication events within each of the two gene lineages. A major duplication event in the AP3 lineage coincides with the base of the higher eudicot radiation and may reflect the evolution of a petal-specific AP3 function in the higher eudicot lineage.

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The utility of genomic prediction models in evolutionary genetics

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0693 ◽

2021 ◽

Vol 288 (1956) ◽

pp. 20210693

Author(s):

Suzanne E. McGaugh ◽

Aaron J. Lorenz ◽

Lex E. Flagel

Keyword(s):

Best Practices ◽

Genomic Prediction ◽

Complex Traits ◽

Genetic Architecture ◽

Prediction Models ◽

Evolutionary Genetics ◽

Breeding Value ◽

Evolutionary Genomics ◽

Genome Wide ◽

Genetic Value

Variation in complex traits is the result of contributions from many loci of small effect. Based on this principle, genomic prediction methods are used to make predictions of breeding value for an individual using genome-wide molecular markers. In breeding, genomic prediction models have been used in plant and animal breeding for almost two decades to increase rates of genetic improvement and reduce the length of artificial selection experiments. However, evolutionary genomics studies have been slow to incorporate this technique to select individuals for breeding in a conservation context or to learn more about the genetic architecture of traits, the genetic value of missing individuals or microevolution of breeding values. Here, we outline the utility of genomic prediction and provide an overview of the methodology. We highlight opportunities to apply genomic prediction in evolutionary genetics of wild populations and the best practices when using these methods on field-collected phenotypes.

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THE MITOTIC APPARATUS

The Journal of Cell Biology ◽

10.1083/jcb.25.1.137 ◽

1965 ◽

Vol 25 (1) ◽

pp. 137-144 ◽

Cited By ~ 65

Author(s):

R. E. Kane

Keyword(s):

Sea Urchin ◽

Alkaline Ph ◽

Experimental Conditions ◽

Mitotic Apparatus ◽

Ph Values ◽

Cent Concentration ◽

Experimental Approaches ◽

The Stability ◽

Related Compounds ◽

Long Chain

Previous investigations have shown that the mitotic apparatus (MA) can be isolated from dividing sea urchin eggs in water buffered at pH 5.6 and that the addition of 1 M hexanediol to the solution raises the usable pH to 6.4. Long chain glycols appeared to be much more effective than related compounds in increasing the stability of the MA, and the aim of the investigations reported here was to determine the basis of this specificity. These experiments show that this impression of specificity is misleading and that under suitable experimental conditions a variety of compounds can be substituted for the glycols. A number of alcohols will duplicate the action of the glycols in stabilizing the MA at pH 6.4, but they must be used at a similar per cent concentration rather than at a similar molar concentration. Increases in the concentration of alcohol or glycol allow isolation at more alkaline pH values, and a pH-concentration relation for the stability of the MA, covering the range from pH 5.6–8, has been determined. These results indicate that the action of these compounds in stabilizing the mitotic apparatus is non-specific and is similar to their effects on the solubility of proteins. The isolation and stabilization of the mitotic apparatus can thus be viewed as a function of the solubility properties of its constituent proteins, opening a variety of new experimental approaches to this problem.

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Classification and phylogeny of the MADS-box multigene family suggest defined roles of MADS-box gene subfamilies in the morphological evolution of eukaryotes

Journal of Molecular Evolution ◽

10.1007/bf02337521 ◽

1996 ◽

Vol 43 (5) ◽

pp. 484-516 ◽

Cited By ~ 284

Author(s):

Günter Theißen ◽

Jan T. Kim ◽

Heinz Saedler

Keyword(s):

Multigene Family ◽

Morphological Evolution ◽

Mads Box ◽

Mads Box Gene

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A quantitative image analysis method for the determination of cocontinuity in polymer blends

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100150307 ◽

1993 ◽

Vol 51 ◽

pp. 894-895

Author(s):

William A. Heeschen

Keyword(s):

Image Analysis ◽

Polymer Blends ◽

Quantitative Measurement ◽

Morphological Evolution ◽

Phase Ratio ◽

Irregular Shapes ◽

Quantitative Image ◽

Discrete Domains ◽

A Domains

Two new morphological measurements based on digital image analysis, CoContinuity and CoContinuity Balance, have been developed and implemented for quantitative measurement of morphology in polymer blends. The morphology of polymer blends varies with phase ratio, composition and processing. A typical morphological evolution for increasing phase ratio of polymer A to polymer B starts with discrete domains of A in a matrix of B (A/B < 1), moves through a cocontinuous distribution of A and B (A/B ≈ 1) and finishes with discrete domains of B in a matrix of A (A/B > 1). For low phase ratios, A is often seen as solid convex particles embedded in the continuous B phase. As the ratio increases, A domains begin to evolve into irregular shapes, though still recognizable as separate domains. Further increase in the phase ratio leads to A domains which extend into and surround the B phase while the B phase simultaneously extends into and surrounds the A phase.

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Organotellurium carboxylates and related compounds: structural and synthetic considerations

Journal of Organometallic Chemistry ◽

10.1016/s0022-328x(00)84278-3 ◽

1974 ◽

Vol 63 (2) ◽

pp. 305-310 ◽

Cited By ~ 1

Author(s):

B Pant

Keyword(s):

Related Compounds

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Learned Placebo Effects in the Immune System

Zeitschrift für Psychologie ◽

10.1027/2151-2604/a000184 ◽

2014 ◽

Vol 222 (3) ◽

pp. 148-153 ◽

Cited By ~ 2

Author(s):

Sabine Vits ◽

Manfred Schedlowski

Keyword(s):

Nervous System ◽

Immune System ◽

Associative Learning ◽

Placebo Response ◽

Immunosuppressive Drug ◽

Immune Functions ◽

Placebo Effects ◽

New Therapeutic Approaches ◽

Biological Variables ◽

Experimental Approaches

Associative learning processes are one of the major neuropsychological mechanisms steering the placebo response in different physiological systems and end organ functions. Learned placebo effects on immune functions are based on the bidirectional communication between the central nervous system (CNS) and the peripheral immune system. Based on this “hardware,” experimental evidence in animals and humans showed that humoral and cellular immune functions can be affected by behavioral conditioning processes. We will first highlight and summarize data documenting the variety of experimental approaches conditioning protocols employed, affecting different immunological functions by associative learning. Taking a well-established paradigm employing a conditioned taste aversion model in rats with the immunosuppressive drug cyclosporine A (CsA) as an unconditioned stimulus (US) as an example, we will then summarize the efferent and afferent communication pathways as well as central processes activated during a learned immunosuppression. In addition, the potential clinical relevance of learned placebo effects on the outcome of immune-related diseases has been demonstrated in a number of different clinical conditions in rodents. More importantly, the learned immunosuppression is not restricted to experimental animals but can be also induced in humans. These data so far show that (i) behavioral conditioned immunosuppression is not limited to a single event but can be reproduced over time, (ii) immunosuppression cannot be induced by mere expectation, (iii) psychological and biological variables can be identified as predictors for this learned immunosuppression. Together with experimental approaches employing a placebo-controlled dose reduction these data provide a basis for new therapeutic approaches to the treatment of diseases where a suppression of immune functions is required via modulation of nervous system-immune system communication by learned placebo effects.

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