Multiple independent recombinations led to hermaphroditism in grapevine

Hermaphroditic (perfect) flowers were a key trait in grapevine domestication, enabling a drastic increase in yields due to the efficiency of self-pollination in the domesticated grapevine (Vitis vinifera L. ssp. vinifera). In contrast, all extant wild Vitis species are dioecious, each plant having only male or female flowers. In this study, we identified the male (M) and female (f) haplotypes of the sex-determining region (SDR) in the wild grapevine species V. cinerea and confirmed the boundaries of the SDR. We also demonstrated that the SDR and its boundaries are precisely conserved across the Vitis genus using shotgun resequencing data of 556 wild and domesticated accessions from North America, East Asia, and Europe. A high linkage disequilibrium was found at the SDR in all wild grape species, while different recombination signatures were observed along the hermaphrodite (H) haplotype of 363 cultivated accessions, revealing two distinct H haplotypes, named H1 and H2. To further examine the H2 haplotype, we sequenced the genome of two grapevine cultivars, 'Riesling' and 'Chardonnay'. By reconstructing the first two H2 haplotypes, we estimated the divergence time between H1 and H2 haplotypes at ∼6 million years ago, which predates the domestication of grapevine (∼8,000 y ago). Our findings emphasize the important role of recombination suppression in maintaining dioecy in wild grape species and lend additional support to the hypothesis that at least two independent recombination events led to the reversion to hermaphroditism in grapevine.

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Heat-induced transposition leads to rapid drought resistance of Arabidopsis thaliana

10.1101/2021.11.25.469987 ◽

2021 ◽

Author(s):

Michael Thieme ◽

Arthur Brêchet ◽

Yann Bourgeois ◽

Bettina Keller ◽

Etienne Bucher ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Drought Resistance ◽

Phenotypic Diversity ◽

Plant Evolution ◽

Loss Of Function ◽

Copy Numbers ◽

Drastic Increase ◽

In The Wild ◽

Rate Of Photosynthesis

Plant genomes comprise a vast diversity of transposable elements (TEs) (Tenaillon et al. 2010)⁠. While their uncontrolled proliferation can have fatal consequences for their host, there is strong evidence for their importance in fueling genetic diversity and plant evolution (Baduel et al. 2021)⁠. However, the number of studies addressing the role of TEs in this process is limited. Here we show that the heat-induced burst of a low-copy TE increases phenotypic diversity and leads to the rapid emergence of more drought-resistant individuals of Arabidopsis thaliana. We exposed TE-high-copy-(hc)lines (Thieme et al. 2017)⁠ with up to ~8 fold increased copy numbers of the heat-responsive ONSEN-TE (AtCOPIA78) (Ito et al. 2011; Cavrak et al. 2014; Tittel-Elmer et al. 2010)⁠ in the wild type background to desiccation as a straightforward and highly relevant selection pressure. We found evidence for a drastic increase of drought resistance in five out of the 23 tested hc-lines and further pinpoint one of the causative mutations to an exonic ONSEN-insertion in the ribose-5-phosphate-isomerase 2 gene. This loss-of-function mutation resulted in a decreased rate of photosynthesis and water consumption. This is one of the rare examples (Esnault et al. 2019)⁠ experimentally demonstrating the adaptive potential of mobilized stress-responsive TEs in eukaryotes. Our results further shed light on the complex relationship between mobile elements and their hosts and substantiate the importance of TE-mediated loss-of-function mutations in stress adaptation, particularly with respect to global warming.

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Role of Mismatch Repair in the Fidelity ofRAD51- andRAD59-Dependent Recombination inSaccharomyces cerevisiae

Genetics ◽

10.1093/genetics/165.4.1733 ◽

2003 ◽

Vol 165 (4) ◽

pp. 1733-1744 ◽

Cited By ~ 2

Author(s):

Rachelle Miller Spell ◽

Sue Jinks-Robertson

Keyword(s):

Mismatch Repair ◽

Genome Instability ◽

Wild Type ◽

Recombination Suppression ◽

Spontaneous Recombination ◽

Mutant Strains ◽

In The Wild ◽

Homeologous Recombination ◽

Recombination Assay

AbstractTo prevent genome instability, recombination between sequences that contain mismatches (homeologous recombination) is suppressed by the mismatch repair (MMR) pathway. To understand the interactions necessary for this regulation, the genetic requirements for the inhibition of homeologous recombination were examined using mutants in the RAD52 epistasis group of Saccharomyces cerevisiae. The use of a chromosomal inverted-repeat recombination assay to measure spontaneous recombination between 91 and 100% identical sequences demonstrated differences in the fidelity of recombination in pathways defined by their dependence on RAD51 and RAD59. In addition, the regulation of homeologous recombination in rad51 and rad59 mutants displayed distinct patterns of inhibition by different members of the MMR pathway. Whereas the requirements for the MutS homolog, MSH2, and the MutL homolog, MLH1, in the suppression of homeologous recombination were similar in rad51 strains, the loss of MSH2 caused a greater loss in homeologous recombination suppression than did the loss of MLH1 in a rad59 strain. The nonequivalence of the regulatory patterns in the wild-type and mutant strains suggests an overlap between the roles of the RAD51 and RAD59 gene products in potential cooperative recombination mechanisms used in wild-type cells.

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Is Empathy Required for Making Moral Judgments?

10.1093/oso/9780190878597.003.0007 ◽

2018 ◽

Author(s):

John Deigh

Keyword(s):

Moral Judgment ◽

Moral Judgments ◽

Psychopathic Personality ◽

Critical Examination ◽

Psychological Profile ◽

Main Thesis ◽

Different Types ◽

Additional Support

This essay is a study of the nature of moral judgment. Its main thesis is that moral judgment is a type of judgment defined by its content and not its psychological profile. The essay arrives at this thesis through a critical examination of Hume’s sentimentalism and the role of empathy in its account of moral judgment. The main objection to Hume’s account is its exclusion of people whom one can describe as making moral judgments though they have no motivation to act on them. Consideration of such people, particularly those with a psychopathic personality, argues for a distinction between different types of moral judgment in keeping with the essay’s main thesis. Additional support for the main thesis is then drawn from Piaget’s theory of moral judgment in children.

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Transcriptome Changes in Pseudomonas putida KT2440 during Medium-Chain-Length Polyhydroxyalkanoate Synthesis Induced by Nitrogen Limitation

International Journal of Molecular Sciences ◽

10.3390/ijms22010152 ◽

2020 ◽

Vol 22 (1) ◽

pp. 152

Author(s):

Dorota Dabrowska ◽

Justyna Mozejko-Ciesielska ◽

Tomasz Pokój ◽

Slawomir Ciesielski

Keyword(s):

Chain Length ◽

Nitrogen Limitation ◽

Stringent Response ◽

Wild Type ◽

Pseudomonas Putida Kt2440 ◽

Medium Chain ◽

Environmental Stimuli ◽

Medium Chain Length ◽

In The Wild

Pseudomonas putida’s versatility and metabolic flexibility make it an ideal biotechnological platform for producing valuable chemicals, such as medium-chain-length polyhydroxyalkanoates (mcl-PHAs), which are considered the next generation bioplastics. This bacterium responds to environmental stimuli by rearranging its metabolism to improve its fitness and increase its chances of survival in harsh environments. Mcl-PHAs play an important role in central metabolism, serving as a reservoir of carbon and energy. Due to the complexity of mcl-PHAs’ metabolism, the manner in which P. putida changes its transcriptome to favor mcl-PHA synthesis in response to environmental stimuli remains unclear. Therefore, our objective was to investigate how the P. putida KT2440 wild type and mutants adjust their transcriptomes to synthesize mcl-PHAs in response to nitrogen limitation when supplied with sodium gluconate as an external carbon source. We found that, under nitrogen limitation, mcl-PHA accumulation is significantly lower in the mutant deficient in the stringent response than in the wild type or the rpoN mutant. Transcriptome analysis revealed that, under N-limiting conditions, 24 genes were downregulated and 21 were upregulated that were common to all three strains. Additionally, potential regulators of these genes were identified: the global anaerobic regulator (Anr, consisting of FnrA, Fnrb, and FnrC), NorR, NasT, the sigma54-dependent transcriptional regulator, and the dual component NtrB/NtrC regulator all appear to play important roles in transcriptome rearrangement under N-limiting conditions. The role of these regulators in mcl-PHA synthesis is discussed.

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Osteoarthritis: Insights Offered by the Study of Bone Mass Genetics

Current Osteoporosis Reports ◽

10.1007/s11914-021-00655-1 ◽

2021 ◽

Vol 19 (2) ◽

pp. 115-122

Author(s):

A. Hartley ◽

C. L. Gregson ◽

L. Paternoster ◽

J. H. Tobias

Keyword(s):

Bone Mass ◽

Causal Effect ◽

Mendelian Randomisation ◽

Mineral Density ◽

High Bone Mass ◽

Increased Risk ◽

High Bone ◽

Genetic Mechanisms ◽

Additional Support

Abstract Purpose of Review This paper reviews how bone genetics has contributed to our understanding of the pathogenesis of osteoarthritis. As well as identifying specific genetic mechanisms involved in osteoporosis which also contribute to osteoarthritis, we review whether bone mineral density (BMD) plays a causal role in OA development. Recent Findings We examined whether those genetically predisposed to elevated BMD are at increased risk of developing OA, using our high bone mass (HBM) cohort. HBM individuals were found to have a greater prevalence of OA compared with family controls and greater development of radiographic features of OA over 8 years, with predominantly osteophytic OA. Initial Mendelian randomisation analysis provided additional support for a causal effect of increased BMD on increased OA risk. In contrast, more recent investigation estimates this relationship to be bi-directional. However, both these findings could be explained instead by shared biological pathways. Summary Pathways which contribute to BMD appear to play an important role in OA development, likely reflecting shared common mechanisms as opposed to a causal effect of raised BMD on OA. Studies in HBM individuals suggest this reflects an important role of mechanisms involved in bone formation in OA development; however further work is required to establish whether the same applies to more common forms of OA within the general population.

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Premating barriers in young sympatric snail species

Scientific Reports ◽

10.1038/s41598-021-84407-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Arina L. Maltseva ◽

Marina A. Varfolomeeva ◽

Arseniy A. Lobov ◽

Polina O. Tikanova ◽

Egor A. Repkin ◽

...

Keyword(s):

Gene Flow ◽

Snail Species ◽

Sympatric Populations ◽

Gastropod Species ◽

Shell Size ◽

Closely Related Species ◽

Partial Canonical Correspondence Analysis ◽

In The Wild ◽

Isolation Index

AbstractSympatric coexistence of recently diverged species raises the question of barriers restricting the gene flow between them. Reproductive isolation may be implemented at several levels, and the weakening of some, e.g. premating, barriers may require the strengthening of the others, e.g. postcopulatory ones. We analysed mating patterns and shell size of mates in recently diverged closely related species of the subgenus Littorina Neritrema (Littorinidae, Caenogastropoda) in order to assess the role of premating reproductive barriers between them. We compared mating frequencies observed in the wild with those expected based on relative densities using partial canonical correspondence analysis. We introduced the fidelity index (FI) to estimate the relative accuracy of mating with conspecific females and precopulatory isolation index (IPC) to characterize the strength of premating barriers. The species under study, with the exception of L. arcana, clearly demonstrated preferential mating with conspecifics. According to FI and IPC, L. fabalis and L. compressa appeared reliably isolated from their closest relatives within Neritrema. Individuals of these two species tend to be smaller than those of the others, highlighting the importance of shell size changes in gastropod species divergence. L. arcana males were often found in pairs with L. saxatilis females, and no interspecific size differences were revealed in this sibling species pair. We discuss the lack of discriminative mate choice in the sympatric populations of L. arcana and L. saxatilis, and possible additional mechanisms restricting gene flow between them.

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Group size and aquatic vegetation modulates male preferences for female shoals in wild zebrafish, Danio rerio

Scientific Reports ◽

10.1038/s41598-020-80913-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Aditya Ghoshal ◽

Anuradha Bhat

Keyword(s):

Group Size ◽

Aquatic Vegetation ◽

Natural Habitat ◽

Ecological Factors ◽

Choice Test ◽

Female Group ◽

Aquatic Flora ◽

In The Wild ◽

The Individual

AbstractShoaling decisions in the wild are determined by a combination of innate preferences of the individual along with the interplay of multiple ecological factors. In their natural habitat as well as in the laboratory, zebrafish is a shoaling fish. Here, we investigate the role of group size and associated vegetation in shaping shoaling preferences of wild male zebrafish. We studied the association preference of males to groups of female shoals in a multi-choice test design. We found that males made greater proportion of visits to an 8-female group compared to 2 and 4-female groups. However, males spent similar proportions of time across the three female-containing groups. When artificial vegetation was incorporated along with female number as an additional factor, we found that males prefer high and moderately vegetated patches compared to low or no-vegetation groups, irrespective of the number of females in these patches. Based on experiments using a novel multi-choice design, our results show that preference for group size can change due to interaction of two separate factors. This work is a first attempt to understand the role of aquatic flora in determining shoaling preferences in zebrafish, using an experimental paradigm consisting of a gradation in female and vegetation densities.

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Evaluation of breeding potential of wild grape originating from Armenia

BIO Web of Conferences ◽

10.1051/bioconf/20191501006 ◽

2019 ◽

Vol 15 ◽

pp. 01006

Author(s):

K. Margaryan ◽

E. Maul ◽

Z. Muradyan ◽

A. Hovhannisyan ◽

G. Melyan ◽

...

Keyword(s):

Vitis Vinifera ◽

Allelic Variation ◽

Resistance Breeding ◽

Crop Wild Relatives ◽

Breeding Programs ◽

Genetic Traits ◽

Breeding Potential ◽

Wild Grape ◽

Wild Grapevine ◽

The Future

Crop wild relatives provide a useful source of genetic variation and represent a large pool of genetic diversity for new allelic variation required in breeding programs. Armenia is an important center of origin both for cultivated Vitis vinifera ssp. sativa and wild Vitis vinifera ssp. sylvestris. Owing to recent prospection in Armenian woods and river floodplains many forms of wild grapevine were discovered and inventoried, which is an important prerequisite to unlock their breeding potential in the future. The fact that some genotypes of V. sylvestris can withstand the diseases is likely to be due to a more efficient basal immunity. The overall goal of the proposed research was to characterize the diversity of V. sylvestris from Armenia with respect to its capacity for stilbene biosynthesis, which might be exploited as genetic resource for resistance breeding. The realized research stimulates the recovery, characterization and preservation of wild grape germplasm, presently at risk of extinction. The recovery and characterization of wild genotypes will be the base of selection of genetic traits important in breeding programs for the generation of biotic and changing climate tolerant grapevine varieties and rootstocks, both necessary for the future of viticulture in Armenia and in Europe.

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Controlled Transcription of Regulator Gene carS by Tet-on or by a Strong Promoter Confirms Its Role as a Repressor of Carotenoid Biosynthesis in Fusarium fujikuroi

Microorganisms ◽

10.3390/microorganisms9010071 ◽

2020 ◽

Vol 9 (1) ◽

pp. 71

Author(s):

Julia Marente ◽

Javier Avalos ◽

M. Carmen Limón

Keyword(s):

Wild Strain ◽

Ring Finger ◽

Carotenoid Biosynthesis ◽

Negative Regulator ◽

Fusarium Fujikuroi ◽

Structural Genes ◽

Gene Encoding ◽

In The Wild ◽

Set Up

Carotenoid biosynthesis is a frequent trait in fungi. In the ascomycete Fusarium fujikuroi, the synthesis of the carboxylic xanthophyll neurosporaxanthin (NX) is stimulated by light. However, the mutants of the carS gene, encoding a protein of the RING finger family, accumulate large NX amounts regardless of illumination, indicating the role of CarS as a negative regulator. To confirm CarS function, we used the Tet-on system to control carS expression in this fungus. The system was first set up with a reporter mluc gene, which showed a positive correlation between the inducer doxycycline and luminescence. Once the system was improved, the carS gene was expressed using Tet-on in the wild strain and in a carS mutant. In both cases, increased carS transcription provoked a downregulation of the structural genes of the pathway and albino phenotypes even under light. Similarly, when the carS gene was constitutively overexpressed under the control of a gpdA promoter, total downregulation of the NX pathway was observed. The results confirmed the role of CarS as a repressor of carotenogenesis in F. fujikuroi and revealed that its expression must be regulated in the wild strain to allow appropriate NX biosynthesis in response to illumination.

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Role of the Mitochondrial Signaling Pathway in Murine Coronavirus-Induced Oligodendrocyte Apoptosis

Journal of Virology ◽

10.1128/jvi.80.1.395-403.2006 ◽

2006 ◽

Vol 80 (1) ◽

pp. 395-403 ◽

Cited By ~ 21

Author(s):

Yin Liu ◽

Yinghui Pu ◽

Xuming Zhang

Keyword(s):

Hepatitis Virus ◽

Mitochondrial Pathway ◽

Caspase 8 ◽

Caspase 9 ◽

Apoptotic Pathway ◽

Antiapoptotic Proteins ◽

Mitochondrial Signaling ◽

Drastic Increase ◽

Infected Cells

ABSTRACT A previous study demonstrated that infection of rat oligodendrocytes by mouse hepatitis virus (MHV) resulted in apoptosis, which is caspase dependent (Y. Liu, Y. Cai, and X. Zhang, J. Virol. 77:11952-11963, 2003). Here we determined the involvement of the mitochondrial pathway in MHV-induced oligodendrocyte apoptosis. We found that caspase-9 activity was 12-fold higher in virus-infected cells than in mock-infected cells at 24 h postinfection (p.i.). Pretreatment of cells with a caspase-9 inhibitor completely blocked caspase-9 activation and partially inhibited the apoptosis mediated by MHV infection. Analyses of cytochrome c release further revealed an activation of the mitochondrial apoptotic pathway. Stable overexpression of the two antiapoptotic proteins Bcl-2 and Bcl-xL significantly, though only partially, blocked apoptosis, suggesting that activation of the mitochondrial pathway is partially responsible for the apoptosis. To identify upstream signals, we determined caspase-8 activity, cleavage of Bid, and expression of Bax and Bad by Western blotting. We found a drastic increase in caspase-8 activity and cleavage of Bid at 24 h p.i. in virus-infected cells, suggesting that Bid may serve as a messenger to relay the signals from caspase-8 to mitochondria. However, treatment with a caspase-8 inhibitor only slightly blocked cytochrome c release from the mitochondria. Furthermore, we found that Bax but not Bad was significantly increased at 12 h p.i. in cells infected with both live and UV-inactivated viruses and that Bax activation was partially blocked by treatment with the caspase-8 inhibitor. These results thus establish the involvement of the mitochondrial pathway in MHV-induced oligodendrocyte apoptosis.

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