Biology subjects

Lee, C.-R.

Publications and source records attributed to Lee, C.-R..

14 recordsLinked to original sources

bioRxiv2025

The demographic history, genomic variation, and transcontinental genotype-phenotype-environment map of mungbean

The breeding of mungbean, a crucial Asian legume, has been hampered by the lack of genomic resources. The International Mungbean Improvement Network (IMIN) aims to ensure global access to diverse germplasms and genomic resources. Using 780 worldwide wild and cultivated accessions, we report this species most comprehensive (pan)genomic variation, demographic history, and genotype-phenotype-environment map. Despite archaeological evidence of the earliest cultivation in South Asia, present-day wild populations only possess relict traces of shared polymorphisms with cultivars. We showed that parallel losses of black seed coats in two Vigna species were caused by the same mutational mechanism in the same gene. In large-scale cross-continent field trials, we found accessions from distant environments from the trial sites have lower performance, especially in high-heritability and high-yield sites, suggesting future breeding priority in benign conditions on accessions from similar environments. Our comprehensive genomic and trial resources facilitate future breeding success of this essential crop.

evolutionary biology↗

bioRxiv2025

Major alleles of CDCA7α shape CG-methylation in Arabidopsis thaliana

DNA methylation is a key epigenetic mark that impacts gene expression and represses transposable elements (TEs) in eukaryotes. Numerous examples of cis-elements targeted by DNA methylation, particularly at CG sites (mCG), have been reported to be under selective pressure in animals and plants. By contrast, there is limited knowledge of trans-regulators of mCG leading to adaptation. Here, using genome-wide association studies, we identify CELL DIVISION CYCLE-ASSOCIATED PROTEIN 7 ALPHA (CDCA7) as a trans-regulator of mCG in natural populations of Arabidopsis thaliana. CDCA7 and its paralog, CDCA7{beta}, directly bind to the chromatin remodeler DECREASE IN DNA METHYLATION 1 (DDM1), which facilitates access of methyltransferases to DNA. CDCA7/{beta} selectively regulates mCG and minimally impacts other DDM1-dependent processes such as non-CG methylation and histone variant deposition. We identify the cis-regulatory sequence modulating CDCA7 expression in natural populations and determining the degree of mCG and TE silencing. The geographic distribution of CDCA7 alleles suggests that new alleles have repeatedly expanded to novel ecological niches, indicating a potential role in local adaptation. Altogether, our findings provide new insight into how changes in global DNA methylation levels through transcriptional regulation of the epigenetic machinery have the capacity to facilitate local adaptation.

plant biology↗

bioRxiv2024

PhoPQ-mediated lipopolysaccharide modification regulates intrinsic resistance to tetracycline and glycylcycline antibiotics in Escherichia coli

Tetracyclines and glycylcycline are among the last-resort antibiotics used to combat infections caused by multidrug-resistant Gram-negative pathogens. Despite the clinical importance of these antibiotics, their mechanisms of resistance remain unclear. In this study, we elucidated a novel mechanism of resistance to tetracycline and glycylcycline antibiotics via lipopolysaccharide (LPS) modification. Disruption of the Escherichia coli PhoPQ two-component system, which regulates the transcription of various genes involved in magnesium transport and LPS modification, leads to increased susceptibility to tetracycline, minocycline, doxycycline, and tigecycline. These phenotypes are caused by enhanced expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core sugar of LPS. PhoPQ-mediated regulation of EptB expression appears to affect the intracellular transportation of doxycycline. Disruption of EptB increases resistance to tetracycline and glycylcycline antibiotics, whereas the other two phosphoethanolamine transferases, EptA and EptC, that participate in the modification of other LPS residues, are not associated with resistance to tetracyclines and glycylcycline. Overall, our results demonstrated that PhoPQ-mediated modification of a specific residue of LPS by phosphoethanolamine transferase EptB regulates resistance to tetracycline and glycylcycline antibiotics. ImportanceElucidating the resistance mechanisms of clinically important antibiotics helps in maintaining the clinical efficacy of antibiotics and in the prescription of adequate antibiotic therapy. Although tetracycline and glycylcycline antibiotics are clinically important in combating multidrug-resistant Gram-negative bacterial infections, their mechanisms of resistance are not fully understood. Our research demonstrates that the Escherichia coli two-component system PhoPQ regulates resistance to tetracycline and glycylcycline antibiotics by controlling the expression of phosphoethanolamine transferase EptB, which catalyzes the modification of the inner core residue of lipopolysaccharide (LPS). Therefore, our findings highlight a novel resistance mechanism to tetracycline and glycylcycline antibiotics and the physiological significance of LPS core modification in E. coli. One sentence summaryLipopolysaccharide modification-mediated tigecycline resistance

microbiology↗

bioRxiv2024

How weedy Arabidopsis thaliana dominated the world: ancestral variation and polygenic adaptation

The composition of a species could change with demographic turnovers, where dominant populations quickly expanded and replaced others. However, whether such events have a genetic basis remains to be investigated. Previous studies showed that Arabidopsis thaliana experienced a significant demographic turnover, where "non-relicts" replaced "relicts" throughout Eurasia. Here, we showed that non-relicts have smaller seeds, more seeds per fruit, and a higher germination rate, making them more competitive over relicts. Using a unique population enriching relict alleles while minimizing population structure, we identified candidate loci and showed that such trait divergence was caused by the divergent sorting of multiple ancient haplotypes in a Mendelian gene and joint allele frequency change of polygenes affecting single-trait divergence and multi-trait covariance. This study is one of the few genetic investigations of species-wide demographic turnover, emphasizing the importance of processes different from the much-focused hard selective sweep.

evolutionary biology↗

bioRxiv2024

Lytic transglycosylase repertoire diversity enables daughter cell separation and antibiotic resistance in Escherichia coli under acidic stress

Peptidoglycan (PG) is an indispensable architectural element that imparts physical toughness and rigidity to the bacterial envelope. It is also a dynamic structure that undergoes continuous turnover or autolysis. Escherichia coli possesses redundant autolytic enzymes responsible for PG turnover; however, the rationale behind the existence of numerous autolytic enzymes remains incompletely understood. In this study, we elucidated the physiological roles of MltE and MltC, members of the lytic transglycosylase (LTG) family that catalyze the cleavage of glycosidic bonds between disaccharide subunits within PG strands. MltE and MltC are acidic LTGs that exhibit increased enzymatic activity and protein levels under acidic pH conditions, respectively. Deletion of these two LTGs results in a pronounced growth defect and elevated membrane permeability at acidic pH. Furthermore, these two LTGs are crucial for resistance against various antibiotics, particularly vancomycin. Intriguingly, inactivation of these LTGs induces a chaining morphology, indicative of daughter cell separation defects, only under acidic pH conditions. Simultaneous deletion of PG amidases, the known contributors to daughter cell separation, exacerbates the chaining phenotype at acidic pH. This suggests that the two LTGs may participate in the cleavage of glycan strands between daughter cells that cannot be resolved by PG amidases under acidic pH conditions. Collectively, our findings highlight the role of LTG repertoire diversity in facilitating bacterial survival and antibiotic resistance under stressful conditions. IMPORTANCEOrchestration of peptidoglycan (PG) synthesis and degradation plays a critical role in bacterial growth and development of antibiotic resistance. Bacteria use a diverse array of enzymes involved in PG synthesis and degradation to navigate the challenging conditions of the periplasm. Although Escherichia coli harbors 12 lytic transglycosylases (LTGs) responsible for cleaving glycosidic bonds between disaccharide subunits within PG strands, the physiological significance of their redundancy remains unclear. In this study, we demonstrated the indispensability of two LTGs, MltE and MltC, for cell growth, daughter cell separation, and antibiotic resistance under acidic stress conditions. Our findings highlight the potential significance of MltE and MltC as primary targets for the development of potentiators to augment the antimicrobial efficacy of antibiotics in acidic pH environments. One sentence summaryAcid stress-specific lytic transglycosylases

microbiology↗

bioRxiv2022

TWAS coupled with eQTL analysis reveals the genetic connection between gene expression and flowering time in Arabidopsis

Genome-wide association study (GWAS) has improved our understanding of complex traits, but challenges exist in distinguishing causation versus association caused by linkage disequilibrium. Instead, the transcriptome-wide association study (TWAS) detects direct associations between expression levels and phenotypic variations, providing an opportunity to better prioritize candidate genes. To assess the feasibility of TWAS, we investigated the association among transcriptomes, genomes, and various traits, including flowering time in Arabidopsis. First, the associated genes formerly known to regulate growth allometry or metabolite production were identified by TWAS. Then, for flowering time, six TWAS-newly identified genes were functionally validated. Analysis of expression quantitative trait locus (eQTL) further revealed a trans-regulatory hotspot affecting the expression of several TWAS-identified genes. The hotspot covers the FRIGIDA (FRI) gene body, which possesses multiple haplotypes differentially affecting the expression of downstream genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1). We also revealed multiple independent paths towards the loss of FRI function in natural accessions. Altogether, this study demonstrates the potential of combining TWAS with eQTL analysis to identify important regulatory modules of the FRI-FLC-SOC1 for quantitative traits in natural populations. HighlightCombining TWAS with eQTL analyses identifies haplotypes connecting flowering genes with their physiological trait, strengthening the importance of FRI-FLC-SOC1 regulatory module on flowering time among the Arabidopsis natural population.

plant biology↗

bioRxiv2022

Ecological and genetic trade-offs drive Arabidopsis thaliana range expansion in Europe

How trade-offs between traits constrain adaptation to contrasted environments is critical to understand the distribution range of a given species. In Arabidopsis thaliana, genetic analyses recently revealed that a group of genotypes successfully recolonized Europe from its center after the last glaciation, outcompeting older lineages and leaving them only at the distribution margins, where environmental conditions are more stressing. However, whether trade-offs between traits related to dispersal, competition, and stress tolerance explain the success and persistence of different lineages across the species geographic range remains an open question. Here, we compared the genetic and phenotypic differentiation between 72 ecotypes originating from three geographical groups in Europe (North, South and Center). We measured key traits related to fecundity, dispersal ability, competition tolerance, and stress tolerance, and used genomic data to infer the effect of selection on these traits. We showed that a trade-off between plant fecundity and seed mass constrains the diversification of A. thaliana in Europe. In particular, the success of the cosmopolitan genotypes that recolonized Europe can be explained by their higher dispersal ability at the expense of their competitive ability and stress tolerance. Inversely, peripheral ecotypes exhibited the opposite trait syndrome: high competition and stress tolerance but low dispersal ability. Moreover, peripheral genotypes tend to differentiate from central ones at genes involved in dispersal and competitive traits such as seed mass. Combining ecological and genomic approaches, our study demonstrated the role of key ecological trade-offs as evolutionary drivers of the distribution of plant populations along a geographic gradient. SignificanceAcross geographic gradients, differential adaptive phenotypes among populations can reduce the risk of local extinctions and favor niche dynamics. However, a phenotypic advantage often comes at a cost. For instance, the competition-colonization trade-off is proposed as an important driver of plant interspecific diversity, but its role for local adaptation at the intraspecific level is still unclear. Using the broadly-distributed species Arabidopsis thaliana, we evaluate how ecological trade-offs have shaped the demography and evolution of central and peripheral populations in its native geographic gradient. Our study demonstrates that the competition-colonization trade-off is responsible of the spatially-structured phenotypic variation of A. thaliana across its geographical range. Our study highlights seed mass as a key trait for plant adaptation across environmental conditions.

ecology↗

bioRxiv2022

Distinct selection signatures during domestication and improvement in crops: a tale of two genes in mungbean

Domestication and improvement are two crucial processes underlying the evolution of crops. Domestication transformed wild plants into a utilizable form for humans; improvement refined cultivars adapting to distinct environments and local preferences. Using whole-genome re-sequencing of Vigna radiata, we investigated the demographic history and compared the genetic footprints of domestication and improvement. The Asian wild population migrated to Australia at about 50 kya, and domestication happened in Asia about 9 kya selecting for non-shattering pods. The key candidate gene for this trait, VrMYB26a, has lower expression in cultivars, consistent with the reduced polymorphism in the promoter region reflecting hard selective sweep. The determinate stems were later selected as an improvement phenotype and associated with the gene VrDet1. Two ancient haplotypes reducing gene expression exhibit intermediate frequencies in cultivars, consistent with selection favoring independent haplotypes in soft selective sweep. Our results suggest domestication and improvement may leave different genomic signatures of selection, reflecting the fundamental differences in the two processes and highlighting the limitations of genome-scan methods relying on hard selective sweep.

plant biology↗

bioRxiv2022

Coordinated and distinct LD-transpeptidase-independent roles of peptidoglycan carboxypeptidases DacC and DacA in stress adaptation and cell shape maintenance

Peptidoglycan (PG) is an essential bacterial architecture pivotal for shape maintenance and adaptation to osmotic stress. Although PG synthesis and modification are tightly regulated under harsh environmental stresses, few related mechanisms have been investigated. In this study, we aimed to investigate the coordinated and distinct roles of the PG carboxypeptidases DacC and DacA, in adaptation to alkaline and salt stresses and shape maintenance in Escherichia coli. We found that DacC is an alkaline PG carboxypeptidase, whose enzyme activity and protein stability are significantly enhanced under alkaline stress. Both DacC and DacA were required for bacterial growth under alkaline stress, whereas only DacA was required for the adaptation to salt stress. Under normal growth conditions, only DacA was necessary for cell shape maintenance, while under alkaline stress conditions, both DacA and DacC were necessary for cell shape maintenance, but their roles were distinct. Notably, all these roles of DacC and DacA were independent of LD-transpeptidases, which are necessary for the formation of PG 3-3 crosslinks and covalent bonds between PG and the outer membrane lipoprotein Lpp. Instead, DacC and DacA interacted with penicillin-binding proteins (PBPs), DD-transpeptidases, mostly in a C-terminal domain-dependent manner, and these interactions were necessary for most of their roles. Collectively, our results demonstrate the coordinated and distinct novel roles of PG carboxypeptidases in stress adaptation and shape maintenance and provide novel insights into the cellular functions of PG carboxypeptidases associated with PBPs.

microbiology↗

bioRxiv2022

The climatic constrains of the historical global spread of mungbean

While the domestication history has been investigated in many crops, the process of cultivation range expansion and factors governing this process received relatively little attention. Here using mungbean (Vigna radiata var. radiata) as a test case, we investigated the genomes of more than one thousand accessions to illustrate climatic adaptations role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East, and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed divergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.

evolutionary biology↗

bioRxiv2022

Divergent LD-transpeptidase-independent effects of peptidoglycan carboxypeptidases on intrinsic ss-lactam and vancomycin resistance

Vancomycin and {beta}-lactams are clinically important antibiotics that inhibit the formation of peptidoglycan cross-links, but their binding targets are different. The binding target of vancomycin is D-alanine-D-alanine (D-Ala-D-Ala), whereas that of {beta}-lactam is penicillin-binding proteins (PBPs). In this study, we revealed the divergent effects of peptidoglycan (PG) carboxypeptidases on vancomycin and {beta}-lactam resistance in Escherichia coli and Bacillus subtilis. The deletion of PG carboxypeptidases induced sensitivity to most {beta}-lactams, whereas it induced strong resistance toward vancomycin. Notably, both of two phenotypes did not have strong association with LD-transpeptidases, which are necessary for the formation of PG 3-3 cross-links and covalent bonds between PG and an Lpp outer membrane (OM) lipoprotein. Vancomycin resistance was induced by increased amount of decoy D-Ala-D-Ala residues within PG, whereas {beta}-lactam sensitivity was associated with physical interactions between PG carboxypeptidase and PBPs. The presence of OM permeability barrier strongly strengthened vancomycin resistance, but it significantly weakened {beta}-lactam sensitivity. Collectively, our results revealed two distinct LD-transpeptidase-independent functions of PG carboxypeptidases, which involved inverse modulation of bacterial resistance to clinically important antibiotics, {beta}-lactams and vancomycin, and presented evidence for a link between PG carboxypeptidase and PBPs. IMPORTANCEBacterial peptidoglycan (PG) hydrolases play important roles in various aspects of bacterial physiology, including cytokinesis, PG synthesis, quality control of PG, PG recycling, and stress adaptation. Of all the PG hydrolases, the role of PG carboxypeptidases is poorly understood, especially regarding their impacts on antibiotic resistance. To date, most studies on PG carboxypeptidases are focused on LD-transpeptidase-related roles. We have revealed two distinct LD-transpeptidase-independent functions of PG carboxypeptidases with respect to antibiotic resistance. The deletion of PG carboxypeptidases led to sensitivity to most {beta}-lactams, while it caused strong resistance to vancomycin. The underlying molecular mechanisms of two phenotypes were not associated with LD-transpeptidases. Therefore, our study provides novel insights into the roles of PG carboxypeptidases in the regulation of antibiotic resistance and a potential clue for the development of a drug to improve the clinical efficacy of {beta}-lactam antibiotics. One sentence summaryEffect of peptidoglycan carboxypeptidase on antibiotic

microbiology↗

bioRxiv2020

The fate of standing variation and new mutation under climate change

Many species face existence threat under anthropogenic climate change, and standing genetic variation was proposed as a way for sessile species to adapt to novel environments. However, it is still unknown whether standing genetic variants, being adaptive to current environmental variability, are sufficient to guarantee future survival. Here we investigate the relative importance of standing variation versus new mutations from the past to infer their future fate in nature. In the wild banana species Musa itinerans where the Taiwanese populations were ancient immigrants from the Chinese populations, new mutations exert larger effect size in precipitation-related variables, where Taiwan contains extreme environments beyond the ancestral climatic range, and new alleles have stronger association with novel environments. For temperature-related variables where Taiwan is within the ancestral climatic range, standing variants are more important than new mutations. The effect sizes of adaptive variants therefore differ under distinct environmental pressures, supporting theoretical predictions that natural selection favors new mutations with larger effect sizes in novel environments where the population is far from the adaptive peak. Despite their importance, large-effect variants also have higher mismatch and may be more vulnerable to future environmental perturbation, leaving minor-effect variants the main source of adaptive response to rapid anthropogenic climate change. Our work provides a support in natural environment to the previous conclusions from theoretical modeling and microbial experiments in well-controlled lab conditions.

evolutionary biology↗

bioRxiv2019

Long-read bitter gourd (Momordica charantia) genome and the genomic architecture of domestication

Bitter gourd (Momordica charantia) is a vegetable and medicinal plant of the family Cucurbitaceae. Here we report a chromosome-level assembly, with highest contig N50 (close to 10 Mb) and proportion of sequences placed on chromosomes (96%) in Cucurbitaceae. Population resequencing revealed the divergence between wild and cultivars at about 6000 years ago. Different cultivar groups have distinct allelic compositions in loci associated with domestication traits, suggesting phenotypic changes were achieved by allele frequency shifts in independent loci. Noticeably, one candidate locus for fruit size locates within a region missing from a recent Illumina-based assembly. Despite breeding efforts to increase female flower proportion, the gynoecy locus exhibits high variation within and low differentiation between wild and cultivar groups, likely because artificial directional selection could not overwhelm natural balancing selection. Our study provides resources to further investigate the genetic architecture of bitter gourd as well highlights the importance of a well-assembled genome.

genomics↗

bioRxiv2018

On the post-glacial spread of human commensal Arabidopsis thaliana: journey to the east

With the availability of more sequenced genomes, our understanding of the evolution and demographic history of the model plant Arabidopsis thaliana is rapidly expanding. Here we compile previously published data to investigate global patterns of genetic variation. While the Southeast African accessions were reported to be the most divergent among worldwide populations, we found accessions from Yunnan, China to be genetically close to the sub-Saharan accessions. Our further investigation of worldwide chloroplast genomes identified several deeply diverged haplogroups existing only in Eurasia, and the African populations have lower variation in many haplogroups they shared with the Eurasian populations. Bayesian inferences of chloroplast demography showed that representative haplogroups of Africa exhibited long-term stable population size, suggesting recent selective sweep or bottleneck is not able to explain the lower chloroplast variation in Africa. Taken together, these patterns cannot be easily explained by a single out-of-Africa event. Several Eurasian chloroplast haplogroups had rapid population growth since 10 kya, presumably reflecting the recent expansion of the weedy non-relicts across Eurasia. Our demographic analysis on a chromosomal region un-affected by relict introgression also suggested the European, Central Asian, and Chinese Yangtze populations diverged no earlier than 15 kya, in contrast to previous estimates of 45 kya inferred from whole genome that likely contains relict admixture. The most recent expansion is observed in the Yangtze population of China less than 2000 years ago. Similar to Iberia, the western end of non-relict expansion reported in our previous study, in this eastern end of Eurasia we find clear traces of gene flow between the Yangtze non-relicts and the Yunnan relicts. Genes under strong selection and previously suggested to contribute to adaptation in the Yangtze valley are enriched for traces of relict introgression, especially those related with biotic and immune responses. The results suggest the ability of non-relicts to obtain locally adaptive alleles through admixture with relicts is an important factor contributing to the rapid expansion across the environmental gradients spanning the eastern to the western coast of Eurasia.

evolutionary biology↗