Graph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening.

Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.

Haplotype-resolved genome assembly provides insights into evolutionary history of the Actinidia arguta tetraploid.

Actinidia arguta, known as hardy kiwifruit, is a widely cultivated species with distinct botanical characteristics such as small and smooth-fruited, rich in beneficial nutrients, rapid softening and tolerant to extremely low temperatures. It contains the most diverse ploidy types, including diploid, tetraploid, hexaploid, octoploid, and decaploid. Here we report a haplotype-resolved tetraploid genome (A. arguta cv. 'Longcheng No.2') containing four haplotypes, each with 40,859, 41,377, 39,833 and 39,222 protein-coding genes. We described the phased genome structure, synteny, and evolutionary analyses to identify and date possible WGD events. Ks calculations for both allelic and paralogous genes pairs throughout the assembled haplotypic individuals showed its tetraploidization is estimated to have formed ~ 1.03 Mya following Ad-α event occurred ~ 18.7 Mya. Detailed annotations of NBS-LRRs or CBFs highlight the importance of genetic variations coming about after polyploidization in underpinning ability of immune responses or environmental adaptability. WGCNA analysis of postharvest quality indicators in combination with transcriptome revealed several transcription factors were involved in regulating ripening kiwi berry texture. Taking together, the assembly of an A. arguta tetraploid genome provides valuable resources in deciphering complex genome structure and facilitating functional genomics studies and genetic improvement for kiwifruit and other crops.

The transcription factor MYB43 antagonizes with ICE1 to regulate freezing tolerance in Arabidopsis.

Previous discovering meticulously illustrates the post-translational modifications and protein stability regulation of ICE1 and their role in cold stress. However, the studies on the interaction of ICE1 with other transcription factors, and their function in modulation cold stress tolerance, as well as in the transition between cold stress and growth are largely insufficient. In this work, we found that maltose binding protein (MBP) 43 directly binds to the promoters of CBF genes to repress their expression, thereby negatively regulating freezing tolerance. Biochemical and genetic analyses showed that MYB43 interacts and antagonizes with ICE1 to regulate the expression of CBF genes and plant's freezing stress tolerance. PLEIOTROPIC REGULATORY LOCUS 1 (PRL1) accumulates under cold stress and promotes MYB43 protein degradation; however, when cold stress disappears, PRL1 restores normal protein levels, causing MYB43 protein to re-accumulate to normal levels. Furthermore, PRL1 positively regulates freezing tolerance by promoting degradation of MYB43 to attenuate its repression of CBF genes and antagonism with ICE1. Thus, our study reveals that MYB43 inhibits CBF genes expression under normal growth condition, while PRL1 promotes MYB43 protein degradation to attenuate its repression of CBF genes and antagonism with ICE1, and thereby to the precise modulation of plant cold stress responses.

Regulatory module WRKY33-ATL31-IRT1 mediates cadmium tolerance in Arabidopsis.

Cadmium (Cd) is one of the most dangerous environmental pollutants among heavy metals, and threatens food safety and human health by accumulating in plant sink tissues. Here, we report a novel regulatory cascade that profoundly influences Cd tolerance in Arabidopsis. Phenotypic analysis showed that an insertional knockdown mutation at the Arabidopsis Tóxicos en Levadura 31 (ATL31) locus resulted in hypersensitivity to Cd stress, most likely due to a significant increase in Cd accumulation. Consistently, ATL31-overexpressing lines exhibited enhanced Cd stress tolerance and reduced Cd accumulation. Further, IRON-REGULATED TRANSPORTER 1 (IRT1) was identified, and yeast two-hybrid, co-immunoprecipitation and bimolecular fluorescence complementation assays demonstrated its interaction with ATL31. Biochemical, molecular, and genetic analyses showed that IRT1 is targeted by ATL31 for ubiquitin-conjugated degradation in response to Cd stress. Intriguingly, transcription of ATL31 was strongly induced by Cd stress. In addition, transgenic and molecular analyses showed that WRKY33 directly activated the transcription of ATL31 in response to Cd stress and positively regulated Cd tolerance. Genetic analysis indicated that ATL31 acts upstream of IRT1 and downstream of WRKY33 to regulate Cd tolerance. Our study revealed that the WRKY33-ATL31-IRT1 module plays a crucial role in timely blocking Cd absorption to prevent metal toxicity in Arabidopsis.

MYB43 as a novel substrate for CRL4PRL1 E3 ligases negatively regulates cadmium tolerance through transcriptional inhibition of HMAs in Arabidopsis.

Controlled stability of proteins is a highly efficient mechanism to direct diverse processes in plants. A key regulatory system for protein stability is given by the CULLIN-RING E3 ligases (CRLs). In this work, MYB43 is identified as a novel target of a CUL4-DDB1-PRL1 (PLEIOTROPIC REGULATORY LOCUS 1)-RING E3 ligase (CRL4PRL1 E3 ligase). Its stability depends on the presence of PRL1, a WD40-containing protein functioning as a substrate receptor of the CRL4 E3 ligases. Genetic studies have indicated that MYB43 is a negative regulator of cadmium (Cd) tolerance in Arabidopsis by transcriptional inhibition of important Cd transporters (HMA2, HMA3 and HMA4), while PRL1 and CUL4 positively regulate Cd tolerance. Expression of CUL4 and PRL1 was enhanced in response to Cd stress, and PRL1 can interact with and target MYB43 for degradation depending on assembly of CRL4PRL1 E3 ligase, and consequently increase the expression of HMA2, HMA3 and HMA4 through attenuating the transcriptional inhibition. HMA2 and HMA4 are shown to transport cadmium ion (Cd2+ ) from the roots of plants to the shoots through the xylem, ultimately increasing the plants' tolerance to Cd stress.

The effect of ABRE BINDING FACTOR 4-mediated FYVE1 on salt stress tolerance in Arabidopsis.

FYVE1 encodes a protein that is localized to the peripheral membrane of late endosomal compartments, and is involved in the regulation of mulitivesicular/prevacuolar compartment protein sorting. It was found that FYVE1 attenuates ABA signaling through degrading ABA receptors PYR1 and PYL4 by ESCRT pathway, and also interacts with transcription factors ABF4 and ABI5 to transcriptionally inhibit ABA signaling pathway by reducing their binding to the cis-regulatory sequences of their downstream genes. However, the mechanisms underlying the transcriptional regulation of FYVE1 and its biological function in salt stress are largely unknown. Here, we show that fyve1 knockdown-mutants show enhanced tolerance to salt stress, while overexpression of FYVE1 results in increased sensitivity to salt stress. Further analysis shows that FYVE1 negatively regulates salt stress tolerance, which is associated with ABA signaling pathway. ABRE BINDING FACTOR 4 (ABF4) directly binds to promoter of FYVE1 to activate its transcription. Moreover, FYVE1 interacts with and promotes degradation of all ABA PYR/PYL receptors. Thus, our results suggest that FYVE1 negatively modulates salt stress tolerance in Arabidopsis via a negative feedback loop.

Determining Interaction Enhanced Valley Susceptibility in Spin-Valley-Locked MoS2.

Two-dimensional transition metal dichalcogenides (TMDCs) are recently emerged electronic systems with various novel properties, such as spin-valley locking, circular dichroism, valley Hall effect, and superconductivity. The reduced dimensionality and large effective masses further produce unconventional many-body interaction effects. Here we reveal strong interaction effects in the conduction band of MoS2 by transport experiment. We study the massive Dirac electron Landau levels (LL) in high-quality MoS2 samples with field-effect mobilities of 24 000 cm2/(V·s) at 1.2 K. We identify the valley-resolved LLs and low-lying polarized LLs using the Lifshitz-Kosevitch formula. By further tracing the LL crossings in the Landau fan diagram, we unambiguously determine the density-dependent valley susceptibility and the interaction enhanced g-factor from 12.7 to 23.6. Near integer ratios of Zeeman-to-cyclotron energies, we discover LL anticrossings due to the formation of quantum Hall Ising ferromagnets, the valley polarizations of which appear to be reversible by tuning the density or an in-plane magnetic field. Our results provide evidence for many-body interaction effects in the conduction band of MoS2 and establish a fertile ground for exploring strongly correlated phenomena of massive Dirac electrons.

Functional and anatomical connectivity-based parcellation of human cingulate cortex.

INTRODUCTION: Human cingulate cortex (CC) has been implicated in many functions, which is highly suggestive of the existence of functional subregions. METHODS: In this study, we used resting-state functional magnetic resonance imaging (rs-fMRI) and diffusion tensor imaging (DTI) to parcellate the human cingulate cortex (CC) based on resting-state functional connectivity (rsFC) patterns and anatomical connectivity (AC) patterns, to analyze the rsFC patterns and the AC patterns of different subregions, and to recognize whether the parcellation results obtained by the two different methods were consistent. RESULTS: The CC was divided into six functional subregions, including the anterior cingulate cortex, dorsal anterior midcingulate cortex, ventral anterior midcingulate cortex, posterior midcingulate cortex, dorsal posterior cingulate cortex, and ventral posterior cingulate cortex. The CC was also divided into ten anatomical subregions, termed Subregion 1 (S1) to Subregion 10 (S10). Each subregion showed specific connectivity patterns, although the functional subregions and the anatomical subregions were internally consistent. CONCLUSIONS: Using different model MRI images, we established a parcellation scheme, which is internally consistent for the human CC, which may provide an in vivo guide for subregion-level studies and improve our understanding of this brain area at subregional levels.