Biology subjects

Zhu, X.-G.

Publications and source records attributed to Zhu, X.-G..

15 recordsLinked to original sources

bioRxiv2024

Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4 grasses

Many of the worlds most productive food and bioenergy crops use C4 photosynthesis, which have high photosynthetic efficiency due to a Kranz anatomy-based CO2 concentrating mechanism. Here, we took a comparative transcriptomics approach using single cell spatial transcriptomes of leaf primordia for maize (Zea mays) and single cell RNA-seq (scRNA-seq) atlases of corresponding leaf tissues for three C4 species (Zea mays, Sorghum bicolor, Setaria viridis) and one C3 rice (Oryza sativa) to study regulatory networks involved in the development and evolution of Kranz anatomy. We show that the formation of Kranz anatomy involves extensive recruitment and modification of pre-existing regulatory modules, especially the SHR-SCR module and the auxin signaling pathway. Members of the INDETERMINATE DOMAIN (IDD) family transcription factors, including IDD7 and IDDP1, contribute to the modification of the involved modules. These extensive recruitment and modification of existing genetic regulatory programs underlie the repeated emergence of C4 photosynthesis during evolution.

plant biology↗

bioRxiv2024

Single-cell resolved differentiation of pre-Kranz anatomy in maize leaf primordia

Typical C4 plants such as maize possess highly optimized Kranz-type leaf anatomy, whereby concentric wreaths of mesophyll and bundle sheath cells surround closely spaced veins. The veins and the cells that surround them are derived from the middle ground meristem (mGM) through processes that are as yet undefined. Here we distinguished the active zone of vascular development within early leaf primordia, and used comparative transcriptomics of sub-sectioned maize and rice primordia to identify cohorts of genes likely involved in early Kranz development. Leveraging single-nucleus RNA sequencing (snRNA-seq) we then explored the cell heterogeneity and developmental trajectories within single maize leaf primordia. Assisted by in situ hybridization, cell clusters of mGM and procambium were identified, with candidate marker genes showing different yet inter-related expression patterns. Localization of the vascular marker ZmSHR1 was preceded by that of ZmEREB161 and ZmEREB114 in terms of procambium initiation. Potential subclusters of bundle sheath cells and different layer of mesophyll cells were depicted from developing cells toward the tip of sub-sectioned maize primordia. Collectively our results identify potential mGM derived or procambium localized Kranz regulators and provide resources for investigating leaf vein development in maize and rice, at sub-primordium and single-cell resolution.

plant biology↗

bioRxiv2023

Regulatory preconditioning for the evolution of C4 photosynthesis revealed by low CO2 treatment of Arabidopsis thaliana

Low CO2 condition was considered a preconditioning or selection pressure for C4 evolution. However, it remains elucidated how low CO2 condition contribute to the evolutionary assembly of the C4 pathway. We conducted a systematic transcriptomics and metabolomics analysis under short-term low CO2 condition and found that Arabidopsis grown under this condition showed increased expression of most genes encoding C4- related enzymes and transporters. Low CO2 condition increased NH4+ content in leaves; as expected, photorespiratory and ammonia refixing pathways were enhanced. Furthermore, we found that compared to low CO2 condition, in vitro treatment with NH4+ induced a similar pattern of changes in C4 related genes and genes involved in ammonia refixation. This supports that increased expression of C4 genes induced by low CO2 condition can supply carbon skeleton for ammonia recycling. This study provides new insight into the regulatory preconditioning which may have facilitated the evolution of C4 photosynthesis under low atmospheric CO2 environments.

evolutionary biology↗

bioRxiv2023

A regulatory circuit involving the NADH dehydrogenase-like complex balances C4 photosynthetic carbon flow and cellular redox in maize

O_LIC4 plants typically operate a CO2 concentration mechanism from mesophyll (M) cells into bundle sheath (BS) cells. NADH dehydrogenase-like (NDH) complex is enriched in the BS cells of many NADP-ME type C4 plants, and is more abundant in C4 than in C3 plants, but to what extent it is involved in the CO2 concentration mechanism remains to be experimentally investigated. C_LIO_LIWe created maize and rice mutants deficient in NDH function, and used a combination of transcriptomic, proteomic, and metabolomic approaches for comparative analysis. C_LIO_LIConsiderable decrease in growth, photosynthetic activities, and levels of key photosynthetic proteins were observed in maize but not rice mutants. However, gene expression for many cyclic electron transport and Calvin-Benson cycle components plus BS specific C4 enzymes, was up-regulated in maize mutants. Metabolite analysis of the maize ndh mutants revealed increased NADPH/NADP ratio, as well as malate, RuBP, FBP, and photorespiration components. C_LIO_LIWe suggest that by optimizing NADPH and malate levels, adjusting NADP-ME activity, NDH functions to balance metabolic and redox states in the BS cells of maize, coordinating photosynthetic gene expression and protein content, thus directly regulating the carbon flow in the two-celled C4 system of maize. C_LI

plant biology↗

bioRxiv2022

Stomatal density affects rice mesophyll cell size and shape and modulates a conserved pattern of cells through the leaf

The structure of the mesophyll influences how light, CO2 and water travels inside a leaf, affecting the rates of both photosynthesis and transpiration. Recent studies in wheat and Arabidopsis have shown that the structure of the mesophyll is influenced by the density and activity of stomata, consistent with the hypothesis that gas flow via stomata can modulate internal cell growth and separation to co-ordinate leaf structure and function. To investigate whether this also occurs in rice, a staple food crop for a large fraction of the worlds population, we examined mesophyll structure in rice mutants with altered stomatal density. Our data show that stomatal function modulates mesophyll structure in rice. Variation in the degree of mesophyll lobing made a major contribution to altered mesophyll structure, suggesting that modified leaf gas flux through stomata influences an aspect of cell shape directly linked to gas exchange capacity in rice. In addition, our analysis revealed a previously unreported underlying pattern in cell size, shape and axiality across layers of the rice mesophyll, which further investigation revealed is present in a range of rice species and cultivars. The potential origin and significance of this mesophyll patterning are discussed. HIGHLIGHTWe describe a previously unreported cellular pattern in rice leaves and show that it is modulated by stomata. These results shed new light on leaf structure and function.

plant biology↗

bioRxiv2022

Born with intronless ERF transcriptional factors: C4 photosynthesis inherits a legacy dating back 450 million years

The genus Flaveria, containing species at different evolutionary stages of the progression from C3 to C4 photosynthesis, is used as a model system to study the evolution of C4 photosynthesis. Here, we report chromosome-scale genome sequences for five Flaveria species, including C3, C4, and intermediate species. Our analyses revealed that both acquiring additional gene copies and recruiting ethylene responsive factor (ERF) cis-regulatory elements (CREs) contributed to the emergence of C4 photosynthesis. ERF transcriptional factors (TFs), especially intronless ERF TFs, were co-opted in dicotyledonous C4 species and monocotyledonous C4 species in parallel. These C4 species co-opted intronless ERF TFs originated from the Late Ordovician mass extinction that occurred [~]450 million years ago in coping with environmental stress. Therefore, this study demonstrated that intronless ERF TFs were acquired during the early evolution of plants and provided the molecular toolbox facilitating multiple subsequent independent evolutions of C4 photosynthesis.

evolutionary biology↗

bioRxiv2022

HY5 Regulates GLK and GNC Transcription Factors to Orchestrate Photomorphogenesis in Arabidopsis thaliana

Light induced de-etiolation is an important aspect of seedling photomorphogenesis. GOLDEN2 LIKE (GLK) transcriptional regulators are involved in chloroplast development, but to what extent they participate in photomorphogenesis is not clear. Here we show that ELONGATED HYPOCOTYL5 (HY5) binds to GLK promoters to activate their expression, and also interacts with GLK proteins. Chlorophyll content in the de-etiolating Arabidopsis seedlings of the hy5 glk2 double mutants was lower than that in hy5 single mutant. GLKs inhibited hypocotyl elongation, and the phenotype could superimpose on the hy5 phenotype. Correspondingly, GLK2 regulates the expression of photosynthesis and cell elongation genes partially independent of HY5. Before exposed to light, the accumulation of GLK proteins was regulated by DE-ETIOLATED 1 (DET1), while also affected (especially for GLK1) transcriptionally by HY5. The enhanced etioplast development and photosystem gene expression observed in det1 mutant were attenuated in det1 glk2 double mutant. Our study reveals that GLKs act down-stream of HY5 and likely cooperate with HY5 and DET1, to orchestrate multiple developmental traits during the light-induced skotomorphogenesis to photomorphogenesis transition in Arabidopsis. One-sentence summaryGLK and GNC act downstream of HY5, and cooperate with HY5 and DET1, to regulate both chloroplast development and hypocotyl elongation during the transition from skotomorphogenesis to photomorphogenesis.

plant biology↗

bioRxiv2022

The genome of Gynandropsis gynandra provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to Arabidopsis. Here, we present a high-quality genome sequence of G. gynandra, anchored onto 17 main super- scaffolds with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. We revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-), then an addition of a third genome (Th-, +1x) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3 T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the impact of gene duplication and gene retention on the evolution of C4 photosynthesis in Cleomaceae.

plant biology↗

bioRxiv2022

Decreasing photosystem antenna size: a double-edged sword for canopy photo-synthetic efficiency

Optimization of antenna size of photosynthetic systems is one strategy to increase plant canopy photosynthesis and crop yield potential. The relationship between antenna size and photosynthesis rate has been extensively studied recently. However, conflicting results have been obtained. Here we show that the extent of decrease in antenna size is a major factor determining the consequences of decreasing antenna on photosynthesis and growth-related parameters. Specifically, we constructed transgenic rice lines with artificial microRNA (amiRNA) targeting to Chlorophyll Synthesis (YGL1) to generate transgene heterozygous and homozygous lines with different leaf chlorophyll contents and antenna sizes. We found that canopy photosynthesis (Ac), biomass and grain yield of the heterozygote were not significantly different from those of WT while the Ac, biomass and grain yield of the homozygote were lower than those of WT. Further, when the maximal quantum yield of photosystem II (Fv/Fm) was larger than 0.8, decreasing antenna size by reducing chlorophyll biosynthesis did not affect leaf photosynthesis; but when Fv/Fm was lower than 0.8, there is a positive relationship between antenna size and leaf photosynthesis. There is large variation in both leaf chlorophyll content and antenna size in elite rice cultivars, suggesting that there is a large scope to decrease leaf chlorophyll content to increase nitrogen use efficiency as long as the quantum yield of PSII is not compromised.

systems biology↗

bioRxiv2020

Bridging Photosynthesis and Crop Yield Formation with a Mechanistic Model of Whole Plant Carbon Nitrogen Interaction

Crop yield is co-determined by potential size of the harvest organ, photosynthetic potential of source organs, and pattern of partitioning and use of photosynthates among sink organs. Given a sufficient potential size of the harvest organ at flowering, how to fully fill them remains a central challenge in crop breeding for high yields. Here, we develop a kinetic model of rice grain filling, scaling primary biochemical and biophysical processes to whole-plant carbon and nitrogen dynamics. Predicted post-anthesis physiological and agronomic behaviors validate experimental observations under six endogenous and external perturbations. By large scale in silico screening, we show here that a stable grain filling rate from flowering to harvest is required to maximize grain yield, which is validated here in two independent super-high yielding rice cultivars (~21 t ha-1 rough rice yield at 14% moisture). On the other hand, we show grain yields in an elite rice cultivar may increase by about 30-40% by stabilizing its grain filling rate. Intriguingly, we have found that the sum of grain filling rates around 15 and 38 days after flowering largely determines grain yield, and have further developed a novel in situ approach quantifying grain filling rates and grain yield precisely with the measurements of ear respiratory rates (r>0.93). Potential post-anthesis molecular targets to maximize rice yield include delaying leaf senescence, enhancing leaf sucrose synthesis and export, limiting root growth, strengthening stem starch synthesis, accelerating endosperm starch synthesis, and moderating endosperm cell division. Our study provides an effective computational framework for post-anthesis crop physiology research and ideotype design.

plant biology↗

bioRxiv2020

Evolution of co-regulatory network of C4 metabolic genes and TFs in the genus Flaveria: go anear or away in the intermediate species?

C4 photosynthesis evolved from the ancestral C3 photosynthesis by recruiting pre-existing genes to fulfill new functions. The enzymes and transporters required for the C4 photosynthesis have been intensively studied; however, the transcription factors (TFs) regulating these C4 metabolic genes are not well understood. In particular, how the TF regulatory network of C4 metabolic genes was rewired during the evolution is unclear. Here, we constructed TFs co-regulatory networks for core C4 metabolic genes (C4GRN) for four evolutionarily closely related species from the genus Flaveria, which represent four different evolutionary stages of the C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that more than half of the co-regulations of TFs and C4 core metabolic genes were species specific. The counterparts of C4 genes in C3 species were already co-regulated with the photosynthesis-related genes; whereas the required TFs for the C4 photosynthesis were recruited later. The type I C3-C4 species recruited 40% of C4 required TFs which co-regulated all core C4 metabolic genes but PEPC; nevertheless, the type II C3-C4 species took on a high divergent C4GRN with C4 species itself. In C4 species, PEPC and PPDK-RP possessed much more co-regulated TFs than other C4 metabolic genes. This study provides for the first time the TFs profiles of the C4 metabolic genes in species with different photosynthetic types and reveal the dynamic of C4 genes-TFs co-regulations along the evolutionary process, providing thereby new insights into the evolution of C4 photosynthesis.

evolutionary biology↗

bioRxiv2020

SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica

Mango (Mangifera indica), a member of the family Anacardiaceae, is one of the worlds most popular tropical fruits. Here we sequenced the variety, "Hong Xiang Ya", and generated a 371.6-Mb mango genome assembly with 34,529 predicted protein-coding genes. Aided with the published genetic map, for the first time, we assembled the M. indica genome to the chromosomes, and finally about 98.77% of the genome assembly was anchored to 20 pseudo-chromosomes. The availability of the chromosome-length genome assembly of M. indica will provide novel insights into genome evolution, understand the genetic basis of specialized phytochemical composites relevant to fruit quality, and enhance allele mining in genomics-assisted breeding for mango genetic improvement.

genomics↗

bioRxiv2020

SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

Asian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10x and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

genomics↗

bioRxiv2018

The Coordination and Jumps along C4 Photosynthesis Evolution in the Genus Flaveria

BackgroundC4 photosynthesis is a remarkable complex trait, elucidations of the evolutionary trajectory of C4 photosynthesis from its ancestral C3 pathway can help us to better understand the generic principles of complex trait evolution and guide engineering of C3 crops for higher yields. We used the genus Flaveria that contains C3, C3-C4, C4-like and C4 species as a system to study the evolution of C4 photosynthesis.\n\nResultsWe mapped transcript abundance, protein sequence, and morphological features to the phylogenetic tree of the genus Flaveria, and calculated the evolutionary correlation of different features. Besides, we predicted the relative changes of ancestral nodes of those features to illustrate the key stages during the evolution of C4 photosynthesis. Gene expression and protein sequence showed consistent modification pattern along the phylogenetic tree. High correlation coefficients ranging from 0.46 to 0.9 among gene expression, protein sequence and morphology were observed, and the greatest modification of those different features consistently occurred at the transition between C3-C4 species and C4-like species.\n\nConclusionsOur data shows highly coordinated changes in gene expression, protein sequence and morphological features. Besides, our results support an obviously evolutionary jump during the evolution of C4 metabolism.

evolutionary biology↗

bioRxiv2017

Wide sampling of natural diversity identifies novel molecular signatures of C4 photosynthesis

Introductory paragraphMuch of biology is associated with convergent traits, and it is challenging to determine the extent to which underlying molecular mechanisms are shared across phylogeny. By analyzing plants representing eighteen independent origins of C4 photosynthesis, we quantified the extent to which this convergent trait utilises identical molecular mechanisms. We demonstrate that biochemical changes that characterise C4 species are recovered by this process, and expand the paradigm by four metabolic pathways not previously associated with C4 photosynthesis. Furthermore, we show that expression of many genes that distinguish C3 and C4 species respond to low CO2, providing molecular evidence that reduction in atmospheric CO2 was a driver for C4 evolution. Thus the origin and architecture of complex traits can be derived from transcriptome comparisons across natural diversity.

plant biology↗