Featured
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Article
| Open AccessCepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery
Cepharanthine is a secondary metabolite isolated from Stephania with a variety of medicinal properties. Here, the authors assembled three Stephania genomes, propose cepharanthine biosynthetic pathway, and assess the antiviral potential of cepharanthine-related metabolites.
- Liang Leng
- , Zhichao Xu
- & Shilin Chen
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Article
| Open AccessGenetic control of thermomorphogenesis in tomato inflorescences
Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.
- Shuai Sun
- , Zhiqiang Liu
- & Xia Cui
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Review Article
| Open AccessChoreographing root architecture and rhizosphere interactions through synthetic biology
Engineering the form and function of root systems and their associated microbiota could provide a means to mitigate adverse climate-driven effects. Here, the authors review the recent developments in plant and rhizobacterial synthetic biology and highlight engineering targets for applications in root systems and rhizosphere.
- Carin J. Ragland
- , Kevin Y. Shih
- & José R. Dinneny
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Article
| Open AccessEpiallelic variation of non-coding RNA genes and their phenotypic consequences
This study uncovers abundant DNA methylation variations of non-coding RNA genes in the natural Arabidopsis population and shows the importance of epigenetic variations in plant phenotypic plasticity and diversity.
- Jie Liu
- & Xuehua Zhong
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Article
| Open AccessChromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana
The role of the nuclear matrix in plant nuclei is unclear. Here the authors reveal that nuclear matrix-associated proteins act as a regulatory hub, recruiting both DNA and transcriptional repressors to the nuclear matrix
- Linhao Xu
- , Shiwei Zheng
- & Hua Jiang
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Article
| Open AccessPhosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation
This paper reports that the Arabidopsis UV-B photoreceptor UVR8 is phosphorylated in vivo and that phosphorylation of Serine 402 modifies UVR8 activity and promotes flavonoid biosynthesis, a key response to UV-B exposure.
- Wei Liu
- , Giovanni Giuriani
- & Gareth I. Jenkins
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Article
| Open AccessA mediator of OsbZIP46 deactivation and degradation negatively regulates seed dormancy in rice
Seed dormancy is the preferred trait in rice production as it can prevent preharvest sprouting. Here, the authors report that MODD (mediator of OsbZIP46 deactivation and degradation) negatively regulates seed dormancy by inhibiting the transcriptional activity of ABSCISIC ACID INSENSITIVES (ABIs).
- Naihui Guo
- , Shengjia Tang
- & Peisong Hu
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Article
| Open AccessPetal abscission is promoted by jasmonic acid-induced autophagy at Arabidopsis petal bases
In angiosperms, petal abscission is crucial for reproductive success and seed dispersion. However, the regulation of this abscission remains unclear. Here, the authors identify a process of petal abscission regulated by jasmonic acid via autophagy at the base of Arabidopsis petals.
- Yuki Furuta
- , Haruka Yamamoto
- & Nobutoshi Yamaguchi
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Article
| Open AccessThe synthetic NLR RGA5HMA5 requires multiple interfaces within and outside the integrated domain for effector recognition
An engineered sensor NLR RGA5HMA5 carrying multiple resurfaced interfaces was generated to confer complete resistance to the rice blast fungus strains expressing the non-corresponding effector AVR-PikD, paving a way to broaden the resistance spectra of NLRs.
- Xin Zhang
- , Yang Liu
- & You-Liang Peng
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Article
| Open AccessPlastid ancestors lacked a complete Entner-Doudoroff pathway, limiting plants to glycolysis and the pentose phosphate pathway
The Enter-Doudoroff (ED) pathway is an alternative to glycolysis present in some prokaryotes. Evans et al. show that its dehydratase enzyme, evolved from a branched chain amino acid pathway paralog, acquired a new function through mutations in its active site.
- Sonia E. Evans
- , Anya E. Franks
- & Michael A. Phillips
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Article
| Open AccessRepeated upslope biome shifts in Saxifraga during late-Cenozoic climate cooling
The origins of alpine plant diversity are unclear. Here, the authors provide a time-calibrated molecular phylogenetic tree for Saxifraga, a diverse alpine plant clade, and show that upslope biome shifts into the alpine zone occurred more often than dispersal between alpine regions.
- Tom Carruthers
- , Michelangelo S. Moerland
- & Wolf L. Eiserhardt
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Article
| Open AccessEffects of climate and environmental heterogeneity on the phylogenetic structure of regional angiosperm floras worldwide
Using a dataset that included 341,846 species in 391 angiosperm floras worldwide, this study finds that the global phylogenetic structure of angiosperms shows clear and meaningful relationships with environmental factors and that current climatic variables have the highest predictive power for phylogenetic metrics reflecting recent evolutionary relationships.
- Hong Qian
- , Shenhua Qian
- & Michael Kessler
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Article
| Open AccessC2-methyladenosine in tRNA promotes protein translation by facilitating the decoding of tandem m2A-tRNA-dependent codons
Duan et al. demonstrate that the m2A modification is ubiquitous in plants and tRNA m2A37 promotes a relaxed conformation of tRNA, enhancing translation efficiency by facilitating decoding of tandem m2A-tRNA-dependent codons.
- Hong-Chao Duan
- , Chi Zhang
- & Guifang Jia
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Article
| Open AccessDysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier
Loss of function alleles of two genetically interacting loci mediate both segregation distortion and interspecific hybrid incompatible via epigenetic regulation in rice.
- Ben Liao
- , You-Huang Xiang
- & Hong-Xuan Lin
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Article
| Open AccessA sequence-aware merger of genomic structural variations at population scale
Existing tools for structural variations (SVs) calling and merging often lead to fragmented SVs and the potential of introducing unnecessary errors. Here, the authors report the PanPop pipeline to address these issues by implementing sequence-aware SV merging algorithm to efficiently merge SVs of various types.
- Zeyu Zheng
- , Mingjia Zhu
- & Yongzhi Yang
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Article
| Open AccessEvolutionary trajectory of pattern recognition receptors in plants
Plant cell-surface receptors perceive both self- and nonself-molecules to regulate biological processes. Here the authors show that a subclass of phytohormone and immune receptors share a common origin, which have diverged to perceive distinct ligands and activate differential downstream responses.
- Bruno Pok Man Ngou
- , Michele Wyler
- & Ken Shirasu
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Article
| Open AccessBCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants
This study uncovers the specialized function of previously elusive BCL7 subunits of SWI/SNF complexes in eukaryotes and reveals the mechanism whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility.
- Yawen Lei
- , Yaoguang Yu
- & Chenlong Li
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Article
| Open AccessIMA peptides regulate root nodulation and nitrogen homeostasis by providing iron according to internal nitrogen status
The authors show IRON MAN peptides have an essential role in symbiotic nitrogen fixation during legume-rhizobium symbiosis. The peptides additionally function to regulate nitrogen homeostasis by controlling nitrogen-iron balance.
- Momoyo Ito
- , Yuri Tajima
- & Takuya Suzaki
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Article
| Open AccessThe nature of carotenoid S* state and its role in the nonphotochemical quenching of plants
Plant Light Harvesting complexes adjust to light conditions via a quenching mechanism involving carotenoids. The authors use computational simulations to reveal how carotenoids’ quenching capacity is tuned by conformational changes of the complex.
- Davide Accomasso
- , Giacomo Londi
- & Benedetta Mennucci
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Article
| Open AccessMicrobiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize
Intercropping has the potential to improve plant nutrition and crop yield. Here, the authors intercrop peanut and maize and show that Pseudomonas secreted siderophore pyoverdine play an important role in plant iron nutrition.
- Nanqi Wang
- , Tianqi Wang
- & Yuanmei Zuo
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Article
| Open AccessPhytophagy impacts the quality and quantity of plant carbon resources acquired by mutualistic arbuscular mycorrhizal fungi
Plant antagonists may disrupt the allocation of carbon resources from plants to mutualistic microorganisms. Here, the authors report how plants attacked by cyst nematodes and aphids maintain carbon transfer to arbuscular mycorrhizal fungi through fatty acid transfer whilst the limiting the loss of sugars.
- C. A. Bell
- , E. Magkourilou
- & K. J. Field
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Article
| Open AccessThe mechanism of low blue light-induced leaf senescence mediated by GmCRY1s in soybean
This study provides insights into how shade induces leaf senescence in soybean. The reduction of blue light intensity deactivates GmCRY1s, leading to the degradation of GmRGAs and the upregulation of WRKY100, ultimately promoting leaf senescence.
- Zhuang Li
- , Xiangguang Lyu
- & Bin Liu
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Article
| Open AccessPredatory protists reduce bacteria wilt disease incidence in tomato plants
Soil organisms are affected by the presence of predatory protists. Here, the authors predatory protists are negatively associated with bacteria wilt disease incidence in tomato plants and that fertilisation enhances the abundance of predatory protists
- Sai Guo
- , Zixuan Jiao
- & Stefan Geisen
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Article
| Open AccessA chromosome-scale assembly reveals chromosomal aberrations and exchanges generating genetic diversity in Coffea arabica germplasm
Coffea arabica is an allotetraploid hybrid of C. eugenioides and C. canephora and contributes to approximately 60% of world coffee production. Here, the authors report its chromosome-level genome assembly and identify that chromosomal abnormalities and introgression from C. canephora may contribute to diversity and pathogen resistance.
- Simone Scalabrin
- , Gabriele Magris
- & Michele Morgante
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Article
| Open AccessDiscovery of plant chemical defence mediated by a two-component system involving β-glucosidase in Panax species
In this work, the authors discovered that Panax species, the valuable medicinal plants, have evolved a two-component chemical defence system comprising a chloroplast-localized β-glucosidase and 20(S)-protopanaxadiol ginsenosides.
- Li-Juan Ma
- , Xiao Liu
- & Jian-Bo Wan
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Article
| Open AccessWheat Pm55 alleles exhibit distinct interactions with an inhibitor to cause different powdery mildew resistance
Powdery mildew threatens worldwide wheat production. Here, the authors report the cloning of two powdery mildew resistant Pm55 alleles and show that they exhibit distinct interactions with the inhibitor SuPm55 to cause different resistance.
- Chuntian Lu
- , Jie Du
- & Ruiqi Zhang
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Article
| Open AccessA CYBDOM protein impacts iron homeostasis and primary root growth under phosphate deficiency in Arabidopsis
Iron deposition in cell walls inhibits Arabidopsis root growth under phosphate deficiency. A protein with iron reductase activity belonging to an uncharacterized CYBDOM family was identified which modulates this process and affects iron homeostasis.
- Joaquín Clúa
- , Jonatan Montpetit
- & Yves Poirier
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Article
| Open AccessFerric reduction by a CYBDOM protein counteracts increased iron availability in root meristems induced by phosphorus deficiency
The study identified an Arabidopsis ascorbate-dependent metalloreductase belonging to the CYBDOM family, which functions in maintaining cell elongation and meristem integrity by preventing iron-dependent root growth arrest under phosphate deficiency.
- Rodolfo A. Maniero
- , Cristiana Picco
- & Ricardo F. H. Giehl
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Article
| Open AccessCommensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS
The plant immune output reactive oxygen species tames a detrimental bacterial commensal from native microbiota by suppressing a bacterial secretion system, allowing the co-existence and turning it into a beneficial bacterium to the host.
- Frederickson Entila
- , Xiaowei Han
- & Kenichi Tsuda
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Comment
| Open AccessIntegrative and inclusive genomics to promote the use of underutilised crops
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
- Oluwaseyi Shorinola
- , Rose Marks
- & Mark A. Chapman
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Article
| Open AccessBPG4 regulates chloroplast development and homeostasis by suppressing GLK transcription factors and involving light and brassinosteroid signaling
The authors identify BPG4, a novel regulator of chloroplast development. BPG4 directly suppresses transcriptional activity of GLK to fine-tune photosynthesis associated nuclear gene expression, and regulates chloroplast development and homeostasis.
- Ryo Tachibana
- , Susumu Abe
- & Takeshi Nakano
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Article
| Open AccessMADS1-regulated lemma and awn development benefits barley yield
HvMADS1 in barley positively regulates awn length and lemma width by promoting cell proliferation through direct action on the expression of HvSHI and HvDL. In wheat, MADS1 conservatively regulates awn length.
- Yueya Zhang
- , Chaoqun Shen
- & Dabing Zhang
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Article
| Open AccessTemporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion
Bivalent histone modifications control various cellular processes in eukaryotes. Here, the authors report that a fungal pathogen deploys bivalent histone modification to fine-tune the expression of BCG1, thereby facilitating successful infection and host immunity evasion.
- Xiaozhen Zhao
- , Yiming Wang
- & Qin Gu
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Article
| Open AccessProximity to Photosystem II is necessary for activation of Plastid Terminal Oxidase (PTOX) for photoprotection
Plastid terminal oxidase (PTOX) is efficient in photoprotection in stress-tolerant plants. Transferring this activity to different species requires modifications to the thylakoid structure to allow PTOX access to the Photosystem II acceptor pool.
- Pablo Ignacio Calzadilla
- , Junliang Song
- & Giles Nicholas Johnson
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Editorial
| Open AccessFeeding the future global population
Climate change is exacerbating challenges both for global food production and from its environmental impacts. Sustainable and socially responsible solutions for future world-wide food security are urgently needed.
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Article
| Open AccessA plant cell death-inducing protein from litchi interacts with Peronophythora litchii pectate lyase and enhances plant resistance
The plant apoplastic space is a critical battlefield in plant-microbe interactions. Here, the authors show that a positive regulator of plant immunity PIP1 recognizes pectate lysates secreted by oomycetes and elicits immunity via SERK3.
- Wen Li
- , Peng Li
- & Zide Jiang
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Article
| Open AccessDecoding the gene regulatory network of endosperm differentiation in maize
The cereal endosperm constitutes most of the grain by volume. Here the authors use single-cell analysis of maize developing endosperm to decode gene regulatory networks that likely control endosperm growth and offer a framework for crop improvement.
- Yue Yuan
- , Qiang Huo
- & Zeyang Ma
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Article
| Open AccessMapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL
The authors employ Micro-C-XL to investigate chromatin structures in plants, specifically focusing on nucleosome-resolution chromatin organizations and enhancer-promoter chromatin loops in Arabidopsis, rice, and soybean.
- Linhua Sun
- , Jingru Zhou
- & Hang He
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Article
| Open AccessLeafhopper salivary vitellogenin mediates virus transmission to plant phloem
A plant virus induces and hijacks vitellogenin (Vg) of insect vector into virus-induced exosomes for release together from salivary glands to plant phloem, where the Vg suppresses H2O2 burst, facilitating insect feeding and viral transmission.
- Yanfei Wang
- , Chengcong Lu
- & Qian Chen
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Article
| Open AccessPrimase promotes the competition between transcription and replication on the same template strand resulting in DNA damage
Resolving R-loops caused by transcription-replication conflicts (TRCs) is vital to genome stability in organisms. Here, the authors show that the chloroplast-localized primase ATH intensifies template strand competition and exacerbates the Head-On TRCs induced DNA damage.
- Weifeng Zhang
- , Zhuo Yang
- & Qianwen Sun
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Article
| Open AccessPervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe
While mycorrhizal-plant interactions are widely studied, other root symbionts may also be ecologically important. Here, the authors show that dark septate endophytes are a strong predictor of rhizosphere and associated soil microbiomes in broad-leaved tree across Europe.
- Tarquin Netherway
- , Jan Bengtsson
- & Mohammad Bahram
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Article
| Open AccessMicrobiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis
The underlying mechanisms of host-driven assembly of phyllosphere microbiota remain largely unknown. Here, 4-hydroxycinnamic acid synthesized by the rice plant’s PAL02 in the phenylpropanoid biosynthesis pathway is shown to be the main driver for enrichment of Pseudomonadales bacteria.
- Pin Su
- , Houxiang Kang
- & Yong Liu
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Article
| Open AccessMultiple independent losses of the biosynthetic pathway for two tropane alkaloids in the Solanaceae family
Hyoscyamine and scopolamine (HS) are two tropane alkaloids with medicinal significance produced by distantly related lineages in the Solanaceae family. Here, the authors assemble the genome of three HS-producing and one non-HS-producing species within Solanaceae, and reveal the evolution of the biosynthetic pathway.
- Jiao Yang
- , Ying Wu
- & Jianquan Liu
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Article
| Open AccessMagnaporthe oryzae effector MoSPAB1 directly activates rice Bsr-d1 expression to facilitate pathogenesis
Magnaporthe oryzae effector MoSPAB1 enters rice nuclei to bind to the promoter of the immunity-brake gene Bsr-d1 and activates its expression by competing with rice MYBS1, which constitute a conserved module that facilitates fungal pathogenesis.
- Ziwei Zhu
- , Jun Xiong
- & Weitao Li
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Article
| Open AccessCell geometry regulates tissue fracture
The epidermal surface of leaves and flower petals often display cells with wavy geometries. Here the authors provide evidence that this pattern represents an energy-efficient mechanism to protect plants from deleterious surface fissures and toughen the plants’ protective surface.
- Amir J. Bidhendi
- , Olivier Lampron
- & Anja Geitmann
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Article
| Open AccessGenome-resolved metatranscriptomics reveals conserved root colonization determinants in a synthetic microbiota
The identification of processes activated by specific microbes during microbiota colonization of plant roots is hampered by technical issues in metatranscriptomics. Here, Vannier et al. colonized germ-free plants with a defined root microbiota comprising over 100 microbial isolates, and addressed those issues in various ways to identify strain-specific processes as well as common gene sets activated by microbes during root colonization.
- Nathan Vannier
- , Fantin Mesny
- & Stéphane Hacquard
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Article
| Open AccessEpigenetic modifications regulate cultivar-specific root development and metabolic adaptation to nitrogen availability in wheat
The analysis of wheat cultivars reveals that variations in histone modification, rather than DNA sequence, are closely linked to the expression of nitrogen metabolism genes and distinct agronomic traits. The findings suggest that epigenetic regulation plays a crucial role in cultivar-specific adaptation to low nitrogen conditions in wheat.
- Hao Zhang
- , Zhiyuan Jin
- & Jun Xiao
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Article
| Open AccessStructural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana
The cryo-EM structures of an FCP trimer and a PSII-FCPII supercomplex from a diatom are revealed, providing detailed insights into the variety of FCPII and their regulatory roles in green light harvesting, energy transfer and dissipation.
- Songhao Zhao
- , Lili Shen
- & Wenda Wang
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Article
| Open AccessControl of compound leaf patterning by MULTI-PINNATE LEAF1 (MPL1) in chickpea
Pinnate compound leaves sequentially produce their leaflets along the longitudinal axes. The study identifies the MPL1 gene as a key regulator in orchestrating an acropetal pattern of leaflet formation during the chickpea pinnate leaf development.
- Ye Liu
- , Yuanfan Yang
- & Liangliang He
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