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Article
| Open AccessThe initial charge separation step in oxygenic photosynthesis
The photosystem II reaction center (PSII-RC) is a model system to understand the initial steps of photosynthesis, but its excited state dynamics is difficult to disentangle with most spectroscopic methods. Here the authors perform a two-dimensional electronic-vibrational spectroscopic study of PSII-RC, providing detailed insight into such dynamics and into the mechanism of charge separation.
- Yusuke Yoneda
- , Eric A. Arsenault
- & Graham R. Fleming
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Article
| Open AccessA dirigent family protein confers variation of Casparian strip thickness and salt tolerance in maize
Most crops are farmed under high transpiring environments, but our understanding of transpiration-dependent salt tolerance (TDST) remains limited. Here, the authors report a dirigent family protein is responsible for TDST by affecting lignin deposition at Casparian strip barrier and transportation of Na+ across the endodermis.
- Yanyan Wang
- , Yibo Cao
- & Caifu Jiang
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Article
| Open AccessA fungal extracellular effector inactivates plant polygalacturonase-inhibiting protein
Plants produce polygalacuturonase-inhibiting proteins (PGIPs) to counteract cell wall degradation by pathogenic microbes. Here the authors show that Sclerotinia sclerotiorum, a fungal pathogen that causes stem rot disease, secretes a PGIP-inactivating effector to diminish plant resistance.
- Wei Wei
- , Liangsheng Xu
- & Weidong Chen
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Article
| Open AccessDeletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata
Unlike Panax species, which can produce dammarane-type saponins, Aralia elata can only synthesize oleananetype saponins. Here, the authors reveal that the loss of the dammaranediol synthase-encoding gene and tandem duplication of triterpene biosynthetic genes drive structural divergences of saponins between the two genera.
- Yu Wang
- , He Zhang
- & Yuhua Li
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Article
| Open AccessA natural allele of OsMS1 responds to temperature changes and confers thermosensitive genic male sterility
Thermosensitive genic male-sterile (TGMS) lines are widely used for two-line hybrid rice breeding, but the mechanism of TGMS has not been fully elucidated. Here, the authors show that natural allele of the OsMS1 gene, encoding a histone binding PHD finger protein, responds to temperature change and confers TGMS in rice.
- Lunying Wu
- , Xiaohui Jing
- & Yunhai Li
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Article
| Open AccessHigh-quality genome and methylomes illustrate features underlying evolutionary success of oaks
The genus Quercus (oaks) has diversified into over 450 species which often play dominant roles in the ecosystems in which they occur. Here the authors present a genome and methylome for a California endemic oak, Quercus lobata, and describe features relevant to its evolutionary success.
- Victoria L. Sork
- , Shawn J. Cokus
- & Steven L. Salzberg
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Article
| Open AccessGenomic distances reveal relationships of wild and cultivated beets
While a large amount of genomic resources is available, the phylogeny of wild and cultivated beets remains unclear. Here, the authors use the k-mer-based Mash method to analyze resequenced genomes of 606 accessions of the genus Beta and reveal Greece as the domestication site of sugar beet.
- Felix L. Sandell
- , Nancy Stralis-Pavese
- & Juliane C. Dohm
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Article
| Open AccessA pair of non-Mendelian genes at the Ga2 locus confer unilateral cross-incompatibility in maize
Unilaterial cross-incompatibility (UCI) systems are regulated by a male-female gene pair that are genetically linked, but no pair of the male and female determinants has been isolated so far. Here, the authors report the cloning of a pair of pectin methylesterases encoding genes at the Ga2 locus confer UCI in maize.
- Zhibin Chen
- , Zhaogui Zhang
- & Huabang Chen
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Article
| Open AccessChromosome evolution and the genetic basis of agronomically important traits in greater yam
While greater yam provides food and income security for millions of people around the world, there are limited genomic resources available. Here, the authors report a chromosome-scale assembly of the greater yam genome as well as quantitative trait loci associated with anthracnose resistance and tuber traits.
- Jessen V. Bredeson
- , Jessica B. Lyons
- & Daniel S. Rokhsar
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Article
| Open AccessGenomic evidence for homoploid hybrid speciation between ancestors of two different genera
Carpinus fangiana exhibits intermediate morphology between C. viminea and Ostrya rehderiana. Here, the authors report that Carpinus sect. Distegocarpus likely originate through homoploid hybrid speciation (HHS) during the early divergence between Carpinus and Ostrya through genomic analyses.
- Zefu Wang
- , Minghui Kang
- & Jianquan Liu
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Article
| Open AccessStructural basis for the assembly and quinone transport mechanisms of the dimeric photosynthetic RC–LH1 supercomplex
Bacterial photosynthesis reflects the early stages of the evolution of photosynthesis. Here, the authors present a systematic study of the cryo-EM structures of the dimeric light harvesting–reaction center complexes and assembly variants from Rhodobacter sphaeroides, which delineated a hierarchical assembly pathway and quinone transport routes of the dimeric photosynthetic RC–LH1 core complex.
- Peng Cao
- , Laura Bracun
- & Lu-Ning Liu
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Article
| Open AccessReshuffling of the ancestral core-eudicot genome shaped chromatin topology and epigenetic modification in Panax
The role of polyploidization generated genomic diversity in shaping the hierarchical genome architecture remains unclear. Here, the authors show that repatterning of the ancestral eudicot genome has resulted in multi-dimensional genome plasticity and secondary metabolite diversification via comparisons of Panax genomes.
- Zhen-Hui Wang
- , Xin-Feng Wang
- & Lin-Feng Li
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Article
| Open AccessAsymmetric structure of the native Rhodobacter sphaeroides dimeric LH1–RC complex
Rhodobacter sphaeroides is a model organism for studying bacterial photosynthesis. Here, the authors present structures of its native dimeric and a protein-U-lacking monomeric light-harvesting-reaction center complexes, which reveal asymmetric features for the dimer and an altered shape for the monomer.
- Kazutoshi Tani
- , Ryo Kanno
- & Zheng-Yu Wang-Otomo
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Article
| Open AccessRadiationless mechanism of UV deactivation by cuticle phenolics in plants
Phenolics are abundant in plant cuticles. Here, via transient absorption spectroscopy and quantum chemical calculations, the authors propose a model by which cuticle phenolics provide photoprotection due to ultrafast and non-radiative excited state deactivation combined with fluorescence emission.
- Ana González Moreno
- , Abel de Cózar
- & Antonio Heredia
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Article
| Open AccessROS homeostasis mediated by MPK4 and SUMM2 determines synergid cell death
Synergid cells undergo programmed cell death following pollen tube reception and successful fertilization. Here the authors show that premature synergid cell death is prevented by the mitogen activated protein kinase MPK4 and the R protein SUMM2 which maintain ROS homeostasis in Arabidopsis.
- Ronny Völz
- , William Harris
- & Yong-Hwan Lee
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Article
| Open AccessStructural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Fucoxanthin chlorophyll a/c-binding proteins (FCPs) harvest light energy in diatoms. The authors analyzed a structure of PSII-FCPII supercomplex at high resolution by cryo-EM, which identified each FCP subunit and pigment network in the supercomplex.
- Ryo Nagao
- , Koji Kato
- & Jian-Ren Shen
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Article
| Open AccessStructure of a tetrameric photosystem I from a glaucophyte alga Cyanophora paradoxa
Photosystem I (PSI) harvest and transfer light energy into chemical energy in photosynthesis. Here, authors analyzed its tetrameric structure from a glaucophyte alga by cryo-EM, providing insights into an evolutionary turning-point of PSI.
- Koji Kato
- , Ryo Nagao
- & Jian-Ren Shen
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Article
| Open AccessCyclophilin anaCyp40 regulates photosystem assembly and phycobilisome association in a cyanobacterium
Cyclophilins are proteins found in many organisms, where they can play roles as chaperones, in signal transduction, or other functions. Here, Yadav et al. show that a cyanobacterial cyclophilin is involved in stress responses and in assembly of photosynthetic complexes, and displays unique structural features.
- Shivam Yadav
- , Martin Centola
- & Enrico Schleiff
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Article
| Open AccessA hierarchical transcriptional network activates specific CDK inhibitors that regulate G2 to control cell size and number in Arabidopsis
Cell division and expansion are carefully coordinated during organ growth. Here, the authors show that the SCL28 and SMOS1 transcription factors interact to regulate cyclin-dependent kinase inhibitors and promote cell size increase over division in Arabidopsis.
- Yuji Nomoto
- , Hirotomo Takatsuka
- & Masaki Ito
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Article
| Open AccessThe phytochrome interacting proteins ERF55 and ERF58 repress light-induced seed germination in Arabidopsis thaliana
Phytochromes regulate light-dependent seed germination in plants. Here the authors show that light-activated phytochromes bind two ERF transcriptional regulators and repress their activity to allow completion of germination.
- Zenglin Li
- , David J. Sheerin
- & Andreas Hiltbrunner
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Article
| Open AccessExploring a blue-light-sensing transcription factor to double the peak productivity of oil in Nannochloropsis oceanica
Microalgae are promising feedstock for oil production. The authors report that a transcription factor NobZIP77 can regulate oil synthesis by sensing the blue light, and explore these findings to greatly enhance oil productivity via genetic and process engineering in Nannochloropsis oceanica.
- Peng Zhang
- , Yi Xin
- & Jian Xu
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Article
| Open AccessAegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62
Aegilops sharonensis is a wild diploid relative of wheat. Here, the authors assemble the genome of Ae. sharonensis and use the assembly as an aid to clone the Ae. sharonensis-derived stem rust resistance gene Sr62 in the allohexaploid genome of wheat.
- Guotai Yu
- , Oadi Matny
- & Brande B. H. Wulff
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Article
| Open AccessMechanistic insights into the regulation of plant phosphate homeostasis by the rice SPX2 – PHR2 complex
SPX receptors regulate plant phosphate response via PHR transcription factors. Here, based on crystal structure analysis of rice PHR2 complexes, the authors propose that SPX2 regulates PHR2 by preventing DNA binding and oligomerisation of the PHR2 CC domain.
- Zeyuan Guan
- , Qunxia Zhang
- & Zhu Liu
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Article
| Open AccessPhylotranscriptomic insights into a Mesoproterozoic–Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae)
“Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
- Zheng Hou
- , Xiaoya Ma
- & Bojian Zhong
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Article
| Open AccessNew recognition specificity in a plant immune receptor by molecular engineering of its integrated domain
Plant NLR proteins trigger immune responses upon recognition of pathogen effectors. Here the authors show that the integrated decoy domain of the rice NLR RGA5 can be engineered to trigger immune responses upon binding a non-cognate effector.
- Stella Cesari
- , Yuxuan Xi
- & Thomas Kroj
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Article
| Open AccessUsing CRISPR-Kill for organ specific cell elimination by cleavage of tandem repeats
How double strand breaks (DSBs) are repaired within the plant 45S rDNA repeats is unclear. Here, the authors show that Cas9-mediated DSBs in 45S rDNA are mainly repaired by cNHEJ and describe CRISPR-Kill as a tool for organ-specific cell elimination by targeting functional repetitive DNA in Arabidopsis.
- Angelina Schindele
- , Fabienne Gehrke
- & Holger Puchta
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Article
| Open AccessExtracellular vesiculo-tubular structures associated with suberin deposition in plant cell walls
Suberizing plant cells export suberin monomers outside of the cell to form a hydrophobic barrier. Here the authors propose a role for extracellular vesiculo-tubular structures in the deposition of suberin monomers.
- Damien De Bellis
- , Lothar Kalmbach
- & Marie Barberon
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Article
| Open AccessParallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages
Detailing how populations adapted to environmental change is needed to predict future responses, but identifying adaptive variants and detailing their fitness effects is rare. Here, the authors show that parallel loss of FRI and FLC function reduces time to flowering and drives adaptation in a drought prone environment.
- Andrea Fulgione
- , Célia Neto
- & Angela M. Hancock
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Article
| Open AccessA peroxisomal heterodimeric enzyme is involved in benzaldehyde synthesis in plants
Benzaldehyde is a simple aromatic aldehyde that attracts pollinators, has antifungal properties and contributes to flavor in many plants. Here the authors show that benzaldehyde is synthesized in petunia via the benzoic acid β-oxidative pathway by a peroxisomal heterodimeric enzyme consisting of α and β subunits.
- Xing-Qi Huang
- , Renqiuguo Li
- & Natalia Dudareva
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Article
| Open AccessApoplastic class III peroxidases PRX62 and PRX69 promote Arabidopsis root hair growth at low temperature
Arabidopsis root hair growth is enhanced at low temperatures. Here the authors show that the class III peroxidases PRX62 and PRX69 modulate ROS homeostasis and cell wall characteristics, and promote root hair elongation at low temperature.
- Javier Martínez Pacheco
- , Philippe Ranocha
- & José M. Estevez
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Article
| Open AccessNorway spruce postglacial recolonization of Fennoscandia
Contrasting theories exist regarding how Norway spruce recolonized Fennoscandia after the last glaciation. Here, the authors provide evidences from sedimentary ancient DNA and modern population genomics to support that Norway spruce was present in southern Fennoscandia shortly after deglaciation and the early Holocene migration from the east.
- Kevin Nota
- , Jonatan Klaminder
- & Laura Parducci
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Article
| Open AccessDNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development
Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.
- Li He
- , Huan Huang
- & Jian-Kang Zhu
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Article
| Open AccessPhylogenomic analyses highlight innovation and introgression in the continental radiations of Fagaceae across the Northern Hemisphere
Fagaceae are diverse family including trees of ecological and economic importance. This phylogenomic analysis of nuclear and plastid genomes reconstructs evolutionary history and finds evidence of multiple adaptive introgression events in this important plant family.
- Biao-Feng Zhou
- , Shuai Yuan
- & Baosheng Wang
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Article
| Open AccessGenotyping-by-sequencing-based identification of Arabidopsis pattern recognition receptor RLP32 recognizing proteobacterial translation initiation factor IF1
Pattern-triggered immunity is activated by recognition of microbe-derived structures by host pattern recognition receptors. Here the authors use a genotype-by sequencing approach to show that bacterial translation initiation factor 1 triggers PTI in Arabidopsis thaliana after recognition by the RLP32 receptor.
- Li Fan
- , Katja Fröhlich
- & Thorsten Nürnberger
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Article
| Open AccessMechanosensory trichome cells evoke a mechanical stimuli–induced immune response in Arabidopsis thaliana
Plant immunity can be induced by pathogen signals or environmental cues. Here, the authors show that plant leaves use trichomes to sense incoming raindrops and trigger basal defence responses to protect against subsequent microbial infection.
- Mamoru Matsumura
- , Mika Nomoto
- & Yasuomi Tada
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Article
| Open AccessArabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading
MicroRNAs regulate gene expression through RNA cleavage or translation repression. Here the authors show that RBV, an evolutionarily conserved WD40 domain protein, acts to promote MIR transcription, pri-miRNA processing and miRNA loading into AGO1.
- Chao Liang
- , Qiang Cai
- & Xuemei Chen
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Comment
| Open AccessBreeding future crops to feed the world through de novo domestication
By the end of this century, a 50% increase in agricultural productivity is required to feed the world. Recent studies have demonstrated de novo domestication of wild plants as a new crop breeding strategy to meet future food challenges.
- Hong Yu
- & Jiayang Li
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Article
| Open AccessSex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA
Most sexual organisms ensure that organelles are inherited from a single parent. Here, the authors describe OTU2p, a Chlamydomonas deubiquitinase that drives uniparental organelle inheritance without gametic dimorphism by preventing proteasome-mediated degradation exclusively in gametes of the plus mating type.
- Sunjoo Joo
- , Thamali Kariyawasam
- & Jae-Hyeok Lee
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Article
| Open AccessTwo zinc finger proteins with functions in m6A writing interact with HAKAI
The components of m6A writer and their interactions are still far from fully understood. Here, the authors identify two HAKAI-interacting zinc finger proteins, HIZ1 and HIZ2, as components of the Arabidopsis m6A writer complex, and show that hiz2 mutant plants have an 85% reduction in m6A abundance and severe developmental defects.
- Mi Zhang
- , Zsuzsanna Bodi
- & Rupert G. Fray
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Article
| Open AccessNatural variation in Glume Coverage 1 causes naked grains in sorghum
Low glume coverage is the preferred for easy threshing in grain production, but the genetic basis remains unclear. Here, the authors report the gene GC1, which encodes an atypical G protein γ subunit, negatively regulates sorghum glume coverage and the naturally truncated alleles can be useful in the naked grain breeding.
- Peng Xie
- , Sanyuan Tang
- & Qi Xie
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Article
| Open AccessHSL1 and BAM1/2 impact epidermal cell development by sensing distinct signaling peptides
HAESA and HSL2 are receptors for IDA/IDL-family signaling peptides in plants. Here the authors show that HSL1, previously shown to recognize CLE9, preferentially binds IDA/IDL peptides and regulates leaf epidermal patterning independently of CLE peptides.
- Andra-Octavia Roman
- , Pedro Jimenez-Sandoval
- & Julia Santiago
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Article
| Open AccessLocal and global crosstalk among heterochromatin marks drives DNA methylome patterning in Arabidopsis
In plant genomes, both mCG and H3K9me2/mCH are important for silencing transposable elements (TEs). Here, the authors show that establishment of mCH is abolished in both TE and active genes when mCG is lost and targeting efficiency of mCH depends on relative levels of mCG within the genome.
- Taiko Kim To
- , Chikae Yamasaki
- & Tetsuji Kakutani
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Article
| Open AccessGenomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
The connection between expression variation and phenotypic diversity in the populations of polyploid crops remains elusive. Here, the authors reveal the impact of genetic variants leading to biased expression of homoeologous genes in hexaploid wheat on agronomic traits.
- Fei He
- , Wei Wang
- & Eduard Akhunov
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Article
| Open AccessPervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants
The small size (≤15-nt) of micorexons poses difficulties for genome annotation and identification using standard RNA sequence mapping approaches. Here, the authors develop computational pipelines to discover and predict microexons in plants and reveal diverse evolutionary trajectories via genomewide microexon modeling.
- Huihui Yu
- , Mu Li
- & Chi Zhang
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Article
| Open AccessCotranslational N-degron masking by acetylation promotes proteome stability in plants
N-terminal protein acetylation is required for plant viability. Here the authors show that reducing N-terminal acetylation by NatA leads to an increase in global protein turnover that is facilitated by absent masking of a novel N-degron
- Eric Linster
- , Francy L. Forero Ruiz
- & Markus Wirtz
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Article
| Open AccessCoat proteins of necroviruses target 14-3-3a to subvert MAPKKKα-mediated antiviral immunity in plants
MAPK cascades play an important role in innate immunity. Here, the authors show that that beet black scorch virus activates MAPK signaling in Nicotiana benthamiana and the viral coat protein counteracts MAPK-mediated defence by competitively binding to a MAPKKKα interactor.
- Zongyu Gao
- , Dingliang Zhang
- & Yongliang Zhang
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Article
| Open AccessArabidopsis guard cell chloroplasts import cytosolic ATP for starch turnover and stomatal opening
Stomatal guard cells require ATP in order to fuel stomatal movements. Here the authors show that guard cell photosynthesis is limited, mitochondria are the main source of ATP and that guard cell chloroplasts import ATP via nucleotide transporters.
- Shey-Li Lim
- , Sabrina Flütsch
- & Boon Leong Lim
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Article
| Open AccessGenomic insights into the evolution of Echinochloa species as weed and orphan crop
Echinochloa is an important genus in the grass family as many of them are either problematic weeds or domesticated millets. Here, the authors assemble three polyploidy genomes in this genus using the diploid-assisted scaffolding method DipHic and provide genomic insights into the dual roles of some species as weeds and orphan crops.
- Dongya Wu
- , Enhui Shen
- & Chu-Yu Ye
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Article
| Open AccessGraph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber
Increasing studies have suggested that single reference genome is insufficient to capture all variations in the genome. Here, the authors report a graph-based cucumber pan-genome by analyzing 12 chromosome-scale assemblies and reveal variations associated with agronomic traits and domestication.
- Hongbo Li
- , Shenhao Wang
- & Zhonghua Zhang
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