Stomatal dynamics are regulated by leaf hydraulic traits and guard cell anatomy in nine true mangrove species

Stomatal regulation is critical for mangroves to survive in the hyper-saline intertidal zone where water stress is severe and water availability is highly fluctuant.However,very little is known about the stomatal sensitivity to vapour pressure deficit(VPD)in mangroves,and its co-ordination with stomatal morphology and leaf hydraulic traits.We measured the stomatal response to a step increase in VPD in situ,stomatal anatomy,leaf hydraulic vulnerability and pressure-volume traits in nine true mangrove species of five families and collected the data of genome size.We aimed to answer two questions:(1)Does stomatal morphology influence stomatal dynamics in response to a high VPD in mangroves?with a consideration of possible influence of genome size on stomatal morphology;and(2)do leaf hydraulic traits influence stomatal sensitivity to VPD in mangroves?We found that the stomata of mangrove plants were highly sensitive to a step rise in VPD and the stomatal responses were directly affected by stomatal anatomy and hydraulic traits.Smaller,denser stomata was correlated with faster stomatal closure at high VPD across the species of Rhizophoraceae,and stomata size negatively and vein density positively correlated with genome size.Less negative leaf osmotic pressure at the full turgor(πo)was related to higher operating steady-state stomatal conductance(gs);and a higher leaf capacitance(Cleaf)and more embolism resistant leaf xylem were associated with slower stomatal responses to an increase in VPD.In addition,stomatal responsiveness to VPD was indirectly affected by leaf morphological traits,which were affected by site salinity and consequently leaf water status.Our results demonstrate that mangroves display a unique relationship between genome size,stomatal size and vein packing,and that stomatal responsiveness to VPD is regulated by leaf hydraulic traits and stomatal morphology.Our work provides a quantitative framework to better understand of stomatal regulation in mangroves in an environment with high salinity and dynamic water availability.

Plant Stem Cell Informatics Database(PSCIdb):A comprehensive computational platform for identifying and analyzing genes related to plant stem cells

Dear Editor,Stem cells in the meristems of land plants share conserved functions,remaining undifferentiated while continually dividing and producing daughter cells that eventually differentiate into various new organs(Meyerowitz,1997;Heidstra and Sabatini,2014).Stem cell activity is therefore essential for sustaining plant growth and development,determining yield and biomass production,and dictating the diversity of body formation and plant architecture across species(Meyerowitz,1997;Heidstra and Sabatini,2014;Harrison,2017;Kitagawa and Jackson,2019).

Hybrid de novo genome assembly of red gromwell(Lithospermum erythrorhizon)reveals evolutionary insight into shikonin biosynthesis

Lithospermum erythrorhizon(red gromwell;zicao)is a medicinal and economically valuable plant belonging to the Boraginaceae family.Roots from L.erythrorhizon have been used for centuries based on the antiviral and woundhealing properties produced from the bioactive compound shikonin and its derivatives.More recently,shikonin,its enantiomer alkannin,and several other shikonin/alkannin derivatives have collectively emerged as valuable natural colorants and as novel drug scaffolds.Despite several transcriptomes and proteomes having been generated from L.erythrorhizon,a reference genome is still unavailable.This has limited investigations into elucidating the shikonin/alkannin pathway and understanding its evolutionary and ecological significance.In this study,we obtained a de novo genome assembly for L.erythrorhizon using a combination of Oxford Nanopore long-read and Illumina short-read sequencing technologies.The resulting genome is∼367.41 Mb long,with a contig N50 size of 314.31 kb and 27,720 predicted protein-coding genes.Using the L.erythrorhizon genome,we identified several additional phydroxybenzoate:geranyltransferase(PGT)homologs and provide insight into their evolutionary history.Phylogenetic analysis of prenyltransferases suggests that PGTs originated in a common ancestor of modern shikonin/alkanninproducing Boraginaceous species,likely from a retrotransposition-derived duplication event of an ancestral prenyltransferase gene.Furthermore,knocking down expression of LePGT1 in L.erythrorhizon hairy root lines revealed that LePGT1 is predominantly responsible for shikonin production early in culture establishment.Taken together,the reference genome reported in this study and the provided analysis on the evolutionary origin of shikonin/alkannin biosynthesis will guide elucidation of the remainder of the pathway.

Chilling stress drives organ-specific transcriptional cascades and dampens diurnal oscillation in tomato

Improving chilling tolerance in cold-sensitive crops,e.g.tomato,requires knowledge of the early molecular response to low temperature in these under-studied species.To elucidate early responding processes and regulators,we captured the transcriptional response at 30 minutes and 3 hours in the shoots and at 3 hours in the roots of tomato post-chilling from 24℃ to 4℃.We used a pre-treatment control and a concurrent ambient temperature control to reveal that majority of the differential expression between cold and ambient conditions is due to severely compressed oscillation of a large set of diurnally regulated genes in both the shoots and roots.This compression happens within 30 minutes of chilling,lasts for the duration of cold treatment,and is relieved within 3 hours of return to ambient temperatures.Our study also shows that the canonical ICE1/CAMTA-to-CBF cold response pathway is active in the shoots,but not in the roots.Chilling stress induces synthesis of known cryoprotectants(trehalose and polyamines),in a CBF-independent manner,and induction of multiple genes encoding proteins of photosystems I and II.This study provides nuanced insights into the organ-specific response in a chilling sensitive plant,as well as the genes influenced by an interaction of chilling response and the circadian clock.

The origin and biosynthesis of the naphthalenoid moiety of juglone in black walnut

Several members of the Juglandaceae family produce juglone,a specialized 1,4-naphthoquinone(1,4-NQ)natural product that is responsible for the notorious allelopathic effects of black walnut(Juglans nigra).Despite its documented ecological roles and potential for being developed as a novel natural product-based herbicide,none of the genes involved in synthesizing juglone have been identified.Based on classical labeling studies,we hypothesized that biosynthesis of juglone’s naphthalenoid moiety is shared with biochemical steps of the phylloquinone pathway.Here,using comparative transcriptomics in combination with targeted metabolic profiling of 1,4-NQs in various black walnut organs,we provide evidence that phylloquinone pathway genes involved in 1,4-dihydroxynaphthoic acid(DHNA)formation are expressed in roots for synthesis of a compound other than phylloquinone.Feeding experiments using axenic black walnut root cultures revealed that stable isotopically labeled L-glutamate incorporates into juglone resulting in the same mass shift as that expected for labeling of the quinone ring in phylloquinone.Taken together,these results indicate that in planta,an intermediate from the phylloquinone pathway provides the naphthalenoid moiety of juglone.Moreover,this work shows that juglone can be de novo synthesized in roots without the contribution of immediate precursors translocated from aerial tissues.The present study illuminates all genes involved in synthesizing the juglone naphthoquinone ring and provides RNA-sequencing datasets that can be used with functional screening studies to elucidate the remaining juglone pathway genes.Translation of the generated knowledge is expected to inform future metabolic engineering strategies for harnessing juglone as a novel natural product-based herbicide.

Combined analyses of translatome and transcriptome in Arabidopsis reveal new players responding to magnesium deficiency

Translational control of gene expression,including recruitment of ribosomes to messenger RNA(mRNA),is particularly important during the response to stress.Purification of ribosomeassociated mRNAs using translating ribosome affinity purification(TRAP)followed by RNAsequencing facilitates the study of mRNAs undergoing active transcription and better proxies the translatome,or protein response,to stimuli.To identify plant responses to Magnesium(Mg)deficiency at the translational level,we combined transcriptome and translatome analyses.Excitingly,we found 26 previously unreported Mg-responsive genes that were only regulated at the translational level and not the transcriptional level,during the early response to Mg deficiency.In addition,mutants of the transcription factor ELONGATED HYPOCOTYL 5(HY5),the H^(+)/CATION EXCHANGER 1 and 3(CAX1 and CAX3),and UBIQUITIN 11(UBQ11)exhibited early chlorosis phenotype under Mg deficiency,supporting their functional involvement in ion homeostasis.Overall,our study strongly supports that TRAP-seq combined with RNA-seq followed by phenotype screening could facilitate the identification of novel players during stress responses.