Peptide REF1 is a local wound signal promoting plant regeneration.

Plants frequently encounter wounding and have evolved an extraordinary regenerative capacity to heal the wounds. However, the wound signal that triggers regenerative responses has not been identified. Here, through characterization of a tomato mutant defective in both wound-induced defense and regeneration, we demonstrate that in tomato, a plant elicitor peptide (Pep), REGENERATION FACTOR1 (REF1), acts as a systemin-independent local wound signal that primarily regulates local defense responses and regenerative responses in response to wounding. We further identified PEPR1/2 ORTHOLOG RECEPTOR-LIKE KINASE1 (PORK1) as the receptor perceiving REF1 signal for plant regeneration. REF1-PORK1-mediated signaling promotes regeneration via activating WOUND-INDUCED DEDIFFERENTIATION 1 (WIND1), a master regulator of wound-induced cellular reprogramming in plants. Thus, REF1-PORK1 signaling represents a conserved phytocytokine pathway to initiate, amplify, and stabilize a signaling cascade that orchestrates wound-triggered organ regeneration. Application of REF1 provides a simple method to boost the regeneration and transformation efficiency of recalcitrant crops.

Tomato MED25 regulates fruit ripening by interacting with EIN3-like transcription factors.

Fruit ripening relies on the precise spatiotemporal control of RNA polymerase II (Pol II)-dependent gene transcription, and the evolutionarily conserved Mediator (MED) coactivator complex plays an essential role in this process. In tomato (Solanum lycopersicum), a model climacteric fruit, ripening is tightly coordinated by ethylene and several key transcription factors. However, the mechanism underlying the transmission of context-specific regulatory signals from these ripening-related transcription factors to the Pol II transcription machinery remains unknown. Here, we report the mechanistic function of MED25, a subunit of the plant Mediator transcriptional coactivator complex, in controlling the ethylene-mediated transcriptional program during fruit ripening. Multiple lines of evidence indicate that MED25 physically interacts with the master transcription factors of the ETHYLENE-INSENSITIVE 3 (EIN3)/EIN3-LIKE (EIL) family, thereby playing an essential role in pre-initiation complex formation during ethylene-induced gene transcription. We also show that MED25 forms a transcriptional module with EIL1 to regulate the expression of ripening-related regulatory as well as structural genes through promoter binding. Furthermore, the EIL1-MED25 module orchestrates both positive and negative feedback transcriptional circuits, along with its downstream regulators, to fine-tune ethylene homeostasis during fruit ripening.

Cationic Zinc(II) Complexes with Carbazole-Type Counter-Anions: Intracomplex Donor/Acceptor Pairs Affording Exciplexes with Thermally Activated Delayed Fluorescence.

Two cationic zinc(II) complexes with carbazole-type counter-anions, namely, [Zn(tpy)2]2+[CAZ-p-BF3-]2 (Zn-p) and [Zn(tpy)2]2+[CAZ-o-BF3-]2 (Zn-o), have been designed and synthesized, where tpy is 2,2':6',2″-terpyridine, CAZ-p-BF3- is 4-((9H-carbazol-9-yl)phenyl)trifluoroborate, and CAZ-o-BF3- is (2-(9H-carbazol-9-yl)phenyl)trifluoroborate. The complex cation [Zn(tpy)2]2+ (as the acceptor) and the carbazole-type counter-anion CAZ-p-BF3- or CAZ-o-BF3- (as the donor) form an intracomplex donor/acceptor pair. Single-crystal structures reveal that compared to Zn-p, Zn-o exhibits a stronger π-π stacking interaction between the carbazole group (as the donor unit) of the counter-anion and the tpy ligand (as the acceptor unit) of [Zn(tpy)2]2+ because of the different anchoring position of the BF3- anion in the counter-anion. In a doped film, Zn-p and Zn-o afford an isolated exciplex formed between the carbazole group and the tpy ligand within the single complex, which gives green-yellow emission with a thermally activated delayed fluorescence (TADF) feature. In crystalline states, Zn-p and Zn-o afford exciplexes with blue emission centered at 468 nm and green-blue emission centered at 508 nm, respectively. The Zn-p crystalline sample shows a relatively large singlet-triplet energy gap (ΔEST) (0.33 eV) and no TADF, whereas the Zn-o crystalline sample exhibits a small ΔEST (0.06 eV) and distinct TADF, with a reverse intersystem crossing rate at 3.3 × 105 s-1. Zn-p and Zn-o both exhibit intriguing mechanochromic luminescence, with largely red-shifted (by over 70 nm) emission and modulated TADF properties upon mechanically grinding the crystalline samples. The work demonstrates that donor/acceptor pairs affording exciplexes can be formed within cationic metal complexes using counter-anions with donor nature, which opens a new avenue toward photo-active metal complexes with rich photophysical properties.

Coordinated cytokinin signaling and auxin biosynthesis mediates arsenate-induced root growth inhibition.

Interactions between plant hormones and environmental signals are important for the maintenance of root growth plasticity under ever-changing environmental conditions. Here, we demonstrate that arsenate (AsV), the most prevalent form of arsenic (As) in nature, restrains elongation of the primary root through transcriptional regulation of local auxin biosynthesis genes in the root tips of Arabidopsis (Arabidopsis thaliana) plants. The ANTHRANILATE SYNTHASE ALPHA SUBUNIT 1 (ASA1) and BETA SUBUNIT 1 (ASB1) genes encode enzymes that catalyze the conversion of chorismate to anthranilate (ANT) via the tryptophan-dependent auxin biosynthesis pathway. Our results showed that AsV upregulates ASA1 and ASB1 expression in root tips, and ASA1- and ASB1-mediated auxin biosynthesis is involved in AsV-induced root growth inhibition. Further investigation confirmed that AsV activates cytokinin signaling by stabilizing the type-B ARABIDOPSIS RESPONSE REGULATOR1 (ARR1) protein, which directly promotes the transcription of ASA1 and ASB1 genes by binding to their promoters. Genetic analysis revealed that ASA1 and ASB1 are epistatic to ARR1 in the AsV-induced inhibition of primary root elongation. Overall, the results of this study illustrate a molecular framework that explains AsV-induced root growth inhibition via crosstalk between two major plant growth regulators, auxin and cytokinin.

Versatile interactions and bioinformatics analysis of noncoding RNAs.

Advances in RNA sequencing technologies and computational methodologies have provided a huge impetus to noncoding RNA (ncRNA) study. Once regarded as inconsequential results of transcriptional promiscuity, ncRNAs were later found to exert great roles in various aspects of biological functions. They are emerging as key players in gene regulatory networks by interacting with other biomolecules (DNA, RNA or protein). Here, we provide an overview of ncRNA repertoire and highlight recent discoveries of their versatile interactions. To better investigate the ncRNA-mediated regulation, it is necessary to make full use of innovative sequencing techniques and computational tools. We further describe a comprehensive workflow for in silico ncRNA analysis, providing up-to-date platforms, databases and tools dedicated to ncRNA identification and functional annotation.

Donor/Acceptor Pairs Created by Electrostatic Interaction: Design, Synthesis, and Investigation on the Exciplex Formed Within the Pair.

Exciplexes formed between donors and acceptors have been widely explored but isolating them from each other and tuning the interaction between the donor and acceptor have remained challenges. Here, we report donor/acceptor (D/A) pairs created by electrostatic interaction between a carbazole-based anionic donor and a 1,3,5-triazine-based cationic acceptor and the exciplex formed within the pair. In a diluted film, the D/A pair affords an isolated exciplex which shows thermally activated delayed fluorescence (TADF). By changing the anchoring position of the imidazolium cation in the cationic acceptor, interactions between the donor and acceptor can be changed. Compared to the conventional exciplex formed in a neat film, the isolated exciplex exhibits a substantially higher luminescence efficiency. The D/A pairs show intriguing mechanochromic luminescence and mechanical grinding-induced/reinforced TADF in the solid state and promising performances as emitters in organic light-emitting diodes.

Cationic Iridium Complexes with 3,4,5-Triphenyl-4H-1,2,4-Triazole Type Cyclometalating Ligands: Synthesis, Characterizations, and Their Use in Light-Emitting Electrochemical Cells.

Cationic iridium complexes that show blue-shifted emission and high phosphorescent efficiency have been pursued for their optoelectronic applications. Five cationic iridium complexes with 3,4,5-triphenyl-4H-1,2,4-triazole (tPhTAZ) type cyclometalating ligands (C^N) and 2,2'-bipyridine or 2-(pyridin-2-yl)-1H-benzo[d]imidazole type ancillary ligands (N^N) have been designed and synthesized. Their structures have been confirmed by X-ray crystallography, and their photophysical and electrochemical properties have been comprehensively characterized. In solution and thin films, the complexes afford efficient yellow to blue-green emission. The highest occupied molecular orbitals (HOMOs) of these complexes are delocalized over the C^N ligand and the iridium ion, and compared with the conventional 2-phenylpyridine (Hppy) ligand, the tPhTAZ ligand largely shifts the emission of the complex toward blue by over 40 nm through stabilizing the HOMO. Moreover, the peripheral phenyl rings in tPhTAZ provide steric hindrance to the complexes, which suppresses phosphorescence concentration-quenching of the complexes, leading to high luminescent efficiencies in neat films. Theoretical calculations have shown that the emission of the complexes originates from either the charge-transfer state (Ir/C^N → N^N) or the C^N/N^N-centered 3π-π* state, depending on the local surrounding of the complex. The complexes exhibit good electrochemical stability with reversible oxidation and reduction processes in solution. Solid-state light emitting electrochemical cells (LECs) using the complexes afford yellow to blue-green emission, with peak current efficiencies of up to 34.7 cd A-1 and maximum brightness of up to 256 cd m-2 at 3.0 V, which are among the highest for LECs based on cationic iridium complexes reported so far, indicating the great potential for the use of tPhTAZ-type C^N ligands in construction of cationic iridium complexes for LEC applications.

Circular RNA: an emerging key player in RNA world.

Insights into the circular RNA (circRNA) exploration have revealed that they are abundant in eukaryotic transcriptomes. Diverse genomic regions can generate different types of RNA circles, implying their diversity. Covalently closed loop structures elevate the stability of this new type of noncoding RNA. High-throughput sequencing analyses suggest that circRNAs exhibit tissue- and developmental-specific expression, indicating that they may play crucial roles in multiple cellular processes. Strikingly, several circRNAs could function as microRNA sponges and regulate gene transcription, highlighting a new class of important regulators. Here, we review the recent advances in knowledge of endogenous circRNA biogenesis, properties and functions. We further discuss the current findings about circRNAs in human diseases. In plants, the roles of circRNAs remain a mystery. Online resources and bioinformatics identification of circRNAs are essential for the analysis of circRNA biology, although different strategies yield divergent results. The understanding of circRNA functions remains limited; however, circRNAs are enriching the RNA world, acting as an emerging key player.

PceRBase: a database of plant competing endogenous RNA.

Competition for microRNA (miRNA) binding between RNA molecules has emerged as a novel mechanism for the regulation of eukaryotic gene expression. Competing endogenous RNA (ceRNA) can act as decoys for miRNA binding, thereby forming a ceRNA network by regulating the abundance of other RNA transcripts which share the same or similar microRNA response elements. Although this type of RNA cross talk was first described in Arabidopsis, and was subsequently shown to be active in animal models, there is no database collecting potential ceRNA data for plants. We have developed a Plant ceRNA database (PceRBase, http://bis.zju.edu.cn/pcernadb/index.jsp) which contains potential ceRNA target-target, and ceRNA target-mimic pairs from 26 plant species. For example, in Arabidopsis lyrata, 311 candidate ceRNAs are identified which could affect 2646 target-miRNA-target interactions. Predicted pairing structure between miRNAs and their target mRNA transcripts, expression levels of ceRNA pairs and associated GO annotations are also stored in the database. A web interface provides convenient browsing and searching for specific genes of interest. Tools are available for the visualization and enrichment analysis of genes in the ceRNA networks. Moreover, users can use PceRBase to predict novel competing mimic-target and target-target interactions from their own data.

Identification and characterization of ncRNA-associated ceRNA networks in Arabidopsis leaf development.

BACKGROUND: Leaf development is a complex biological process that is accompanied by wide transcriptional changes. Many protein-coding genes have been characterized in plant leaves, but little attention has been given to noncoding RNAs (ncRNAs). Moreover, increasing evidence indicates that an intricate interplay among RNA species, including protein-coding RNAs and ncRNAs, exists in eukaryotic transcriptomes, however, it remains elusive in plant leaves. RESULTS: We detected novel ncRNAs, such as circular RNAs (circRNAs) and long noncoding RNAs (lncRNAs), and further constructed and analyzed their associated competitive endogenous RNA (ceRNA) networks in Arabidopsis leaves. Transcriptome profiling showed extensive changes during leaf development. In addition, comprehensive detection of circRNAs in other plant leaves suggested that circRNAs are widespread in plant leaves. To investigate the complex post-transcriptional interactions in Arabidopsis leaves, we constructed a global circRNA/lncRNA-associated ceRNA network. Functional analysis revealed that ceRNAs were highly correlated with leaf development. These ceRNAs could be divided into six clusters, which were enriched for different functional classes. Stage-specific ceRNA networks were further constructed and comparative analysis revealed different roles of stage common and specific hub ceRNAs. CONCLUSIONS: Our results demonstrate that understanding the ceRNA interactions will lead insights into gene regulations implicated in leaf development.

CircPro: an integrated tool for the identification of circRNAs with protein-coding potential.

SUMMARY: Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5' caps or 3' polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome. To gain insights into the new area of circRNA translation, we introduce an integrated tool capable of detecting circRNAs with protein-coding potential from high-throughput sequencing data. AVAILABILITY AND IMPLEMENTATION: CircPro is available at http://bis.zju.edu.cn/CircPro. CONTACT: mchen@zju.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genome-Wide Analysis of the Distinct Types of Chromatin Interactions in Arabidopsis thaliana.

The three-dimensional shapes of chromosomes regulate gene expression and genome function. Our knowledge of the role of chromatin interaction is evolving rapidly. Here, we present a study of global chromatin interaction patterns in Arabidopsis thaliana. High-throughput experimental techniques have been developed to map long-range interactions within chromatin. We have integrated data from multiple experimental sources including Hi-C, BS-seq, ChIP-chip and ChIP-seq data for 17 epigenetic marks and 35 transcription factors. We identified seven groups of interacting loci, which can be distinguished by their epigenetic profiles. Furthermore, the seven groups of interacting loci can be divided into three types of chromatin linkages based on expression status. We observed that two interacting loci sometimes share common epigenetic and transcription factor-binding profiles. Different groups of loci display very different relationships between epigenetic marks and the binding of transcription factors. Distinctive types of chromatin linkages exhibit different gene expression profiles. Our study unveils an entirely unexplored regulatory interaction, linking epigenetic profiles, transcription factor binding and the three-dimensional spatial organization of the Arabidopsis nuclear genome.

Genome-wide characterization and evolution analysis of miniature inverted-repeat transposable elements (MITEs) in moso bamboo (Phyllostachys heterocycla).

MAIN CONCLUSION: Moso bamboo MITEs were genome-wide identified first time, and data shows that MITEs contribute to the genomic diversity and differentiation of bamboo. Miniature inverted-repeat transposable elements (MITEs) are widespread in animals and plants. There are a large number of transposable elements in moso bamboo (Phyllostachys heterocycla var. pubescens) genome, but the genome-wide information of moso bamboo MITEs is not known yet. Here we identified 362 MITE families with a total of 489,592 MITE-related sequences, accounting for 4.74 % of the moso bamboo genome. The 362 MITE families are clustered into six known and one unknown super-families. Our analysis indicated that moso bamboo MITEs preferred to reside in or near the genes that might be involved in regulation of host gene expression. Of the seven super-families, three might undergo major expansion event twice, respectively, during 8-11 million years ago (mya) ago and 22-28 mya ago; two might experience a long expansion period from 6 to 13 mya. Almost 1/3 small RNAs might be derived from the MITE sequences. Some MITE families generate small RNAs mainly from the terminals, while others predominantly from the central region. Given the high copy number of MITEs, many siRNAs and miRNAs derived from MITE sequences and the preferential insertion of MITE into gene regions, MITEs may contribute to the genomic diversity and differentiation of bamboo.

Genome-wide identification and evolution of HECT genes in soybean.

Proteins containing domains homologous to the E6-associated protein (E6-AP) carboxyl terminus (HECT) are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.

A natural variation in SlSCaBP8 promoter contributes to the loss of saline-alkaline tolerance during tomato improvement.

Saline-alkaline stress is a worldwide problem that threatens the growth and yield of crops. However, how crops adapt to saline-alkaline stress remains less studied. Here we show that saline-alkaline tolerance was compromised during tomato domestication and improvement, and a natural variation in the promoter of SlSCaBP8, an EF-hand Ca2+ binding protein, contributed to the loss of saline-alkaline tolerance during tomato improvement. The biochemical and genetic data showed that SlSCaBP8 is a positive regulator of saline-alkaline tolerance in tomato. The introgression line Pi-75, derived from a cross between wild Solanum pimpinellifolium LA1589 and cultivar E6203, containing the SlSCaBP8LA1589 locus, showed stronger saline-alkaline tolerance than E6203. Pi-75 and LA1589 also showed enhanced saline-alkaline-induced SlSCaBP8 expression than that of E6203. By sequence analysis, a natural variation was found in the promoter of SlSCaBP8 and the accessions with the wild haplotype showed enhanced saline-alkaline tolerance compared with the cultivar haplotype. Our studies clarify the mechanism of saline-alkaline tolerance conferred by SlSCaBP8 and provide an important natural variation in the promoter of SlSCaBP8 for tomato breeding.

Chromosome-level genome assembly of Solanum pimpinellifolium.

Solanum pimpinellifolium, the closest wild relative of the domesticated tomato, has high potential for use in breeding programs aimed at developing multi-pathogen resistance and quality improvement. We generated a chromosome-level genome assembly of S. pimpinellifolium LA1589, with a size of 833 Mb and a contig N50 of 31 Mb. We anchored 98.80% of the contigs into 12 pseudo-chromosomes, and identified 74.47% of the sequences as repetitive sequences. The genome evaluation revealed BUSCO and LAI score of 98.3% and 14.49, respectively, indicating high quality of this assembly. A total of 41,449 protein-coding genes were predicted in the genome, of which 89.17% were functionally annotated. This high-quality genome assembly serves as a valuable resource for accelerating the biological discovery and molecular breeding of this important horticultural crop.

Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution.

BACKGROUND: Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. METHODS: Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. RESULTS: We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.

The complete chloroplast genome and phylogenetic analysis of Syringa reticulata subsp. amurensis (Rupr.) P.S.Green & M.C.Chang from Qinghai Province, China.

Syringa reticulata subsp. amurensis (Rupr.) P. S. Green & M. C. Chang (Oleaceae) is a shrub or tree with high medicinal value as well as great ecological significance as an urban garden plant. To better understand the molecular genetics and evolutionary of S. reticulata subsp. amurensis, its complete chloroplast genome was sequenced and annotated. The assembled chloroplast genome is a circular 156,141 bp sequence, consisting of 87,108 bp large single copy (LSC) region and 17,239 bp small single copy (SSC) region, which were flanked by a pair of 25,897 bp inverted repeats (IRs). The GC content of the chloroplast genome is 36.14%. Moreover, a total of 132 functional genes were annotated, including 88 protein-coding, 36 tRNA, and eight rRNA genes. Phylogenetic analysis showed that S. reticulata subsp. amurensis was most closely related to S. reticulata subsp. Pekinensis and the genus Syringa is paraphyletic group. This study provides important information for further phylogenetic studies on S. reticulata subsp. amurensis and its allies.

Sky-blue-emitting cationic iridium complexes with carbazole-type counter-anions and their use for efficient solution-processed organic light-emitting diodes.

The control of counter-anion is a facile approach to tune the overall properties of cationic iridium complexes for optoelectronic applications. Here, we report for the first time the use of electron-rich carbazole-type counter-anions in cationic iridium complexes and the use of such complexes as dopants in solution-processed organic light-emitting diodes (OLEDs). PF6-, 4-(9H-carbazol-9-yl)benzenesulfonate (CAZ-SO3-), and 4-(9'H-[9,3':6',9''-tercarbazol]-9'-yl)benzenesulfonate (TCAZ-SO3-) have been employed as the counter-anions of sky-blue-emitting complexes R, 1 and 2, respectively. The carbazole-type counter-anions do not largely disturb the phosphorescence of the cations and the complexes show similar emission properties in solution and films. The close proximity of the carbazole-type anions to the phosphorescent cations allows efficient energy-transfer from the former to the latter in films. When used as dopants in solution-processed OLEDs, complexes 1 and 2 show higher performances than complex R because the hole-trapping effects of the carbazole-type counter-anions largely improve the carrier-recombination balance in the emissive layers. In particular, the double-layer sky-blue device based on complex 2 with strong hole-trapping by TCAZ-SO3- affords a high peak current efficiency of 27.1 cd A-1. The work reveals that electron-rich carbazole-type anions are promising counter-anions for cationic iridium complexes toward optoelectronic applications.

The complete chloroplast genome of Syringa oblata (Oleaceae).

Syringa oblata Lindl. is a popular ornamental shrub with aroma compounds. Here, we sequenced and assembled the complete chloroplast genome of S. oblata. The complete chloroplast genome of S. oblata is 155,648 bp in length, containing a pair of inverted repeated (IRa and IRb) region of 25,732 bp that are separated by a large single copy (LSC) region of 86,247 bp, and a small single copy (SSC) region of 17,937 bp. A total of 132 functional genes were annotated, including 88 protein-coding genes, 36 tRNA genes, and eight rRNA genes. The Neighbour-joining phylogenetic tree based on complete chloroplast genomes suggested that S. oblata is most closely related to S. vulgaris.