A story of two kingdoms: unravelling the intricacies of protein phase separation in plants and animals.

The biomolecular condensates (BCs) formed by proteins through phase separation provide the necessary space and raw materials for the orderly progression of cellular activities, and on this basis, various membraneless organelles (MLOs) are formed. The occurrence of eukaryotic phase separation is driven by multivalent interactions from intrinsically disordered regions (IDRs) and/or specific protein/nucleic acid binding domains and is regulated by various environmental factors. In plant and animal cells, the MLOs involved in gene expression regulation, stress response, and mitotic control display similar functions and mechanisms.

Alternative splicing of VRF1 acts as a molecular switch to regulate stress-induced early flowering.

Plants frequently evade extreme environmental stress by initiating early flowering, yet the underlying mechanisms remain incompletely understood. Here, through extensive mutant screening, we identify a vegetative growth to reproductive growth transition factor (vrf1) mutant, which exhibits a deficiency in drought escape. Alternative splicing of VRF1 generates four isoforms, of which two encode functional proteins, VRF1-AS1 and VRF1-AS3.

Six Species of with Three New Taxa on Grass from Sichuan Province, China.

(, ) species are parasitic fungi with a wide global distribution, causing tar spots on plants. In this study, we describe three newly discovered species: , , and from in China. These species were characterized using morphological traits and multi-locus phylogeny based on the internal transcribed spacer region (ITS) with the intervening 5.

Morphological and molecular analyses reveal two new species of (Nectriaceae, Hypocreales) associated with scale insects on walnut in China.

The fungal genus consists of species mostly occurring as parasites of scale insects, but are also commonly isolated from soil or lichens. In the present study, we surveyed the diversity and assess the taxonomy of entomopathogenic fungi in Sichuan Province, China. Two new species of , viz.

Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis.

Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing.

Morphology and phylogeny of ascomycetes associated with walnut trees () in Sichuan province, China.

In Sichuan province, walnuts, consisting of , , and the hybrid × , are commercially important edible nuts, and is the most widespread plant. To date, the diversity and distribution of fungi inhabiting on have not received enough attention, although there have been studies focusing on pathogens from fruit and stem. In order to update the checklist of fungi associated with Sichuan walnuts, a survey on fungi associated with the three species from 15 representative regions in Sichuan was conducted.

Morpho-Molecular Characterization of Microfungi Associated with (Poaceae) in Sichuan, China.

In the present study, we surveyed the ascomycetes from bamboo of across Sichuan Province, China. A biphasic approach based on morphological characteristics and multigene phylogeny confirmed seven species, including one new genus, two new species, and five new host record species. A novel genus is introduced to accommodate that was collected from leaves of .

In Situ Observation of Abscisic Acid Distribution in Major Crop Species by Immunofluorescence Labeling.

Immunofluorescent approach uses fluorophore-conjugated antibodies to target molecules of interest for the observation of their distribution and microenvironment at cellular or tissue level. In connection with modern fluorescence microscopy, immunofluorescence has high sensitivity and specificity, resulting in a wide range of applications in animal studies. However, the protocols of immunofluorescence are seldom reported.

Phylogeny and conservation of plant U2A/U2A', a core splicing component in U2 spliceosomal complex.

This study systematically identifies 112 U2A genes from 80 plant species by combinatory bioinformatics analysis, which is important for understanding their phylogenetic history, expression profiles and for predicting specific functions. In eukaryotes, a pre-mRNA can generate multiple transcripts by removing certain introns and joining corresponding exons, thus greatly expanding the transcriptome and proteome diversity. The spliceosome is a mega-Dalton ribonucleoprotein (RNP) complex that is essential for the process of splicing.

Insight into the Systematics of Novel Entomopathogenic Fungi Associated with Armored Scale Insect, (Hemiptera: Diaspididae) in China.

This study led to the discovery of three entomopathogenic fungi associated with , a scale insect on (fishscale bamboo) and (bitter bamboo) in China. Two of these species belong to : X.L.

Phylogenetic comparison and splice site conservation of eukaryotic U1 snRNP-specific U1-70K gene family.

Eukaryotic cells can expand their coding ability by using their splicing machinery, spliceosome, to process precursor mRNA (pre-mRNA) into mature messenger RNA. The mega-macromolecular spliceosome contains multiple subcomplexes, referred to as small nuclear ribonucleoproteins (snRNPs). Among these, U1 snRNP and its central component, U1-70K, are crucial for splice site recognition during early spliceosome assembly.

SWATH-MS-Based Proteomics: Strategies and Applications in Plants.

Most applied proteomic approaches require labeling steps. Recent technological advances provide an alternative label-free proteomics approach: SWATH-MS. This powerful tool is now widely used in animal studies but has drawn far less attention in plants.

Morpho-molecular diversity of Linocarpaceae (Chaetosphaeriales): gen. nov. from decaying branches of .

In this paper, in Linocarpaceae is introduced from in Sichuan Province, China. The new genus is characterised by its distinct morphological characters, such as ostiole with periphyses, asci with a thick doughnut-shaped, J- apical ring and clavate ascospore without septum-like band and appendage. Maximum Likelihood and Bayesian Inference phylogenetic analyses, based on DNA sequence data from ITS, LSU, SSU and TEF-1α regions, provide further evidence that the fungus is a distinct genus within this family.

Comprehensive transcriptome and proteome analyses reveal a novel sodium chloride responsive gene network in maize seed tissues during germination.

Germination is a plant developmental process by which radicle of mature seeds start to penetrate surrounding barriers for seedling establishment and multiple environmental factors have been shown to affect it. Little is known how high salinity affects seed germination of C4 plant, Zea mays. Preliminary germination assay suggested that isolated embryo alone was able to germinate under 200 mM NaCl treatment, whereas the intact seeds were highly repressed.

Full-Length Transcript-Based Proteogenomics of Rice Improves Its Genome and Proteome Annotation.

Rice () molecular breeding has gained considerable attention in recent years, but inaccurate genome annotation hampers its progress and functional studies of the rice genome. In this study, we applied single-molecule long-read RNA sequencing (lrRNA_seq)-based proteogenomics to reveal the complexity of the rice transcriptome and its coding abilities. Surprisingly, approximately 60% of loci identified by lrRNA_seq are associated with natural antisense transcripts (NATs).

SWATH-MS-facilitated proteomic profiling of fruit skin between Fuji apple and a red skin bud sport mutant.

Background: Apple is one of the most popular fruit crops world-wide and its skin color is an important quality consideration essential for commercial value. However, the strategy on genetic breeding for red skin apple and the genetic basis of skin color differentiation is very limited and still largely unknown.

Results: Here, we reported a bud sport mutant of Fuji apple with red skin color and enhanced anthocyanins accumulation.

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight.

Rhizosheath comprises soil that adheres firmly to roots. In this study, two ecotypes of switchgrass with different rhizosheath sizes after drought stress were analyzed which showed metabolic differences under drought conditions. The rhizosheath comprises soil that adheres firmly to roots by a combination of root hairs and mucilage and may aid in root growth under soil drying.

Abscisic Acid Regulates Auxin Distribution to Mediate Maize Lateral Root Development Under Salt Stress.

Roots are important plant organs. Lateral root (LR) initiation (LRI) and development play a central role in environmental adaptation. The mechanism of LR development has been well investigated in .

gen. et sp. nov. (Phaeosphaeriaceae, Pleosporales) on (Poaceae) from Sichuan Province, China.

sp. nov. was found on collected from Sichuan Province in China and is introduced in a new genus gen.

Alternative splicing and translation play important roles in hypoxic germination in rice.

Post-transcriptional mechanisms (PTMs), including alternative splicing (AS) and alternative translation initiation (ATI), may explain the diversity of proteins involved in plant development and stress responses. Transcriptional regulation is important during the hypoxic germination of rice seeds, but the potential roles of PTMs in this process have not been characterized. We used a combination of proteomics and RNA sequencing to discover how AS and ATI contribute to plant responses to hypoxia.

Genome-wide identification and functional analysis of the splicing component SYF2/NTC31/p29 across different plant species.

This study systematically identifies plant SYF2/NTC31/p29 genes from 62 plant species by a combinatory bioinformatics approach, revealing the importance of this gene family in phylogenetics, duplication, transcriptional, and post-transcriptional regulation. Alternative splicing is a post-transcriptional regulatory mechanism, which is critical for plant development and stress responses. The entire process is strictly attenuated by a complex of splicing-related proteins, designated splicing factors.

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants.

Background: The next-generation sequencing (NGS) technology has greatly facilitated genomic and transcriptomic studies, contributing significantly in expanding the current knowledge on genome and transcriptome. However, the continually evolving variety of sequencing platforms, protocols and analytical pipelines has led the research community to focus on cross-platform evaluation and standardization. As a NGS pioneer in China, the Beijing Genomics Institute (BGI) has announced its own NGS platform designated as BGISEQ-500, since 2016.