Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice

Fusion transcripts in plants: hidden layer of transcriptome complexity

In the realm of genetic information, fusion transcripts contribute to the intricate complexity of the transcriptome across various organisms. Recently, Cong et al. investigated these RNAs in rice, maize, soybean, and arabidopsis (Arabidopsis thaliana), revealing conserved characteristics. These findings enhance our understanding of the functional roles and evolutionary significance of these fusion transcripts.

The landscape of fusion transcripts in plants: a new insight into genome complexity

BACKGROUND

Fusion transcripts (FTs), generated by the fusion of genes at the DNA level or RNA-level splicing events significantly contribute to transcriptome diversity. FTs are usually considered unique features of neoplasia and serve as biomarkers and therapeutic targets for multiple cancers. The latest findings show the presence of FTs in normal human physiology. Several discrete reports mentioned the presence of fusion transcripts in planta, has important roles in stress responses, morphological alterations, or traits (e.g. seed size, etc.).

RESULTS

In this study, we identified 169,197 fusion transcripts in 2795 transcriptome datasets of Arabidopsis thaliana, Cicer arietinum, and Oryza sativa by using a combination of tools, and confirmed the translational activity of 150 fusion transcripts through proteomic datasets. Analysis of the FT junction sequences and their association with epigenetic factors, as revealed by ChIP-Seq datasets, demonstrated an organised process of fusion formation at the DNA level. We investigated the possible impact of three-dimensional chromatin conformation on intra-chromosomal fusion events by leveraging the Hi-C datasets with the incidence of fusion transcripts. We further utilised the long-read RNA-Seq datasets to validate the most reoccurring fusion transcripts in each plant species followed by further authentication through RT-PCR and Sanger sequencing.

CONCLUSIONS

Our findings suggest that a significant portion of fusion events may be attributed to alternative splicing during transcription, accounting for numerous fusion events without a proportional increase in the number of RNA pairs. Even non-nuclear DNA transcripts from mitochondria and chloroplasts can participate in intra- and inter-chromosomal fusion formation. Genes in close spatial proximity are more prone to undergoing fusion formation, especially in intra-chromosomal FTs. Most of the fusion transcripts may not undergo translation and serve as long non-coding RNAs. The low validation rate of FTs in plants indicated that the fusion transcripts are expressed at very low levels, like in the case of humans. FTs often originate from parental genes involved in essential biological processes, suggesting their relevance across diverse tissues and stress conditions. This study presents a comprehensive repository of fusion transcripts, offering valuable insights into their roles in vital physiological processes and stress responses.

PFusionDB: a comprehensive database of plant-specific fusion transcripts

Fusion transcripts (FTs) are well known cancer biomarkers, relatively understudied in plants. Here, we developed PFusionDB (www.nipgr.ac.in/PFusionDB), a novel plant-specific fusion-transcript database. It is a comprehensive repository of 80,170, 39,108, 83,330, and 11,500 unique fusions detected in 1280, 637, 697, and 181 RNA-Seq samples of Arabidopsis thaliana, Oryza sativa japonica, Oryza sativa indica, and Cicer arietinum respectively. Here, a total of 76,599 (Arabidopsis thaliana), 35,480 (Oryza sativa japonica), 72,099 (Oryza sativa indica), and 9524 (Cicer arietinum) fusion transcripts are non-recurrent i.e., only found in one sample. Identification of FTs was performed by using a total of five tools viz. EricScript-Plants, STAR-Fusion, TrinityFusion, SQUID, and MapSplice. At PFusionDB, available fundamental details of fusion events includes the information of parental genes, junction sequence, expression levels of fusion transcripts, breakpoint coordinates, strand information, tissue type, treatment information, fusion type, PFusionDB ID, and Sequence Read Archive (SRA) ID. Further, two search modules: 'Simple Search' and 'Advanced Search', along with a 'Browse' option to data download, are present for the ease of users. Three distinct modules viz. 'BLASTN', 'SW Align', and 'Mapping' are also available for efficient query sequence mapping and alignment to FTs. PFusionDB serves as a crucial resource for delving into the intricate world of fusion transcript in plants, providing researchers with a foundation for further exploration and analysis. Database URL: www.nipgr.ac.in/PFusionDB.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04132-1.

Orphan gene BR2 positively regulates bolting resistance through the vernalization pathway in Chinese cabbage

Orphan genes (OGs) are unique to the specific species or lineage, and whose homologous sequences cannot be found in other species or lineages. Furthermore, these genes lack recognizable domains or functional motifs, which make their characterization difficult. Here, we identified a Brassica rapa  OG named BOLTING RESISTANCE 2 (BR2) that could positively modulate bolting resistance. The expression of BR2 was developmentally regulated and the BR2 protein was localized to the cell membrane. BR2 overexpression not only markedly delayed flowering time in Arabidopsis transgenic plants, but substantially affected the development of leaves and flower organs. Flowering repressor AtFLC gene was significantly up-regulated transcribed in Arabidopsis BR2 overexpression lines, while AtFT and AtSOC1 expression was decreased. In addition, the BR2 expression was enhanced in bolting-resistant type Chinese cabbage and was reduced in non-resistant type. Moreover, chilling stress inhibited the BR2 expression levels. Overexpression of BR2 also delayed flowering time in Chinese cabbage. In vernalized Chinese cabbage BR2 overexpression plants, BrVIN3.b and BrFRI were significantly down-regulated, while BrFLC5 was substantially up-regulated. Key floral factors, including three BrSOC1s, two BrLFYs, and four BrFTs were down-regulated. The expression changes of these key genes were consistent with the delayed flowering phenotype of Chinese cabbage BR2 overexpressing plants. Thus, we predicted that BR2 may predominantly function via the vernalization pathway. Our findings propose that the OG  BR2 acts as a novel modulator of flowering time in Chinese cabbage, which provides a new insight on the breeding of varieties that are resistant to bolting.

Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh

Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

The ORFans' tale: new insights in plant biology

Orphan genes (OGs) are protein-coding genes without a significant sequence similarity in closely related species. Despite their functional importance, very little is known about the underlying molecular mechanisms by which OGs participate in diverse biological processes. Here, we discuss the evolutionary mechanisms of OGs' emergence with relevance to species-specific adaptations. We also provide a mechanistic view of the involvement of OGs in multiple processes, including growth, development, reproduction, and carbon-metabolism-mediated immunity. We highlight the interconnection between OGs and the sucrose nonfermenting 1 (SNF1)-related protein kinases (SnRKs)-target of rapamycin (TOR) signaling axis for phytohormone signaling, nutrient metabolism, and stress responses. Finally, we propose a high-throughput pipeline for OGs' interspecies and intraspecies gene transfer through a transgenic approach for future biotechnological advances.

Rice domestication-associated transcription factor PROSTRATE GROWTH 1 controls plant and panicle architecture by regulating the expression of LAZY 1 and OsGIGANTEA, respectively

Plant architecture and panicle architecture are two critical agronomic traits that greatly affect the yield of rice (Oryza sativa). PROSTRATE GROWTH 1 (PROG1) encodes a key C2H2-type zinc-finger transcription factor and has pleiotropic effects on the regulation of both plant and panicle architecture, thereby influencing the grain yield. However, the molecular mechanisms through which PROG1 controls plant and panicle architecture remain unclear. In this study, we showed that PROG1 directly binds the LAZY 1 (LA1) promoter and acts as a repressor to inhibit LA1 expression. Conversely, LA1 acts as a repressor of PROG1 by directly binding to the PROG1 promoter. These two genes play antagonistic roles in shaping plant architecture by regulating both tiller angle and tiller number. Interestingly, our data showed that PROG1 controls panicle architecture through direct binding to the intragenic regulatory regions of OsGIGANTEA (OsGI) and subsequent activation of its expression. Collectively, we have identified two crucial targets of PROG1, LA1 and OsGI, shedding light on the molecular mechanisms underlying plant and panicle architecture control by PROG1. Our study provides valuable insights into the regulation of key domestication-related traits in rice and identifies potential targets for future high-yield rice breeding.

Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis

Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.

Research Advances and Prospects of Orphan Genes in Plants

Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.

Molecular and Genetic Aspects of Grain Number Determination in Rice (Oryza sativa L.)

Rice grain yield is a complex trait determined by three components: panicle number, grain number per panicle (GNPP) and grain weight. GNPP is the major contributor to grain yield and is crucial for its improvement. GNPP is determined by a series of physiological and biochemical steps, including inflorescence development, formation of rachis branches such as primary rachis branches and secondary rachis branches, and spikelet specialisation (lateral and terminal spikelets). The molecular genetic basis of GNPP determination is complex, and it is regulated by numerous interlinked genes. In this review, panicle development and the determination of GNPP is described briefly, and GNPP-related genes that influence its determination are categorised according to their regulatory mechanisms. We introduce genes related to rachis branch development and their regulation of GNPP, genes related to phase transition (from rachis branch meristem to spikelet meristem) and their regulation of GNPP, and genes related to spikelet specialisation and their regulation of GNPP. In addition, we describe other GNPP-related genes and their regulation of GNPP. Research on GNPP determination suggests that it is possible to cultivate rice varieties with higher grain yield by modifying GNPP-related genes.

A Novel Mutation of the NARROW LEAF 1 Gene Adversely Affects Plant Architecture in Rice (Oryza sativa L.)

Plant architecture is critical for enhancing the adaptability and productivity of crop plants. Mutants with an altered plant architecture allow researchers to elucidate the genetic network and the underlying mechanisms. In this study, we characterized a novel nal1 rice mutant with short height, small panicle, and narrow and thick deep green leaves that was identified from a cross between a rice cultivar and a weedy rice accession. Bulked segregant analysis coupled with genome re-sequencing and cosegregation analysis revealed that the overall mutant phenotype was caused by a 1395-bp deletion spanning over the last two exons including the transcriptional end site of the nal1 gene. This deletion resulted in chimeric transcripts involving nal1 and the adjacent gene, which were validated by a reference-guided assembly of transcripts followed by PCR amplification. A comparative transcriptome analysis of the mutant and the wild-type rice revealed 263 differentially expressed genes involved in cell division, cell expansion, photosynthesis, reproduction, and gibberellin (GA) and brassinosteroids (BR) signaling pathways, suggesting the important regulatory role of nal1. Our study indicated that nal1 controls plant architecture through the regulation of genes involved in the photosynthetic apparatus, cell cycle, and GA and BR signaling pathways.

Identification of Orphan Genes in Unbalanced Datasets Based on Ensemble Learning

Orphan genes are associated with regulatory patterns, but experimental methods for identifying orphan genes are both time-consuming and expensive. Designing an accurate and robust classification model to detect orphan and non-orphan genes in unbalanced distribution datasets poses a particularly huge challenge. Synthetic minority over-sampling algorithms (SMOTE) are selected in a preliminary step to deal with unbalanced gene datasets. To identify orphan genes in balanced and unbalanced Arabidopsis thaliana gene datasets, SMOTE algorithms were then combined with traditional and advanced ensemble classified algorithms respectively, using Support Vector Machine, Random Forest (RF), AdaBoost (adaptive boosting), GBDT (gradient boosting decision tree), and XGBoost (extreme gradient boosting). After comparing the performance of these ensemble models, SMOTE algorithms with XGBoost achieved an F1 score of 0.94 with the balanced A. thaliana gene datasets, but a lower score with the unbalanced datasets. The proposed ensemble method combines different balanced data algorithms including Borderline SMOTE (BSMOTE), Adaptive Synthetic Sampling (ADSYN), SMOTE-Tomek, and SMOTE-ENN with the XGBoost model separately. The performances of the SMOTE-ENN-XGBoost model, which combined over-sampling and under-sampling algorithms with XGBoost, achieved higher predictive accuracy than the other balanced algorithms with XGBoost models. Thus, SMOTE-ENN-XGBoost provides a theoretical basis for developing evaluation criteria for identifying orphan genes in unbalanced and biological datasets.