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Main conclusion
Alternative splicing EVENTS were genome-wide identified for four legume species, and nitrogen fixation-related gene families and evolutionary analysis was also performed.
Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. Investigation of the genome-wide conserved AS eve...
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Rhizobial infection of legume roots during development of nitrogen fixing root nodules occurs either intracellularly though plant derived infection threads traversing the epidermal and cortical cell layers to deliver the bacteria or intercellularly via bacterial entry between epidermal plant cells. Although, around 25% of all legume genera are post...
Citations
... Additionally, the computed incidence of AS in V. mungo (42.4%) is lower than Arabidopsis (61%) yet substantially greater when compared to Oryza sativa (21.2%). Considering the legumes, the share of the AS genes is marginally higher than those reported in V. radiata (37.9%) (Satyawan et al. 2017), soybean (38.87%), chickpea (33.7%), and Medicago (28.39%) (Wang et al. 2019), thereby bringing the proportion closer to other legume species. In accordance with the findings of Koralewski and Krutovsky (2011), the close association between exon length and exon number suggests a propensity of multiexon genes with short exons in V. mungo. ...
Vigna mungo, a highly consumed crop in the pan-Asian countries, is vulnerable to several biotic and abiotic stresses. Understanding the post-transcriptional gene regulatory cascades, especially alternative splicing (AS), may underpin large-scale genetic improvements to develop stress-resilient varieties. Herein, a transcriptome based approach was undertaken to decipher the genome-wide AS landscape and splicing dynamics in order to establish the intricacies of their functional interactions in various tissues and stresses. RNA sequencing followed by high-throughput computational analyses identified 54,526 AS events involving 15,506 AS genes that generated 57,405 transcripts isoforms. Enrichment analysis revealed their involvement in diverse regulatory functions and demonstrated that transcription factors are splicing-intensive, splice variants of which are expressed differentially across tissues and environmental cues. Increased expression of a splicing regulator NHP2L1/SNU13 was found to co-occur with lower intron retention events. The host transcriptome is significantly impacted by differential isoform expression of 1172 and 765 AS genes that resulted in 1227 (46.8% up and 53.2% downregulated) and 831 (47.5% up and 52.5% downregulated) transcript isoforms under viral pathogenesis and Fe2+ stressed condition, respectively. However, genes experiencing AS operate differently from the differentially expressed genes, suggesting AS is a unique and independent mode of regulatory mechanism. Therefore, it can be inferred that AS mediates a crucial regulatory role across tissues and stressful situations and the results would provide an invaluable resource for future endeavours in V. mungo genomics.
... A total of 14,070 complete and 19,983 internal AS events were obtained from 30% of all consensus expression genes corresponding to those reported earlier in rice (48%), Arabidopsis (61%), and maize (40%) [2][3][4]. In addition, the frequency of AS events in lotus is also comparable with that in Lotus japonicus (~30%) and Medicago truncatula (~28%) [32]. Among them, 445 complete AS also contain the internal AS events. ...
Sacred lotus (Nelumbo nucifera) is a typical aquatic plant, belonging to basal eudicot plant, which is ideal for genome and genetic evolutionary study. Understanding lotus gene diversity is important for the study of molecular genetics and breeding. In this research, public RNA-seq data and the annotated reference genome were used to identify the genes in lotus. A total of 26,819 consensus and 1,081 novel genes were identified. Meanwhile, a comprehensive analysis of gene alternative splicing events was conducted, and a total of 19,983 “internal” alternative splicing (AS) events and 14,070 “complete” AS events were detected in 5,878 and 5,881 multi-exon expression genes, respectively. Observations made from the AS events show the predominance of intron retention (IR) subtype of AS events representing 33%. IR is followed by alternative acceptor (AltA), alternative donor (AltD) and exon skipping (ES), highlighting the universality of the intron definition model in plants. In addition, functional annotations of the gene with AS indicated its relationship to a number of biological processes such as cellular process and metabolic process, showing the key role for alternative splicing in influencing the growth and development of lotus. The results contribute to a better understanding of the current gene diversity in lotus, and provide an abundant resource for future functional genome analysis in lotus.
... Similarly, differential expression changes in chlorophyll-and photosynthesis-related genes, together with a disturbance of carbohydrates, were found in heat-treated rice anthers . In rice, salicylic acid may increase the HS tolerance of pollen mother cells through hydrogen peroxide (H 2 O 2 )mediated signaling pathways (Feng et al., 2018) and catalase (CAT)mediated detoxification of reactive oxygen species (ROS) (Zhao et al., 2018;Gong et al., 2019). Furthermore, the exogenous application of abscisic acid prior to HS enhanced sucrose transport and accelerated sucrose metabolism to maintain the carbon balance and energy homeostasis, which consequently mitigated the heat damage to anthers (Rezaul et al., 2019). ...
... The same genes from different rice genotypes carried out differential AS regulations in response to salt stress stimulation (Jian et al., 2022). Interestingly, not only growth conditions but also nutrition status affect AS regulation of related genes in different plants (Zhang Y. M. et al., 2012;Li H. et al., 2016;Nishida et al., 2017;Wang et al., 2019). For example, nutrient stress caused differential AS regulation of the NRR gene in rice (Zhang Y. M. et al., 2012). ...
Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA ), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.
... Among the four mechanisms (ES, IR, A5SS, A3SS) [29], ES is the most common in animals, whereas IR is more frequent in plants. For example, IR and ES account for 3% and 40% of all AS events in human [30], and 43.86% and 8.68% of all AS events in 84K poplar leaves, respectively. ...
Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar ( P . alba × P . glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.
... Although the functions of alternative splicing in animals and plants are similar, some differences exist between them in some aspects. For example, intron retention (IR) has been reported to be the most frequent AS event in plants, whereas exon skipping (ES) is the major type in humans and animals (Xu et al., 2002;Wang et al., 2008;Ruan et al., 2018;Ma et al., 2019;Wang Z. et al., 2019). The Suppressor of Morphological defects on Genitalia (SMG) gene family (SMG 1-7), which plays an important role in the AS-coupled-NMD pathway, has been widely reported in animals; however, no SMG 5 and SMG 6 paralogs have been identified in plants. ...
Alternative splicing (AS) plays pivotal roles in regulating plant growth and development, flowering, biological rhythms, signal transduction, and stress responses. However, no studies on AS have been performed in Liriodendron chinense, a deciduous tree species that has high economic and ecological value. In this study, we used multiple tools and algorithms to analyze transcriptome data derived from seven tissues via hybrid sequencing. Although only 17.56% (8,503/48,408) of genes in L. chinense were alternatively spliced, these AS genes occurred in 37,844 AS events. Among these events, intron retention was the most frequent AS event, producing 1,656 PTC-containing and 3,310 non-PTC-containing transcripts. Moreover, 183 long noncoding RNAs (lncRNAs) also underwent AS events. Furthermore, weighted gene coexpression network analysis (WGCNA) revealed that there were great differences in the activities of transcription and post-transcriptional regulation between pistils and leaves, and AS had an impact on many physiological and biochemical processes in L. chinense, such as photosynthesis, sphingolipid metabolism, fatty acid biosynthesis and metabolism. Moreover, our analysis showed that the features of genes may affect AS, as AS genes and non-AS genes had differences in the exon/intron length, transcript length, and number of exons/introns. In addition, the structure of AS genes may impact the frequencies and types of AS because AS genes with more exons or introns tended to exhibit more AS events, and shorter introns tended to be retained, whereas shorter exons tended to be skipped. Furthermore, eight AS genes were verified, and the results were consistent with our analysis. Overall, this study reveals that AS and gene interaction are mutual—on one hand, AS can affect gene expression and translation, while on the other hand, the structural characteristics of the gene can also affect AS. This work is the first to comprehensively report on AS in L. chinense, and it can provide a reference for further research on AS in L. chinense.
... Alternative splicing (AS) is a key regulatory mechanism that increases proteome diversity. A comparative analysis of the AS landscape across four legume species (soybean, M. truncatula, L. japonicus and Cicer arietinum) revealed that the percentage of nitrogen fixation-related genes subjected to AS ranges from 27% to 43% depending on the species [32]. The study of Traubenik et al. also evaluated the translational status of alternative spliced variants at genome-wide level, identifying 122 genes with one or more AS variants differentially translated in response to rhizobia. ...
Many plant NLR (nucleotide-binding, leucine-rich repeat) immune receptors require other NLRs for their function. In pairs of chromosomally adjacent sensor/helper NLRs, the sensor typically carries an integrated domain (ID) that mimics the authentic target of a pathogen effector. The RPW8-NLR clade supports the function of many diverse plant NLRs, particularly those with a TIR N-terminal domain, in concert with a family of EP-domain containing signalling partners. The NRC clade of NLRs are required for the function of many unlinked sensor NLRs in Solanaceous plants. We evaluate recent advances in paired NLR biology in the context of the structure and possible mechanisms of the first defined plant inflammasome containing ZAR1.
... Alternative splicing (AS) is a key regulatory mechanism that increases proteome diversity. A comparative analysis of the AS landscape across four legume species (soybean, M. truncatula, L. japonicus and Cicer arietinum) revealed that the percentage of nitrogen fixation-related genes subjected to AS ranges from 27% to 43% depending on the species [32]. The study of Traubenik et al. also evaluated the translational status of alternative spliced variants at genome-wide level, identifying 122 genes with one or more AS variants differentially translated in response to rhizobia. ...
Post-transcriptional control of gene expression allows plants to rapidly adapt to changes in their environment. Under low nitrogen conditions, legume plants engage into a symbiosis with soil bacteria that results in the formation of root nodules, where bacteria are allocated and fix atmospheric nitrogen for the plant’s benefit. Recent studies highlighted the importance of small RNA-mediated mechanisms in the control of bacterial infection, nodule organogenesis, and the long-distance signaling that balances plant growth and nodulation. Examples of such mechanisms are shoot-to-root mobile microRNAs and small RNA fragments derived from degradation of bacterial transfer RNAs that repress complementary mRNAs in the host plant. Mechanisms of selective mRNA translation also contribute to rapidly modulate the expression of nodulation genes in a cell-specific manner during symbiosis. Here, the most recent advances made on the regulation of mRNA stability and translatability, and the emerging roles of long non-coding RNAs in symbiosis are summarized.
... TGS methods have been applied in sequencing of animals and humans and have proven superior to short-read sequencing methods due to the advantage of obtaining full-length transcripts [16]. Thus, they can be used to identify complex AS events, which can greatly increase transcriptome diversity. ...
Background:
The number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio sequencing, whereas ONT is rarely used. Therefore, in this study, we examined ONT RNA sequencing methods in plants. We performed a detailed evaluation of reads from PacBio, Nanopore direct cDNA (ONT Dc), and Nanopore PCR cDNA (ONT Pc) sequencing including characteristics of raw data and identification of transcripts. In addition, matched Illumina data were generated for comparison.
Results:
ONT Pc showed overall better raw data quality, whereas PacBio generated longer read lengths. In the transcriptome analysis, PacBio and ONT Pc performed similarly in transcript identification, simple sequence repeat analysis, and long non-coding RNA prediction. PacBio was superior in identifying alternative splicing events, whereas ONT Pc could estimate transcript expression levels.
Conclusions:
This paper made a comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome, the results indicate that ONT Pc is more cost-effective for generating extremely long reads and can characterise the transcriptome as well as quantify transcript expression. Therefore, ONT Pc is a new cost-effective and worthwhile method for full-length single-molecule transcriptome analysis in plants.
... Mostly likely we have missed out some publications related RNA-seq applications in soybean research, however, we noticed that most of transcriptome analyses, as reviewed above, performed identification of DEGs, GO analysis and pathway analysis. Only a few of published articles carried out AS analysis (Wang et al., 2014;Aghamirzaie et al., 2015;Wang et al., 2019b;Song et al. 2020). Given the importance of AS in regulation of gene functions in growth and development and in response to various biotic and abiotic stresses (Reddy et al., 2013;Staiger and Brown, 2013), AS analysis needs to be included as an essential part of RNA-seq data analysis in plants. ...
... TGS methods have been applied in sequencing of animals and humans and have proven superior to short-read sequencing methods due to the advantage of obtaining full-length transcripts [16]. Thus, they can be used to identify complex AS events, which can greatly increase transcriptome diversity. ...
Background The number of studies using third-generation sequencing using Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research areas. Among them, plant full-length single-molecule transcriptome studies have mostly used PacBio sequencing, whereas ONT is rarely used. Therefore, in this study, we examined ONT RNA sequencing methods in plants. We performed a detailed evaluation of reads from PacBio, Nanopore direct cDNA (ONT Dc), and Nanopore PCR cDNA (ONT Pc) sequencing including characteristics of raw data and identification of transcripts. In addition, matched Illumina data were generated for comparison.
Results ONT Pc showed overall better raw data quality, whereas PacBio generated longer read lengths. In the transcriptome analysis, PacBio and ONT Pc performed similarly in transcript identification, simple sequence repeat analysis, and long non-coding RNA prediction. PacBio was superior in identifying alternative splicing events, whereas ONT Pc could estimate transcript expression levels.
Conclusions This paper made a comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome, the results indicate that ONT Pc is more cost-effective for generating extremely long reads and can characterise the transcriptome as well as quantify transcript expression. Therefore, ONT Pc is a new cost-effective and worthwhile method for full-length single-molecule transcriptome analysis in plants.
