A large number of noncoding circular RNAs (circRNAs) with regulatory potency have been identified in animals, but little attention has been given to plant circRNAs.
We performed genome-wide ...identification of circRNAs in Oryza sativa and Arabidopsis thaliana using publically available RNA-Seq data, analyzed and compared features of plant and animal circRNAs.
circRNAs (12037 and 6012) were identified in Oryza sativa and Arabidopsis thaliana, respectively, with 56% (10/18) of the sampled rice exonic circRNAs validated experimentally. Parent genes of over 700 exonic circRNAs were orthologues between rice and Arabidopsis, suggesting conservation of circRNAs in plants. The introns flanking plant circRNAs were much longer than introns from linear genes, and possessed less repetitive elements and reverse complementary sequences than the flanking introns of animal circRNAs. Plant circRNAs showed diverse expression patterns, and 27 rice exonic circRNAs were found to be differentially expressed under phosphate-sufficient and -starvation conditions. A significantly positive correlation was observed for the expression profiles of some circRNAs and their parent genes.
Our results demonstrated that circRNAs are widespread in plants, revealed the common and distinct features of circRNAs between plants and animals, and suggested that circRNAs could be a critical class of noncoding regulators in plants.
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The debilitating effects on hand function from a number of a neurologic disorders has given rise to the development of rehabilitative robotic devices aimed at restoring hand function in these ...patients. To combat the shortcomings of previous traditional robotics, soft robotics are rapidly emerging as an alternative due to their inherent safety, less complex designs, and increased potential for portability and efficacy. While several groups have begun designing devices, there are few devices that have progressed enough to provide clinical evidence of their design's therapeutic abilities. Therefore, a global review of devices that have been previously attempted could facilitate the development of new and improved devices in the next step towards obtaining clinical proof of the rehabilitative effects of soft robotics in hand dysfunction.
A literature search was performed in SportDiscus, Pubmed, Scopus, and Web of Science for articles related to the design of soft robotic devices for hand rehabilitation. A framework of the key design elements of the devices was developed to ease the comparison of the various approaches to building them. This framework includes an analysis of the trends in portability, safety features, user intent detection methods, actuation systems, total DOF, number of independent actuators, device weight, evaluation metrics, and modes of rehabilitation.
In this study, a total of 62 articles representing 44 unique devices were identified and summarized according to the framework we developed to compare different design aspects. By far, the most common type of device was that which used a pneumatic actuator to guide finger flexion/extension. However, the remainder of our framework elements yielded more heterogeneous results. Consequently, those results are summarized and the advantages and disadvantages of many design choices as well as their rationales were highlighted.
The past 3 years has seen a rapid increase in the development of soft robotic devices for hand rehabilitative applications. These mostly preclinical research prototypes display a wide range of technical solutions which have been highlighted in the framework developed in this analysis. More work needs to be done in actuator design, safety, and implementation in order for these devices to progress to clinical trials. It is our goal that this review will guide future developers through the various design considerations in order to develop better devices for patients with hand impairments.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
More than half of the calories consumed by humans are provided by three major cereal crops (rice, maize, and wheat). Orphan crops are usually well adapted to low-input agricultural conditions, and ...they not only play vital roles in local areas but can also contribute to food and nutritional needs worldwide. Interestingly, many wild relatives of orphan crops are important weeds of major crops. Although orphan crops and their wild relatives have received little attentions from researchers for many years, genomic studies have recently been performed on these plants. Here, we provide an overview of genomic studies on orphan crops, with a focus on orphan cereals and their wild relatives. The genomes of at least 12 orphan cereals and/or their wild relatives have been sequenced. In addition to genomic benefits for orphan crop breeding, we discuss the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives (including weeds) and provide perspectives on genetic improvement of both orphan and major crops (including de novo domestication of orphan crops) in the coming genomic era.
Orphan crops play important roles in global food and nutrition security and represent a broad gene pool. This article provides an overview of genomic studies on orphan crops and their wild relatives (including weeds) and discusses the potential ways for mutual utilization of genomic data from major crops, orphan crops, and their wild relatives.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Summary
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared with its parents. The underlying molecular basis for heterosis, particularly ...for allopolyploids, remains elusive. In this study we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormone (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines. We also found evidence for decreased expression divergence of the homoeologous gene pairs in the allopolyploid F1 hybrids and suggest that high‐parental expression‐level dominance plays an important role in heterosis. Small RNA and methylation studies aimed at examining the epigenetic effect of the changes in gene expression level in the F1 hybrids showed that the majority of the small interfering RNA (siRNA) clusters had a higher expression level in the F1 hybrids than in the parents, and that there was an increase in genome‐wide DNA methylation in the F1 hybrid. Transposable elements associated with siRNA clusters had a higher level of methylation and a lower expression level in the F1 hybrid, implying that the non‐additively expressed siRNA clusters resulted in lower activity of the transposable elements through DNA methylation in the hybrid. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms contribute to heterosis during early flower development in allopolyploid B. napus.
Significance Statement
We found that the majority of small interfering RNA clusters had a higher expression level in F1 hybrids than in the parents, and there was an increase in the genome‐wide DNA methylation of F1 hybrids. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms play in heterosis during early flower development in allopolyploid B. napus.
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Recent origination of circular RNAs in plants Chu, Qinjie; Ding, Yuwen; Xu, Xiaoxu ...
The New phytologist,
January 2022, 2022-01-00, 20220101, Volume:
233, Issue:
1
Journal Article
Peer reviewed
Open access
Summary
Circular RNA (circRNA) is a kind of new regulatory RNA with diverse biological functions. Numerous circRNAs have been identified in many plant species; however, evolution of plant circRNAs ...remains largely unknown.
In this study, we assembled full‐length sequences of 6519 rice (Oryza sativa) circRNAs and analyzed their conservation in another 46 plant species based on comparison of sequences and expression patterns.
We found that, at the genomic level, 8.7% of the 6519 circRNAs were conserved in dicotyledonous plants and 49.1% in Oryza genus. Meanwhile, 57.8% of parental protein‐coding genes of the rice circRNAs originated recently after divergence of monocotyledonous plants, implying recent origin of the majority of rice circRNAs, a conclusion further supported by the results based on analysis of 4663 full‐length circRNAs in Arabidopsis thaliana. Accordingly, we proposed three models to address the origination of different types of circRNAs.
Taken together, the results obtained in this study provide new insights for the evolutionary dynamics of plant circRNAs and candidate circRNAs for further functional exploration.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SBCE, SBMB, UL, UM, UPUK
A total of 2 542 lincRNAs were identified from Populus trichocarpa and some of them play key roles in drought stress tolerance or regulate microRNA through target mimicry patterns.
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Over past several years, machine learning, or more generally artificial intelligence, has generated overwhelming research interest and attracted unprecedented public attention. As tomographic imaging ...researchers, we share the excitement from our imaging perspective item 1) in the Appendix, and organized this special issue dedicated to the theme of "Machine learning for image reconstruction." This special issue is a sister issue of the special issue published in May 2016 of this journal with the theme "Deep learning in medical imaging" item 2) in the Appendix. While the previous special issue targeted medical image processing/analysis, this special issue focuses on data-driven tomographic reconstruction. These two special issues are highly complementary, since image reconstruction and image analysis are two of the main pillars for medical imaging. Together we cover the whole workflow of medical imaging: from tomographic raw data/features to reconstructed images and then extracted diagnostic features/readings.
Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, ...but the evolution of rice is still under debate.
Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice.
This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
Abstract
Circular RNA (circRNA) is a kind of covalently closed single-stranded RNA molecules that have been proved to play important roles in transcriptional regulation of genes in diverse species. ...With the rapid development of bioinformatics tools, a huge number (95143) of circRNAs have been identified from different plant species, providing an opportunity for uncovering the overall characteristics of plant circRNAs. Here, based on publicly available circRNAs, we comprehensively analyzed characteristics of plant circRNAs with the help of various bioinformatics tools as well as in-house scripts and workflows, including the percentage of coding genes generating circRNAs, the frequency of alternative splicing events of circRNAs, the non-canonical splicing signals of circRNAs and the networks involving circRNAs, miRNAs and mRNAs. All this information has been integrated into an upgraded online database, PlantcircBase 3.0 (http://ibi.zju.edu.cn/plantcircbase/). In this database, we provided browse, search and visualization tools as well as a web-based blast tool, BLASTcirc, for prediction of circRNAs from query sequences based on searching against plant genomes and transcriptomes.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
SUMMARY
Momilactone A, an important plant labdane‐related diterpenoid, functions as a phytoalexin against pathogens and an allelochemical against neighboring plants. The genes involved in the ...biosynthesis of momilactone A are found in clusters, i.e., momilactone A biosynthetic gene clusters (MABGCs), in the rice and barnyardgrass genomes. In addition, we know little about the origin and evolution of MABGCs. Here, we integrated results from comprehensive phylogeny and comparative genomic analyses of the core genes of MABGC‐like clusters and MABGCs in 40 monocot plant genomes, providing convincing evidence for the birth and evolution of MABGCs in grass species. The MABGCs found in the PACMAD clade of the core grass lineage (including Panicoideae and Chloridoideae) originated from a MABGC‐like cluster in Triticeae (BOP clade) via lateral gene transfer (LGT) and followed by recruitment of MAS1/2 and CYP76L1 genes. The MABGCs in Oryzoideae originated from PACMAD through another LGT event and lost CYP76L1 afterwards. The Oryza MABGC and another Oryza diterpenoid cluster c2BGC are two distinct clusters, with the latter originating from gene duplication and relocation within Oryzoideae. Further comparison of the expression patterns of the MABGC genes between rice and barnyardgrass in response to pathogen infection and allelopathy provides novel insights into the functional innovation of MABGCs in plants. Our results demonstrate LGT‐mediated origination of MABGCs in grass and shed lights into the evolutionary innovation and optimization of plant biosynthetic pathways.
Significance Statement
How biosynthetic gene clusters (BGCs) originate and evolve is less known in eukaryotes. Momilactone A, an important defensive and allelopathic secondary chemical in plants, is synthesized by momilactone A BGCs (MABGCs). By exploiting the phylogeny and comparative genomics of the core genes of MABGC‐like clusters and MABGCs across 40 plant species, we reconstruct the evolutionary trajectory of MABGCs in grass, i.e., the PACMAD clade (including Panicoideae and Chloridoideae) acquired MABGCs from Triticeae via lateral gene transfer (LGT) of a MABGC‐like cluster and another LGT event passed the PACMAD MABGC on to Oryza. The composition of MABGCs is dynamic with gain and/or loss of genes in the recipient species after LGT. The study demonstrates that, like prokaryotes, plants are capable of moving a cluster of genes involved in the same biosynthesis pathway by LGT. The results shed light into the evolutionary innovation of BGCs and optimization of a biosynthetic pathway via synthetic biology.
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