51
|
Khemka NK, Singh U, Dwivedi AK, Jain M. Machine Learning-Based Annotation of Long Noncoding RNAs Using PLncPRO. Methods Mol Biol 2021; 2107:253-260. [PMID: 31893451 DOI: 10.1007/978-1-0716-0235-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long noncoding RNAs (lncRNAs) are noncoding RNAs with transcript length more than 200 nucleotides. Although poorly conserved, lncRNAs are expressed across diverse species, including plants and animals, and are known to be involved in regulation of various biological processes. To understand their biological significance, we first need to identify the lncRNAs accurately. However, distinguishing lncRNAs from coding transcripts is still a challenging task. Here, we describe a machine learning-based approach to accurately identify the plant lncRNAs. We describe the usage of plant long noncoding RNA prediction by random forests (PLncPRO), which employs machine learning-based random forest algorithm to recognize the lncRNAs from the set of given transcript sequences. Stepwise instructions have been provided to use PLncPRO to annotate the lncRNA sequences.
Collapse
Affiliation(s)
- Niraj K Khemka
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Urminder Singh
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj K Dwivedi
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
| |
Collapse
|
52
|
Duan Y, Zhang W, Cheng Y, Shi M, Xia XQ. A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs. RNA (NEW YORK, N.Y.) 2021; 27:80-98. [PMID: 33055239 PMCID: PMC7749630 DOI: 10.1261/rna.074724.120] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
High-throughput RNA sequencing unveiled the complexity of transcriptome and significantly increased the records of long noncoding RNAs (lncRNAs), which were reported to participate in a variety of biological processes. Identification of lncRNAs is a key step in lncRNA analysis, and a bunch of bioinformatics tools have been developed for this purpose in recent years. While these tools allow us to identify lncRNA more efficiently and accurately, they may produce inconsistent results, making selection a confusing issue. We compared the performance of 41 analysis models based on 14 software packages and different data sets, including high-quality data and low-quality data from 33 species. In addition, computational efficiency, robustness, and joint prediction of the models were explored. As a practical guidance, key points for lncRNA identification under different situations were summarized. In this investigation, no one of these models could be superior to others under all test conditions. The performance of a model relied to a great extent on the source of transcripts and the quality of assemblies. As general references, FEELnc_all_cl, CPC, and CPAT_mouse work well in most species while COME, CNCI, and lncScore are good choices for model organisms. Since these tools are sensitive to different factors such as the species involved and the quality of assembly, researchers must carefully select the appropriate tool based on the actual data. Alternatively, our test suggests that joint prediction could behave better than any single model if proper models were chosen. All scripts/data used in this research can be accessed at http://bioinfo.ihb.ac.cn/elit.
Collapse
Affiliation(s)
- You Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingyin Cheng
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mijuan Shi
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiao-Qin Xia
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
53
|
Xia W, Dou Y, Liu R, Gong S, Huang D, Fan H, Xiao Y. Genome-wide discovery and characterization of long noncoding RNAs in African oil palm ( Elaeis guineensis Jacq.). PeerJ 2020; 8:e9585. [PMID: 33194332 PMCID: PMC7643553 DOI: 10.7717/peerj.9585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 06/30/2020] [Indexed: 01/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are an important class of genes and play important roles in a range of biological processes. However, few reports have described the identification of lncRNAs in oil palm. In this study, we applied strand specific RNA-seq with rRNA removal to identify 1,363 lncRNAs from the equally mixed tissues of oil palm spear leaf and six different developmental stages of mesocarp (8–24 weeks). Based on strand specific RNA-seq data and 18 released oil palm transcriptomes, we systematically characterized the expression patterns of lncRNA loci and their target genes. A total of 875 uniq target genes for natural antisense lncRNAs (NAT-lncRNA, 712), long intergenic noncoding RNAs (lincRNAs, 92), intronic-lncRNAs (33), and sense-lncRNAs (52) were predicted. A majority of lncRNA loci (77.8%–89.6%) had low expression in 18 transcriptomes, while only 89 lncRNA loci had medium to high expression in at least one transcriptome. Coexpression analysis between lncRNAs and their target genes indicated that 6% of lncRNAs had expression patterns positively correlated with those of target genes. Based on single nucleotide polymorphism (SNP) markers derived from our previous research, 6,882 SNPs were detected for lncRNAs and 28 SNPs belonging to 21 lncRNAs were associated with the variation of fatty acid contents. Moreover, seven lncRNAs showed expression patterns positively correlated expression pattern with those of genes in de novo fatty acid synthesis pathways. Our study identified a collection of lncRNAs for oil palm and provided clues for further research into lncRNAs that may regulate mesocarp development and lipid metabolism.
Collapse
Affiliation(s)
- Wei Xia
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yajing Dou
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rui Liu
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Shufang Gong
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Haikuo Fan
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| | - Yong Xiao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, China
| |
Collapse
|
54
|
Genome-wide analysis of long non-coding RNAs responsive to multiple nutrient stresses in Arabidopsis thaliana. Funct Integr Genomics 2020; 21:17-30. [PMID: 33130916 DOI: 10.1007/s10142-020-00758-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 10/19/2020] [Accepted: 10/25/2020] [Indexed: 01/23/2023]
Abstract
Nutrient stress is the most important environmental stress that limits plant growth and development. Although recent evidence highlights the vital functions of long non-coding RNAs (lncRNA) in response to single nutrient stress in some model plants, a comprehensive investigation of the effect of lncRNAs in response to nutrient stress has not been performed in Arabidopsis thaliana. Here, we presented the identification and characterization of lncRNAs under seven nutrient stress conditions. The expression pattern analysis revealed that aberrant expression of lncRNAs is a stress-specific manner under nutrient stress conditions and that lncRNAs are more sensitive to nutrient stress than protein-coding genes (PCGs). Moreover, competing endogenous RNA (ceRNA) network and lncRNA-mRNA co-expression network (CEN) were constructed to explore the potential function of these lncRNAs under nutrient stress conditions. We further combined different expressed lncRNAs with ceRNA network and CEN to select key lncRNAs in response to nutrient stress. Together, our study provides important information for further insights into the role of lncRNAs in response to stress in plants.
Collapse
|
55
|
Li K, Ren X, Song X, Li X, Zhou Y, Harlev E, Sun D, Nevo E. Incipient sympatric speciation in wild barley caused by geological-edaphic divergence. Life Sci Alliance 2020; 3:3/12/e202000827. [PMID: 33082129 PMCID: PMC7652381 DOI: 10.26508/lsa.202000827] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022] Open
Abstract
Sympatric speciation is still contentious but here based on genome-wide analysis; we show incipient sympatric speciation of an emerging new wild barley species from Hordeum spontaneum, the progenitor of all cultivated barleys at “Evolution Plateau” (EP), Upper Galilee, Israel. Sympatric speciation (SS) has been contentious since the idea was suggested by Darwin. Here, we show in wild barley SS due to geologic and edaphic divergence in “Evolution Plateau,” Upper Galilee, Israel. Our whole genome resequencing data showed SS separating between the progenitor old Senonian chalk and abutting derivative young Pleistocene basalt wild barley populations. The basalt wild barley species unfolds larger effective population size, lower recombination rates, and larger genetic diversity. Both species populations show similar descending trend ∼200,000 yr ago associated with the last glacial maximum. Coalescent demography analysis indicates that SS was local, primary, in situ, and not due to a secondary contact from ex situ allopatric population. Adaptive divergent putatively selected genes were identified in both populations. Remarkably, disease resistant genes were selected in the wet basalt population, and genes related to flowering time, leading to temporal reproductive isolation, were selected in the chalk population. The evidence substantiates adaptive ecological SS in wild barley, highlighting the genome landscape during SS with gene flow, due to geologic-edaphic divergence.
Collapse
Affiliation(s)
- Kexin Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.,State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China.,Institute of Evolution, University of Haifa, Haifa, Israel
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaoying Song
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yu Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eli Harlev
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, Israel
| |
Collapse
|
56
|
Jha UC, Nayyar H, Jha R, Khurshid M, Zhou M, Mantri N, Siddique KHM. Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation. BMC PLANT BIOLOGY 2020; 20:466. [PMID: 33046001 PMCID: PMC7549229 DOI: 10.1186/s12870-020-02595-x] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The immobile nature of plants means that they can be frequently confronted by various biotic and abiotic stresses during their lifecycle. Among the various abiotic stresses, water stress, temperature extremities, salinity, and heavy metal toxicity are the major abiotic stresses challenging overall plant growth. Plants have evolved complex molecular mechanisms to adapt under the given abiotic stresses. Long non-coding RNAs (lncRNAs)-a diverse class of RNAs that contain > 200 nucleotides(nt)-play an essential role in plant adaptation to various abiotic stresses. RESULTS LncRNAs play a significant role as 'biological regulators' for various developmental processes and biotic and abiotic stress responses in animals and plants at the transcription, post-transcription, and epigenetic level, targeting various stress-responsive mRNAs, regulatory gene(s) encoding transcription factors, and numerous microRNAs (miRNAs) that regulate the expression of different genes. However, the mechanistic role of lncRNAs at the molecular level, and possible target gene(s) contributing to plant abiotic stress response and adaptation, remain largely unknown. Here, we review various types of lncRNAs found in different plant species, with a focus on understanding the complex molecular mechanisms that contribute to abiotic stress tolerance in plants. We start by discussing the biogenesis, type and function, phylogenetic relationships, and sequence conservation of lncRNAs. Next, we review the role of lncRNAs controlling various abiotic stresses, including drought, heat, cold, heavy metal toxicity, and nutrient deficiency, with relevant examples from various plant species. Lastly, we briefly discuss the various lncRNA databases and the role of bioinformatics for predicting the structural and functional annotation of novel lncRNAs. CONCLUSIONS Understanding the intricate molecular mechanisms of stress-responsive lncRNAs is in its infancy. The availability of a comprehensive atlas of lncRNAs across whole genomes in crop plants, coupled with a comprehensive understanding of the complex molecular mechanisms that regulate various abiotic stress responses, will enable us to use lncRNAs as potential biomarkers for tailoring abiotic stress-tolerant plants in the future.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Rintu Jha
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Muhammad Khurshid
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Nitin Mantri
- School of Science, RMIT University, Plenty Road, Bundoora. Victoria. 3083., Australia
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6001, Australia.
| |
Collapse
|
57
|
Long non-coding RNA LINC00511/miR-150/MMP13 axis promotes breast cancer proliferation, migration and invasion. Biochim Biophys Acta Mol Basis Dis 2020; 1867:165957. [PMID: 33031905 DOI: 10.1016/j.bbadis.2020.165957] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022]
Abstract
Breast cancer is the most common cancer affecting women and one of the leading causes of cancer-related deaths worldwide. In existing studies, some long non-coding RNAs (lncRNAs) are considered to have important regulatory roles in the development of cancers. However, the pathogenic significance of LINC00511 in breast cancer is unclear. In this study, LINC00511 was significantly up-regulated in breast cancer, and its expression level was correlated to poor prognosis of patients with breast cancer. To further study the role of LINC00511 in breast cancer, we knocked down the expression of LINC00511 using siRNAs. Cells transfected with siRNA-2 proliferated, and its metastasis was suppressed. RNA-seq analysis revealed 182 potential targets for LINC00511. The in-silico analysis revealed that differently expressed genes were closely related to signaling mediated by p38-alpha and p38-beta. Subcellular localization showed that LINC00511 was mainly located in the cytoplasm, and knocking down the LINC00511 gene could down-regulate the expression of MMP13. Using bioinformatics analysis combined with dual-luciferase report assay, we finally determined that miR-150 was the direct target of LINC00511. The dual-luciferase report assays also showed that MMP13 was the target of miR-150. LINC00511 knockdown significantly reduced MMP13 protein levels, and miR-150 gene knockdown significantly rescued the down-regulation of MMP13 caused by LINC00511 gene silencing. Moreover, silencing MMP13 and overexpression of miR-150 could reduce the proliferation of breast cancer cells. In conclusion, our data show that LINC00511 is a breast cancer promoter, and the LINC00511/miR-150/MMP13 axis may be a new therapeutic strategy for breast cancer patients.
Collapse
|
58
|
Single-Molecule Real-Time Transcript Sequencing of Turnips Unveiling the Complexity of the Turnip Transcriptome. G3-GENES GENOMES GENETICS 2020; 10:3505-3514. [PMID: 32769136 PMCID: PMC7534443 DOI: 10.1534/g3.120.401434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To generate the full-length transcriptome of Xinjiang green and purple turnips, Brassica rapa var. Rapa, using single-molecule real-time (SMRT) sequencing. The samples of two varieties of Brassica rapa var. Rapa at five developmental stages were collected and combined to perform SMRT sequencing. Meanwhile, next generation sequencing was performed to correct SMRT sequencing data. A series of analyses were performed to investigate the transcript structure. Finally, the obtained transcripts were mapped to the genome of Brassica rapa ssp. pekinesis Chiifu to identify potential novel transcripts. For green turnip (F01), a total of 19.54 Gb clean data were obtained from 8 cells. The number of reads of insert (ROI) and full-length non-chimeric (FLNC) reads were 510,137 and 267,666. In addition, 82,640 consensus isoforms were obtained in the isoform sequences clustering, of which 69,480 were high-quality, and 13,160 low-quality sequences were corrected using Illumina RNA seq data. For purple turnip (F02), there were 20.41 Gb clean data, 552,829 ROIs, and 274,915 FLNC sequences. A total of 93,775 consensus isoforms were obtained, of which 78,798 were high-quality, and the 14,977 low-quality sequences were corrected. Following the removal of redundant sequences, there were 46,516 and 49,429 non-redundant transcripts for F01 and F02, respectively; 7,774 and 9,385 alternative splicing events were predicted for F01 and F02; 63,890 simple sequence repeats, 59,460 complete coding sequences, and 535 long-non coding RNAs were predicted. Moreover, 5,194 and 5,369 novel transcripts were identified by mapping to Brassica rapa ssp. pekinesis Chiifu. The obtained transcriptome data may improve turnip genome annotation and facilitate further study of the Brassica rapa var. Rapa genome and transcriptome.
Collapse
|
59
|
Hung FY, Chen C, Yen MR, Hsieh JWA, Li C, Shih YH, Chen FF, Chen PY, Cui Y, Wu K. The expression of long non-coding RNAs is associated with H3Ac and H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex in Arabidopsis. NAR Genom Bioinform 2020; 2:lqaa066. [PMID: 33575615 PMCID: PMC7671367 DOI: 10.1093/nargab/lqaa066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/21/2020] [Accepted: 08/25/2020] [Indexed: 01/03/2023] Open
Abstract
In recent years, eukaryotic long non-coding RNAs (lncRNAs) have been identified as important factors involved in a wide variety of biological processes, including histone modification, alternative splicing and transcription enhancement. The expression of lncRNAs is highly tissue-specific and is regulated by environmental stresses. Recently, a large number of plant lncRNAs have been identified, but very few of them have been studied in detail. Furthermore, the mechanism of lncRNA expression regulation remains largely unknown. Arabidopsis HISTONE DEACETYLASE 6 (HDA6) and LSD1-LIKE 1/2 (LDL1/2) can repress gene expression synergistically by regulating H3Ac/H3K4me. In this research, we performed RNA-seq and ChIP-seq analyses to further clarify the function of HDA6-LDL1/2. Our results indicated that the global expression of lncRNAs is increased in hda6/ldl1/2 and that this increased lncRNA expression is particularly associated with H3Ac/H3K4me2 changes. In addition, we found that HDA6-LDL1/2 is important for repressing lncRNAs that are non-expressed or show low-expression, which may be strongly associated with plant development. GO-enrichment analysis also revealed that the neighboring genes of the lncRNAs that are upregulated in hda6/ldl1/2 are associated with various developmental processes. Collectively, our results revealed that the expression of lncRNAs is associated with H3Ac/H3K4me2 changes regulated by the HDA6-LDL1/2 histone modification complex.
Collapse
Affiliation(s)
- Fu-Yu Hung
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Chen Chen
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Ming-Ren Yen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | | | - Chenlong Li
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Yuan-Hsin Shih
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Fang-Fang Chen
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| | - Pao-Yang Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Yuhai Cui
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3 Canada
| | - Keqiang Wu
- Institute of Plant Biology, National Taiwan University, Taipei 10617 Taiwan
| |
Collapse
|
60
|
Sun K, Wang H, Sun H. NAMS webserver: coding potential assessment and functional annotation of plant transcripts. Brief Bioinform 2020; 22:5906158. [PMID: 33080021 PMCID: PMC8138890 DOI: 10.1093/bib/bbaa200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 07/23/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
Recent advances in transcriptomics have uncovered lots of novel transcripts in plants. To annotate such transcripts, dissecting their coding potential is a critical step. Computational approaches have been proven fruitful in this task; however, most current tools are designed/optimized for mammals and only a few of them have been tested on a limited number of plant species. In this work, we present NAMS webserver, which contains a novel coding potential classifier, NAMS, specifically optimized for plants. We have evaluated the performance of NAMS using a comprehensive dataset containing more than 3 million transcripts from various plant species, where NAMS demonstrates high accuracy and remarkable performance improvements over state-of-the-art software. Moreover, our webserver also furnishes functional annotations, aiming to provide users informative clues to the functions of their transcripts. Considering that most plant species are poorly characterized, our NAMS webserver could serve as a valuable resource to facilitate the transcriptomic studies. The webserver with testing dataset is freely available at http://sunlab.cpy.cuhk.edu.hk/NAMS/.
Collapse
Affiliation(s)
- Kun Sun
- Corresponding authors: Kun Sun, Shenzhen Bay Laboratory, Shenzhen 518132, China. Tel.: +86-0755-2641-9310; Fax: +86-755-8696-7710. E-mail: ; Hao Sun, Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong SAR 999077, China. Tel.: +852-3763-6048; Fax: +852-2636-5090. E-mail:
| | | | | |
Collapse
|
61
|
Abstract
Epigenetic mechanisms play fundamental roles in regulating numerous biological processes in various developmental and environmental contexts. Three highly interconnected epigenetic control mechanisms, including small noncoding RNAs, DNA methylation, and histone modifications, contribute to the establishment of plant epigenetic profiles. During the past decade, a growing body of experimental work has revealed the intricate, diverse, and dynamic roles that epigenetic modifications play in plant-nematode interactions. In this review, I summarize recent progress regarding the functions of small RNAs in mediating plant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRNAs. I also recapitulate recent advances in genome-wide DNA methylation analysis and discuss how cyst nematodes induce extensive and dynamic changes in the plant methylome that impact the transcriptional activity of genes and transposable elements. Finally, the potential role of nematode effector proteins in triggering such epigenome changes is discussed.
Collapse
Affiliation(s)
- Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA;
| |
Collapse
|
62
|
Sang J, Zou D, Wang Z, Wang F, Zhang Y, Xia L, Li Z, Ma L, Li M, Xu B, Liu X, Wu S, Liu L, Niu G, Li M, Luo Y, Hu S, Hao L, Zhang Z. IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 18:161-172. [PMID: 32683045 PMCID: PMC7646092 DOI: 10.1016/j.gpb.2018.12.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 11/28/2018] [Accepted: 12/29/2018] [Indexed: 12/19/2022]
Abstract
Genome reannotation aims for complete and accurate characterization of gene models and thus is of critical significance for in-depth exploration of gene function. Although the availability of massive RNA-seq data provides great opportunities for gene model refinement, few efforts have been made to adopt these precious data in rice genome reannotation. Here we reannotate the rice (Oryza sativa L. ssp. japonica) genome based on integration of large-scale RNA-seq data and release a new annotation system IC4R-2.0. In general, IC4R-2.0 significantly improves the completeness of gene structure, identifies a number of novel genes, and integrates a variety of functional annotations. Furthermore, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are systematically characterized in the rice genome. Performance evaluation shows that compared to previous annotation systems, IC4R-2.0 achieves higher integrity and quality, primarily attributable to massive RNA-seq data applied in genome annotation. Consequently, we incorporate the improved annotations into the Information Commons for Rice (IC4R), a database integrating multiple omics data of rice, and accordingly update IC4R by providing more user-friendly web interfaces and implementing a series of practical online tools. Together, the updated IC4R, which is equipped with the improved annotations, bears great promise for comparative and functional genomic studies in rice and other monocotyledonous species. The IC4R-2.0 annotation system and related resources are freely accessible at http://ic4r.org/.
Collapse
Affiliation(s)
- Jian Sang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhennan Wang
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fan Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuansheng Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Xia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaohua Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lina Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengwei Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingxiang Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaonan Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuangyang Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangyi Niu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Man Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingfeng Luo
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songnian Hu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lili Hao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
63
|
Tian H, Guo F, Zhang Z, Ding H, Meng J, Li X, Peng Z, Wan S. Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L. BMC PLANT BIOLOGY 2020; 20:308. [PMID: 32615935 PMCID: PMC7330965 DOI: 10.1186/s12870-020-02510-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 06/22/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. RESULTS A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. CONCLUSIONS This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.
Collapse
Affiliation(s)
- Haiying Tian
- College of Life Science, Shandong University, Jinan, 250014 China
| | - Feng Guo
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhimeng Zhang
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Hong Ding
- Peanut Research Institute of Shandong, Qingdao, 266100 China
| | - Jingjing Meng
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Xinguo Li
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Zhenying Peng
- College of Life Science, Shandong University, Jinan, 250014 China
- Bio-Tech Research Center, Shandong Academy of Agricultural Science/Shandong Provincial Key Laboratory of Genetic Improvement, Ecology and Physiology of Crops, Jinan, 250014 China
| | - Shubo Wan
- College of Life Science, Shandong University, Jinan, 250014 China
- Shandong Academy of Agricultural Science, Jinan, 250014 China
| |
Collapse
|
64
|
Glazinska P, Kulasek M, Glinkowski W, Wysocka M, Kosiński JG. LuluDB-The Database Created Based on Small RNA, Transcriptome, and Degradome Sequencing Shows the Wide Landscape of Non-coding and Coding RNA in Yellow Lupine ( Lupinus luteus L.) Flowers and Pods. Front Genet 2020; 11:455. [PMID: 32499815 PMCID: PMC7242762 DOI: 10.3389/fgene.2020.00455] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 11/13/2022] Open
Abstract
Yellow lupine (Lupinus luteus L.) belongs to a legume family that benefits from symbiosis with nitrogen-fixing bacteria. Its seeds are rich in protein, which makes it a valuable food source for animals and humans. Yellow lupine is also the model plant for basic research on nodulation or abscission of organs. Nevertheless, the knowledge about the molecular regulatory mechanisms of its generative development is still incomplete. The RNA-Seq technique is becoming more prominent in high-throughput identification and expression profiling of both coding and non-coding RNA sequences. However, the huge amount of data generated with this method may discourage other scientific groups from making full use of them. To overcome this inconvenience, we have created a database containing analysis-ready information about non-coding and coding L. luteus RNA sequences (LuluDB). LuluDB was created on the basis of RNA-Seq analysis of small RNA, transcriptome, and degradome libraries obtained from yellow lupine cv. Taper flowers, pod walls, and seeds in various stages of development, flower pedicels, and pods undergoing abscission or maintained on the plant. It contains sequences of miRNAs and phased siRNAs identified in L. luteus, information about their expression in individual samples, and their target sequences. LuluDB also contains identified lncRNAs and protein-coding RNA sequences with their organ expression and annotations to widely used databases like GO, KEGG, NCBI, Rfam, Pfam, etc. The database also provides sequence homology search by BLAST using, e.g., an unknown sequence as a query. To present the full capabilities offered by our database, we performed a case study concerning transcripts annotated as DCL 1–4 (DICER LIKE 1–4) homologs involved in small non-coding RNA biogenesis and identified miRNAs that most likely regulate DCL1 and DCL2 expression in yellow lupine. LuluDB is available at http://luluseqdb.umk.pl/basic/web/index.php.
Collapse
Affiliation(s)
- Paulina Glazinska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Milena Kulasek
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Wojciech Glinkowski
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Torun, Poland.,Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Torun, Poland
| | - Marta Wysocka
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Jan Grzegorz Kosiński
- Department of Computational Biology, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| |
Collapse
|
65
|
Xiao L, Liu X, Lu W, Chen P, Quan M, Si J, Du Q, Zhang D. Genetic dissection of the gene coexpression network underlying photosynthesis in Populus. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1015-1026. [PMID: 31584236 PMCID: PMC7061883 DOI: 10.1111/pbi.13270] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 09/09/2019] [Accepted: 09/29/2019] [Indexed: 05/06/2023]
Abstract
Photosynthesis is a key reaction that ultimately generates the carbohydrates needed to form woody tissues in trees. However, the genetic regulatory network of protein-encoding genes (PEGs) and regulatory noncoding RNAs (ncRNAs), including microRNAs (miRNAs) and long noncoding RNAs (lncRNAs), underlying the photosynthetic pathway is unknown. Here, we integrated data from coexpression analysis, association studies (additive, dominance and epistasis), and expression quantitative trait nucleotide (eQTN) mapping to dissect the causal variants and genetic interaction network underlying photosynthesis in Populus. We initially used 30 PEGs, 6 miRNAs and 12 lncRNAs to construct a coexpression network based on the tissue-specific gene expression profiles of 15 Populus samples. Then, we performed association studies using a natural population of 435 unrelated Populus tomentosa individuals, and identified 72 significant associations (P ≤ 0.001, q ≤ 0.05) with diverse additive and dominance patterns underlying photosynthesis-related traits. Analysis of epistasis and eQTNs revealed that the complex genetic interactions in the coexpression network contribute to phenotypes at various levels. Finally, we demonstrated that heterologously expressing the most highly linked gene (PtoPsbX1) in this network significantly improved photosynthesis in Arabidopsis thaliana, pointing to the functional role of PtoPsbX1 in the photosynthetic pathway. This study provides an integrated strategy for dissecting a complex genetic interaction network, which should accelerate marker-assisted breeding efforts to genetically improve woody plants.
Collapse
Affiliation(s)
- Liang Xiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Xin Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Wenjie Lu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Panfei Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Mingyang Quan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Jingna Si
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Qingzhang Du
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Deqiang Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignBeijing Forestry UniversityBeijingChina
- National Engineering Laboratory for Tree BreedingCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental PlantsMinistry of EducationCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| |
Collapse
|
66
|
Pereira WJ, Melo ATDO, Coelho ASG, Rodrigues FA, Mamidi S, Alencar SAD, Lanna AC, Valdisser PAMR, Brondani C, Nascimento-Júnior IRD, Borba TCDO, Vianello RP. Genome-wide analysis of the transcriptional response to drought stress in root and leaf of common bean. Genet Mol Biol 2020; 43:e20180259. [PMID: 31429863 PMCID: PMC7307723 DOI: 10.1590/1678-4685-gmb-2018-0259] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 02/22/2019] [Indexed: 12/30/2022] Open
Abstract
Genes related to the response to drought stress in leaf and root tissue of
drought-susceptible (DS) and tolerant (DT) genotypes were characterized by
RNA-Seq. In total, 54,750 transcripts, representative of 28,590 genes, were
identified; of these, 1,648 were of high-fidelity (merge of 12 libraries) and
described for the first time in the Andean germplasm. From the 1,239
differentially expressed genes (DEGs), 458 were identified in DT, with a
predominance of genes in categories of oxidative stress, response to stimulus
and kinase activity. Most genes related to oxidation-reduction terms in roots
were early triggered in DT (T75) compared to DS (T150) suggestive of a mechanism
of tolerance by reducing the damage from ROS. Among the KEGG enriched by DEGs
up-regulated in DT leaves, two related to the formation of Sulfur-containing
compounds, which are known for their involvement in tolerance to abiotic
stresses, were common to all treatments. Through qPCR, 88.64% of the DEGs were
validated. A total of 151,283 variants were identified and functional effects
estimated for 85,780. The raw data files were submitted to the NCBI database. A
transcriptome map revealed new genes and isoforms under drought. These results
supports a better understanding of the drought tolerance mechanisms in
beans.
Collapse
Affiliation(s)
- Wendell Jacinto Pereira
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Goiânia, GO, Brazil.,Universidade de Brasília, Departamento de Biologia Celular, Brasília, DF, Brazil
| | | | | | | | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sérgio Amorim de Alencar
- Universidade Católica de Brasília, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Brasília, DF, Brazil
| | - Anna Cristina Lanna
- EMBRAPA Arroz e Feijão, Rod. GO - 462, Km 12, Santo Antônio de Goiás, GO, Brazil
| | | | - Claudio Brondani
- EMBRAPA Arroz e Feijão, Rod. GO - 462, Km 12, Santo Antônio de Goiás, GO, Brazil
| | | | | | | |
Collapse
|
67
|
Zhu C, Zhang S, Fu H, Zhou C, Chen L, Li X, Lin Y, Lai Z, Guo Y. Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea ( Camellia sinensis) in Solar-Withering. FRONTIERS IN PLANT SCIENCE 2019; 10:1638. [PMID: 31929782 PMCID: PMC6941427 DOI: 10.3389/fpls.2019.01638] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/20/2019] [Indexed: 05/08/2023]
Abstract
Oolong tea is a popular and semi-fermented beverage. During the processing of tea leaves, withering is the first indispensable process for improving flavor. However, the roles of long non-coding RNAs (lncRNAs) and the characteristic secondary metabolites during the withering of oolong tea leaves remain unknown. In this study, phytochemical analyses indicated that total polyphenols, flavonoids, catechins, epigallocatechin (EGC), catechin gallate (CG), gallocatechin gallate (GCG), epicatechin gallate (ECG), and epigallocatechin gallate (EGCG) were all less abundant in the solar-withered leaves (SW) than in the fresh leaves (FL) and indoor-withered leaves (IW). In contrast, terpenoid, jasmonic acid (JA), and methyl jasmonate (MeJA) contents were higher in the SW than in the FL and IW. By analyzing the transcriptome data, we detected 32,036 lncRNAs. On the basis of the Kyoto Encyclopedia of Genes and Genomes analysis, the flavonoid metabolic pathway, the terpenoid metabolic pathway, and the JA/MeJA biosynthesis and signal transduction pathway were enriched pathways. Additionally, 63 differentially expressed lncRNAs (DE-lncRNAs) and 23 target genes were identified related to the three pathways. A comparison of the expression profiles of the DE-lncRNAs and their target genes between the SW and IW revealed four up-regulated genes (FLS, CCR, CAD, and HCT), seven up-regulated lncRNAs, four down-regulated genes (4CL, CHI, F3H, and F3'H), and three down-regulated lncRNAs related to flavonoid metabolism; nine up-regulated genes (DXS, CMK, HDS, HDR, AACT, MVK, PMK, GGPPS, and TPS), three up-regulated lncRNAs, and six down-regulated lncRNAs related to terpenoid metabolism; as well as six up-regulated genes (LOX, AOS, AOC, OPR, ACX, and MFP2), four up-regulated lncRNAs, and three down-regulated lncRNAs related to JA/MeJA biosynthesis and signal transduction. These results suggested that the expression of DE-lncRNAs and their targets involved in the three pathways may be related to the low abundance of the total polyphenols, flavonoids, and catechins (EGC, CG, GCG, ECG, and EGCG) and the high abundance of terpenoids in the SW. Moreover, solar irradiation, high JA and MeJA contents, and the endogenous target mimic (eTM)-related regulatory mechanism in the SW were also crucial for increasing the terpenoid levels. These findings provide new insights into the greater contribution of solar-withering to the high-quality flavor of oolong tea compared with the effects of indoor-withering.
Collapse
Affiliation(s)
- Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
68
|
Unver T, Tombuloglu H. Barley long non-coding RNAs (lncRNA) responsive to excess boron. Genomics 2019; 112:1947-1955. [PMID: 31730798 DOI: 10.1016/j.ygeno.2019.11.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/06/2019] [Accepted: 11/11/2019] [Indexed: 02/01/2023]
Abstract
Long non-coding RNA (lncRNA) has a misleading name, since although they do not encode proteins, they may encode small peptides. Such transcripts are emerging as regulatory molecules. With the advent of next-generation sequencing technologies and novel bioinformatics tools, a tremendous amount of lncRNAs have been identified in several plant species. Recent reports demonstrated roles of plant lncRNAs such as development and environmental response. Here, we reported a genome-wide discovery of ~8000 barley lncRNAs and measured their expression pattern upon excessive boron (B) treatment. According to the tissue-based comparison, leaves have a greater number of B-responsive differentially expressed lncRNAs than the root. Functional annotation of the coding transcripts, which were co-expressed with lncRNAs, revealed that molecular function of the ion transport, establishment of localization, and response to stimulus significantly enriched only in the leaf. On the other hand, 32 barley endogenous target mimics (eTM) as lncRNAs, which potentially decoy the transcriptional suppression activity of 18 miRNAs, were obtained. Also, six lncRNAs, differentially expressed upon B-treatment, were selected and quantitatively analyzed in both B-sensitive and B-tolerant cultivars treated by excess B-level. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis confirmed the B-responsive expressional changes obtained by RNA sequencing. Notably, some lncRNAs (i.e., TCONS_00045190 and TCONS_00056415) over-expressed only in B-tolerant cultivar upon excess B treatment. Presented data including identification, expression measurement, and functional characterization of barley lncRNAs suggest that B-stress response might also be regulated by lncRNA expression, via cooperative interaction of miRNA-eTM-coding target transcript modules.
Collapse
Affiliation(s)
- Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, No: 1/1/76, 06378, Yenimahalle, Ankara, Turkey.
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| |
Collapse
|
69
|
Zhou GF, Zhang LP, Li BX, Sheng O, Wei QJ, Yao FX, Guan G, Liu GD. Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange ( Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency. Int J Mol Sci 2019; 20:ijms20215419. [PMID: 31683503 PMCID: PMC6862649 DOI: 10.3390/ijms20215419] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/28/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.
Collapse
Affiliation(s)
- Gao-Feng Zhou
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| | - Li-Ping Zhang
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| | - Bi-Xian Li
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
| | - Qing-Jiang Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Feng-Xian Yao
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| | - Guan Guan
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| | - Gui-Dong Liu
- National Navel Orange Engineering Research Center, College of Navel Orange, Gannan Normal University, Ganzhou 341000, China.
| |
Collapse
|
70
|
Durut N, Mittelsten Scheid O. The Role of Noncoding RNAs in Double-Strand Break Repair. FRONTIERS IN PLANT SCIENCE 2019; 10:1155. [PMID: 31611891 PMCID: PMC6776598 DOI: 10.3389/fpls.2019.01155] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 08/23/2019] [Indexed: 06/10/2023]
Abstract
Genome stability is constantly threatened by DNA lesions generated by different environmental factors as well as endogenous processes. If not properly and timely repaired, damaged DNA can lead to mutations or chromosomal rearrangements, well-known reasons for genetic diseases or cancer in mammals, or growth abnormalities and/or sterility in plants. To prevent deleterious consequences of DNA damage, a sophisticated system termed DNA damage response (DDR) detects DNA lesions and initiates DNA repair processes. In addition to many well-studied canonical proteins involved in this process, noncoding RNA (ncRNA) molecules have recently been discovered as important regulators of the DDR pathway, extending the broad functional repertoire of ncRNAs to the maintenance of genome stability. These ncRNAs are mainly connected with double-strand breaks (DSBs), the most dangerous type of DNA lesions. The possibility to intentionally generate site-specific DSBs in the genome with endonucleases constitutes a powerful tool to study, in vivo, how DSBs are processed and how ncRNAs participate in this crucial event. In this review, we will summarize studies reporting the different roles of ncRNAs in DSB repair and discuss how genome editing approaches, especially CRISPR/Cas systems, can assist DNA repair studies. We will summarize knowledge concerning the functional significance of ncRNAs in DNA repair and their contribution to genome stability and integrity, with a focus on plants.
Collapse
|
71
|
He L, Wang Q, Gu Z, Liao Q, Palukaitis P, Du Z. A conserved RNA structure is essential for a satellite RNA-mediated inhibition of helper virus accumulation. Nucleic Acids Res 2019; 47:8255-8271. [PMID: 31269212 PMCID: PMC6735963 DOI: 10.1093/nar/gkz564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/30/2019] [Accepted: 06/20/2019] [Indexed: 12/15/2022] Open
Abstract
As a class of parasitic, non-coding RNAs, satellite RNAs (satRNAs) have to compete with their helper virus for limited amounts of viral and/or host resources for efficient replication, by which they usually reduce viral accumulation and symptom expression. Here, we report a cucumber mosaic virus (CMV)-associated satRNA (sat-T1) that ameliorated CMV-induced symptoms, accompanied with a significant reduction in the accumulation of viral genomic RNAs 1 and 2, which encode components of the viral replicase. Intrans replication assays suggest that the reduced accumulation is the outcome of replication competition. The structural basis of sat-T1 responsible for the inhibition of viral RNA accumulation was determined to be a three-way branched secondary structure that contains two biologically important hairpins. One is indispensable for the helper virus inhibition, and the other engages in formation of a tertiary pseudoknot structure that is essential for sat-T1 survival. The secondary structure containing the pseudoknot is the first RNA element with a biological phenotype experimentally identified in CMV satRNAs, and it is structurally conserved in most CMV satRNAs. Thus, this may be a generic method for CMV satRNAs to inhibit the accumulation of the helper virus via the newly-identified RNA structure.
Collapse
Affiliation(s)
- Lu He
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Qian Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Zhouhang Gu
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Qiansheng Liao
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| | - Peter Palukaitis
- Department of Horticultural Sciences, Seoul Women's University, Nowon-gu, Seoul 01797, Republic of Korea
| | - Zhiyou Du
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China
| |
Collapse
|
72
|
Ma J, Bai X, Luo W, Feng Y, Shao X, Bai Q, Sun S, Long Q, Wan D. Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars. Front Genet 2019; 10:777. [PMID: 31543901 PMCID: PMC6739720 DOI: 10.3389/fgene.2019.00777] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
Collapse
Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yannan Feng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shujiao Sun
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiming Long
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| |
Collapse
|
73
|
Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
|
74
|
Tian Y, Bai S, Dang Z, Hao J, Zhang J, Hasi A. Genome-wide identification and characterization of long non-coding RNAs involved in fruit ripening and the climacteric in Cucumis melo. BMC PLANT BIOLOGY 2019; 19:369. [PMID: 31438855 PMCID: PMC6704668 DOI: 10.1186/s12870-019-1942-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/18/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND Cucumis melo is a suitable study material for investigation of fruit ripening owing to its climacteric nature. Long non-coding RNAs have been linked to many important biological processes, such as fruit ripening, flowering time regulation, and abiotic stress responses in plants. However, knowledge of the regulatory roles of lncRNAs underlying the ripening process in C. melo are largely unknown. In this study the complete transcriptome of Cucumis melo L. cv. Hetao fruit at four developmental stages was sequenced and analyzed. The potential role of lncRNAs was predicted based on the function of differentially expressed target genes and correlated genes. RESULTS In total, 3857 lncRNAs were assembled and annotated, of which 1601 were differentially expressed between developmental stages. The target genes of these lncRNAs and the regulatory relationship (cis- or trans-acting) were predicted. The target genes were enriched with GO terms for biological process, such as response to auxin stimulus and hormone biosynthetic process. Enriched KEGG pathways included plant hormone signal transduction and carotenoid biosynthesis. Co-expression network construction showed that LNC_002345 and LNC_000154, which were highly expressed, might co-regulate with mutiple genes associated with auxin signal transduction and acted in the same pathways. We identified lncRNAs (LNC_000987, LNC_000693, LNC_001323, LNC_003610, LNC_001263 and LNC_003380) that were correlated with fruit ripening and the climacteric, and may participate in the regulation of ethylene biosynthesis and metabolism and the ABA signaling pathway. A number of crucial transcription factors, such as ERFs, WRKY70, NAC56, and NAC72, may also play important roles in the regulation of fruit ripening in C. melo. CONCLUSIONS Our results predict the regulatory functions of the lncRNAs during melon fruit development and ripening, and 142 highly expressed lncRNAs (average FPKM > 100) were identified. These lncRNAs participate in the regulation of auxin signal transduction, ethylene, sucrose biosynthesis and metabolism, the ABA signaling pathway, and transcription factors, thus regulating fruit development and ripening.
Collapse
Affiliation(s)
- Yunyun Tian
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| | - Selinge Bai
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| | - Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| | - Jinfeng Hao
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| | - Jin Zhang
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, Inner Mongolia People’s Republic of China
| |
Collapse
|
75
|
Salih H, Gong W, He S, Xia W, Odongo MR, Du X. Long non-coding RNAs and their potential functions in Ligon-lintless-1 mutant cotton during fiber development. BMC Genomics 2019; 20:661. [PMID: 31426741 PMCID: PMC6700839 DOI: 10.1186/s12864-019-5978-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/16/2019] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) are part of genes, which are not translated into proteins and play a vital role in plant growth and development. Nevertheless, the presence of LncRNAs and how they functions in Ligon-lintless-1 mutant during the early cessation of cotton fiber development are still not well understood. In order to investigate the function of LncRNAs in cotton fiber development, it is necessary and important to identify LncRNAs and their potential roles in fiber cell development. RESULTS In this work, we identified 18,333 LncRNAs, with the proportion of long intergenic noncoding RNAs (LincRNAs) (91.5%) and anti-sense LncRNAs (8.5%), all transcribed from Ligon-lintless-1 (Li1) and wild-type (WT). Expression differences were detected between Ligon-lintless-1 and wild-type at 0 and 8 DPA (day post anthesis). Pathway analysis and Gene Ontology based on differentially expressed LncRNAs on target genes, indicated fatty acid biosynthesis and fatty acid elongation being integral to lack of fiber in mutant cotton. The result of RNA-seq and RT-qPCR clearly singles out two potential LncRNAs, LNC_001237 and LNC_017085, to be highly down-regulated in the mutant cotton. The two LncRNAs were found to be destabilized or repressed by ghr-miR2950. Both RNA-seq analysis and RT-qPCR results in Ligon-lintless-1 mutant and wild-type may provide strong evidence of LNC_001237, LNC_017085 and ghr-miR2950 being integral molecular elements participating in various pathways of cotton fiber development. CONCLUSION The results of this study provide fundamental evidence for the better understanding of LncRNAs regulatory role in the molecular pathways governing cotton fiber development. Further research on designing and transforming LncRNAs will help not only in the understanding of their functions but will also in the improvement of fiber quality.
Collapse
Affiliation(s)
- Haron Salih
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
- Zalingei University, Central Darfur, Sudan
| | - Wenfang Gong
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Wang Xia
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Magwanga Richard Odongo
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000 China
| |
Collapse
|
76
|
Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences. G3-GENES GENOMES GENETICS 2019; 9:2749-2760. [PMID: 31239292 PMCID: PMC6686930 DOI: 10.1534/g3.119.400196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Polyadenylation is an essential post-transcriptional modification of eukaryotic transcripts that plays critical role in transcript stability, localization, transport, and translational efficiency. About 70% genes in plants contain alternative polyadenylation (APA) sites. Despite availability of vast amount of sequencing data, to date, a comprehensive map of the polyadenylation events in maize is not available. Here, 9.48 billion RNA-Seq reads were analyzed to characterize 95,345 Poly(A) Clusters (PAC) in 23,705 (51%) maize genes. Of these, 76% were APA genes. However, most APA genes (55%) expressed a dominant PAC rather than favoring multiple PACs equally. The lincRNA genes with PACs were significantly longer in length than the genes without any PAC and about 48% genes had APA sites. Heterogeneity was observed in 52% of the PACs supporting the imprecise nature of the polyadenylation process. Genomic distribution revealed that the majority of the PACs (78%) were located in the genic regions. Unlike previous studies, large number of PACs were observed in the intergenic (n = 21,264), 5′-UTR (735), CDS (2,542), and the intronic regions (12,841). The CDS and introns with PACs were longer in length than without PACs, whereas intergenic PACs were more often associated with transcripts that lacked annotated 3′-UTRs. Nucleotide composition around PACs demonstrated AT-richness and the common upstream motif was AAUAAA, which is consistent with other plants. According to this study, only 2,830 genes still maintained the use of AAUAAA motif. This large-scale data provides useful insights about the gene expression regulation and could be utilized as evidence to validate the annotation of transcript ends.
Collapse
|
77
|
Paschoal AR, Lozada-Chávez I, Domingues DS, Stadler PF. ceRNAs in plants: computational approaches and associated challenges for target mimic research. Brief Bioinform 2019; 19:1273-1289. [PMID: 28575144 DOI: 10.1093/bib/bbx058] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/27/2017] [Indexed: 11/13/2022] Open
Abstract
The competing endogenous RNA hypothesis has gained increasing attention as a potential global regulatory mechanism of microRNAs (miRNAs), and as a powerful tool to predict the function of many noncoding RNAs, including miRNAs themselves. Most studies have been focused on animals, although target mimic (TMs) discovery as well as important computational and experimental advances has been developed in plants over the past decade. Thus, our contribution summarizes recent progresses in computational approaches for research of miRNA:TM interactions. We divided this article in three main contributions. First, a general overview of research on TMs in plants is presented with practical descriptions of the available literature, tools, data, databases and computational reports. Second, we describe a common protocol for the computational and experimental analyses of TM. Third, we provide a bioinformatics approach for the prediction of TM motifs potentially cross-targeting both members within the same or from different miRNA families, based on the identification of consensus miRNA-binding sites from known TMs across sequenced genomes, transcriptomes and known miRNAs. This computational approach is promising because, in contrast to animals, miRNA families in plants are large with identical or similar members, several of which are also highly conserved. From the three consensus TM motifs found with our approach: MIM166, MIM171 and MIM159/319, the last one has found strong support on the recent experimental work by Reichel and Millar [Specificity of plant microRNA TMs: cross-targeting of mir159 and mir319. J Plant Physiol 2015;180:45-8]. Finally, we stress the discussion on the major computational and associated experimental challenges that have to be faced in future ceRNA studies.
Collapse
Affiliation(s)
| | - Irma Lozada-Chávez
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Germany
| | - Douglas Silva Domingues
- Department of Botany, Institute of Biosciences, S~ao Paulo State University (UNESP) in Rio Claro, Brazil
| | | |
Collapse
|
78
|
Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava. BMC Genomics 2019; 20:514. [PMID: 31226927 PMCID: PMC6588902 DOI: 10.1186/s12864-019-5895-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Background Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are involved in drought tolerance in various crops. Results Herein, we demonstrate that tetraploidy potentiates tolerance to drought stress in cassava (Manihot esculenta Crantz). Autotetraploidy reduces transpiration by lesser extent increasing of stomatal density, smaller stomatal aperture size, or greater stomatal closure, and reducing accumulation of H2O2 under drought stress. Transcriptome analysis of autotetraploid samples revealed down-regulation of genes involved in photosynthesis under drought stress, and less down-regulation of subtilisin-like proteases involved in increasing stomatal density. UDP-glucosyltransferases were increased more or reduced less in dehydrated leaves of autotetraploids compared with controls. Strand-specific RNA-seq data (validated by quantitative real time PCR) identified 2372 lncRNAs, and 86 autotetraploid-specific lncRNAs were differentially expressed in stressed leaves. The co-expressed network analysis indicated that LNC_001148 and LNC_000160 in autotetraploid dehydrated leaves regulated six genes encoding subtilisin-like protease above mentioned, thereby result in increasing the stomatal density to a lesser extent in autotetraploid cassava. Trans-regulatory network analysis suggested that autotetraploid-specific differentially expressed lncRNAs were associated with galactose metabolism, pentose phosphate pathway and brassinosteroid biosynthesis, etc. Conclusion Tetraploidy potentiates tolerance to drought stress in cassava, and LNC_001148 and LNC_000160 mediate drought tolerance by regulating stomatal density in autotetraploid cassava. Electronic supplementary material The online version of this article (10.1186/s12864-019-5895-7) contains supplementary material, which is available to authorized users.
Collapse
|
79
|
Emamjomeh A, Zahiri J, Asadian M, Behmanesh M, Fakheri BA, Mahdevar G. Identification, Prediction and Data Analysis of Noncoding RNAs: A Review. Med Chem 2019; 15:216-230. [PMID: 30484409 DOI: 10.2174/1573406414666181015151610] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Revised: 06/03/2018] [Accepted: 09/30/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Noncoding RNAs (ncRNAs) which play an important role in various cellular processes are important in medicine as well as in drug design strategies. Different studies have shown that ncRNAs are dis-regulated in cancer cells and play an important role in human tumorigenesis. Therefore, it is important to identify and predict such molecules by experimental and computational methods, respectively. However, to avoid expensive experimental methods, computational algorithms have been developed for accurately and fast prediction of ncRNAs. OBJECTIVE The aim of this review was to introduce the experimental and computational methods to identify and predict ncRNAs structure. Also, we explained the ncRNA's roles in cellular processes and drugs design, briefly. METHOD In this survey, we will introduce ncRNAs and their roles in biological and medicinal processes. Then, some important laboratory techniques will be studied to identify ncRNAs. Finally, the state-of-the-art models and algorithms will be introduced along with important tools and databases. RESULTS The results showed that the integration of experimental and computational approaches improves to identify ncRNAs. Moreover, the high accurate databases, algorithms and tools were compared to predict the ncRNAs. CONCLUSION ncRNAs prediction is an exciting research field, but there are different difficulties. It requires accurate and reliable algorithms and tools. Also, it should be mentioned that computational costs of such algorithm including running time and usage memory are very important. Finally, some suggestions were presented to improve computational methods of ncRNAs gene and structural prediction.
Collapse
Affiliation(s)
- Abbasali Emamjomeh
- Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Plant Breeding and Biotechnology (PBB), University of Zabol, Zabol, Iran
| | - Javad Zahiri
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Asadian
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Barat A Fakheri
- Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran
| | - Ghasem Mahdevar
- Department of Mathematics, Faculty of Sciences, University of Isfahan, Isfahan, Iran
| |
Collapse
|
80
|
Wekesa JS, Luan Y, Chen M, Meng J. A Hybrid Prediction Method for Plant lncRNA-Protein Interaction. Cells 2019; 8:E521. [PMID: 31151273 PMCID: PMC6627874 DOI: 10.3390/cells8060521] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 01/23/2023] Open
Abstract
Long non-protein-coding RNAs (lncRNAs) identification and analysis are pervasive in transcriptome studies due to their roles in biological processes. In particular, lncRNA-protein interaction has plausible relevance to gene expression regulation and in cellular processes such as pathogen resistance in plants. While lncRNA-protein interaction has been studied in animals, there has yet to be extensive research in plants. In this paper, we propose a novel plant lncRNA-protein interaction prediction method, namely PLRPIM, which combines deep learning and shallow machine learning methods. The selection of an optimal feature subset and subsequent efficient compression are significant challenges for deep learning models. The proposed method adopts k-mer and extracts high-level abstraction sequence-based features using stacked sparse autoencoder. Based on the extracted features, the fusion of random forest (RF) and light gradient boosting machine (LGBM) is used to build the prediction model. The performances are evaluated on Arabidopsis thaliana and Zea mays datasets. Results from experiments demonstrate PLRPIM's superiority compared with other prediction tools on the two datasets. Based on 5-fold cross-validation, we obtain 89.98% and 93.44% accuracy, 0.954 and 0.982 AUC for Arabidopsis thaliana and Zea mays, respectively. PLRPIM predicts potential lncRNA-protein interaction pairs effectively, which can facilitate lncRNA related research including function prediction.
Collapse
Affiliation(s)
- Jael Sanyanda Wekesa
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116023, Liaoning, China.
- Department of Information Technology, Jomo Kenyatta University of Agriculture and Technology, Nairobi 62000-00200, Kenya.
| | - Yushi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116023, Liaoning, China.
| | - Ming Chen
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China.
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116023, Liaoning, China.
| |
Collapse
|
81
|
Blyuss KB, Fatehi F, Tsygankova VA, Biliavska LO, Iutynska GO, Yemets AI, Blume YB. RNAi-Based Biocontrol of Wheat Nematodes Using Natural Poly-Component Biostimulants. FRONTIERS IN PLANT SCIENCE 2019; 10:483. [PMID: 31057585 PMCID: PMC6479188 DOI: 10.3389/fpls.2019.00483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
With the growing global demands on sustainable food production, one of the biggest challenges to agriculture is associated with crop losses due to parasitic nematodes. While chemical pesticides have been quite successful in crop protection and mitigation of damage from parasites, their potential harm to humans and environment, as well as the emergence of nematode resistance, have necessitated the development of viable alternatives to chemical pesticides. One of the most promising and targeted approaches to biocontrol of parasitic nematodes in crops is that of RNA interference (RNAi). In this study we explore the possibility of using biostimulants obtained from metabolites of soil streptomycetes to protect wheat (Triticum aestivum L.) against the cereal cyst nematode Heterodera avenae by means of inducing RNAi in wheat plants. Theoretical models of uptake of organic compounds by plants, and within-plant RNAi dynamics, have provided us with useful insights regarding the choice of routes for delivery of RNAi-inducing biostimulants into plants. We then conducted in planta experiments with several streptomycete-derived biostimulants, which have demonstrated the efficiency of these biostimulants at improving plant growth and development, as well as in providing resistance against the cereal cyst nematode. Using dot blot hybridization we demonstrate that biostimulants trigger a significant increase of the production in plant cells of si/miRNA complementary with plant and nematode mRNA. Wheat germ cell-free experiments show that these si/miRNAs are indeed very effective at silencing the translation of nematode mRNA having complementary sequences, thus reducing the level of nematode infestation and improving plant resistance to nematodes. Thus, we conclude that natural biostimulants produced from metabolites of soil streptomycetes provide an effective tool for biocontrol of wheat nematode.
Collapse
Affiliation(s)
| | - Farzad Fatehi
- Department of Mathematics, University of Sussex, Brighton, United Kingdom
| | - Victoria A. Tsygankova
- Department of Chemistry of Bioactive Nitrogen-Containing Heterocyclic Compounds, Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Liudmyla O. Biliavska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Galyna O. Iutynska
- Department of General and Soil Microbiology, Zabolotny Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alla I. Yemets
- Department of Cell Biology and Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Yaroslav B. Blume
- Department of Genomics and Molecular Biotechnology, Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| |
Collapse
|
82
|
Barrera-Redondo J, Ibarra-Laclette E, Vázquez-Lobo A, Gutiérrez-Guerrero YT, Sánchez de la Vega G, Piñero D, Montes-Hernández S, Lira-Saade R, Eguiarte LE. The Genome of Cucurbita argyrosperma (Silver-Seed Gourd) Reveals Faster Rates of Protein-Coding Gene and Long Noncoding RNA Turnover and Neofunctionalization within Cucurbita. MOLECULAR PLANT 2019; 12:506-520. [PMID: 30630074 DOI: 10.1016/j.molp.2018.12.023] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 05/19/2023]
Abstract
Whole-genome duplications are an important source of evolutionary novelties that change the mode and tempo at which genetic elements evolve within a genome. The Cucurbita genus experienced a whole-genome duplication around 30 million years ago, although the evolutionary dynamics of the coding and noncoding genes in this genus have not yet been scrutinized. Here, we analyzed the genomes of four Cucurbita species, including a newly assembled genome of Cucurbita argyrosperma, and compared the gene contents of these species with those of five other members of the Cucurbitaceae family to assess the evolutionary dynamics of protein-coding and long intergenic noncoding RNA (lincRNA) genes after the genome duplication. We report that Cucurbita genomes have a higher protein-coding gene birth-death rate compared with the genomes of the other members of the Cucurbitaceae family. C. argyrosperma gene families associated with pollination and transmembrane transport had significantly faster evolutionary rates. lincRNA families showed high levels of gene turnover throughout the phylogeny, and 67.7% of the lincRNA families in Cucurbita showed evidence of birth from the neofunctionalization of previously existing protein-coding genes. Collectively, our results suggest that the whole-genome duplication in Cucurbita resulted in faster rates of gene family evolution through the neofunctionalization of duplicated genes.
Collapse
Affiliation(s)
- Josué Barrera-Redondo
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico
| | - Enrique Ibarra-Laclette
- Departamento de Estudios Moleculares Avanzados, Instituto de Ecología A.C., Carretera Antigua a Coatepec No. 351, Col. El Haya. C.P., Xalapa, Veracruz 91070, Mexico
| | - Alejandra Vázquez-Lobo
- Centro de Investigaciones en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, Cuernavaca, Morelos 62209, Mexico
| | - Yocelyn T Gutiérrez-Guerrero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico
| | - Guillermo Sánchez de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Km 6.5 Carretera Celaya-San Miguel de Allende, Celaya, Guanajuato 38110, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, Tlanepantla, Edo. de Mex 54090, Mexico.
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510 Ciudad de México, Mexico.
| |
Collapse
|
83
|
Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine. Sci Rep 2019; 9:3552. [PMID: 30837504 PMCID: PMC6401051 DOI: 10.1038/s41598-019-38989-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
Collapse
|
84
|
Jha UC, Bohra A, Jha R, Parida SK. Salinity stress response and 'omics' approaches for improving salinity stress tolerance in major grain legumes. PLANT CELL REPORTS 2019; 38:255-277. [PMID: 30637478 DOI: 10.1007/s00299-019-02374-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/04/2019] [Indexed: 05/21/2023]
Abstract
Sustaining yield gains of grain legume crops under growing salt-stressed conditions demands a thorough understanding of plant salinity response and more efficient breeding techniques that effectively integrate modern omics knowledge. Grain legume crops are important to global food security being an affordable source of dietary protein and essential mineral nutrients to human population, especially in the developing countries. The global productivity of grain legume crops is severely challenged by the salinity stress particularly in the face of changing climates coupled with injudicious use of irrigation water and improper agricultural land management. Plants adapt to sustain under salinity-challenged conditions through evoking complex molecular mechanisms. Elucidating the underlying complex mechanisms remains pivotal to our knowledge about plant salinity response. Improving salinity tolerance of plants demand enriching cultivated gene pool of grain legume crops through capitalizing on 'adaptive traits' that contribute to salinity stress tolerance. Here, we review the current progress in understanding the genetic makeup of salinity tolerance and highlight the role of germplasm resources and omics advances in improving salt tolerance of grain legumes. In parallel, scope of next generation phenotyping platforms that efficiently bridge the phenotyping-genotyping gap and latest research advances including epigenetics is also discussed in context to salt stress tolerance. Breeding salt-tolerant cultivars of grain legumes will require an integrated "omics-assisted" approach enabling accelerated improvement of salt-tolerance traits in crop breeding programs.
Collapse
Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
| | - Rintu Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067, India
| |
Collapse
|
85
|
Spatio-Temporal Transcriptional Dynamics of Maize Long Non-Coding RNAs Responsive to Drought Stress. Genes (Basel) 2019; 10:genes10020138. [PMID: 30781862 PMCID: PMC6410058 DOI: 10.3390/genes10020138] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response.
Collapse
|
86
|
Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
Collapse
Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
87
|
Yang Y, Liu T, Shen D, Wang J, Ling X, Hu Z, Chen T, Hu J, Huang J, Yu W, Dou D, Wang MB, Zhang B. Tomato yellow leaf curl virus intergenic siRNAs target a host long noncoding RNA to modulate disease symptoms. PLoS Pathog 2019; 15:e1007534. [PMID: 30668603 PMCID: PMC6366713 DOI: 10.1371/journal.ppat.1007534] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 02/07/2019] [Accepted: 12/16/2018] [Indexed: 11/19/2022] Open
Abstract
Tomato yellow leaf curl virus (TYLCV) and its related begomoviruses cause fast-spreading diseases in tomato worldwide. How this virus induces diseases remains largely unclear. Here we report a noncoding RNA-mediated model to elucidate the molecular mechanisms of TYLCV-tomato interaction and disease development. The circular ssDNA genome of TYLCV contains a noncoding intergenic region (IR), which is known to mediate viral DNA replication and transcription in host cells, but has not been reported to contribute directly to viral disease development. We demonstrate that the IR is transcribed in dual orientations during plant infection and confers abnormal phenotypes in tomato independently of protein-coding regions of the viral genome. We show that the IR sequence has a 25-nt segment that is almost perfectly complementary to a long noncoding RNA (lncRNA, designated as SlLNR1) in TYLCV-susceptible tomato cultivars but not in resistant cultivars which contains a 14-nt deletion in the 25-nt region. Consequently, we show that viral small-interfering RNAs (vsRNAs) derived from the 25-nt IR sequence induces silencing of SlLNR1 in susceptible tomato plants but not resistant plants, and this SlLNR1 downregulation is associated with stunted and curled leaf phenotypes reminiscent of TYLCV symptoms. These results suggest that the lncRNA interacts with the IR-derived vsRNAs to control disease development during TYLCV infection. Consistent with its possible function in virus disease development, over-expression of SlLNR1 in tomato reduces the accumulation of TYLCV. Furthermore, gene silencing of the SlLNR1 in the tomato plants induced TYLCV-like leaf phenotypes without viral infection. Our results uncover a previously unknown interaction between vsRNAs and host lncRNA, and provide a plausible model for TYLCV-induced diseases and host antiviral immunity, which would help to develop effective strategies for the control of this important viral pathogen.
Collapse
Affiliation(s)
- Yuwen Yang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tingli Liu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jinyan Wang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xitie Ling
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Zhongze Hu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jieli Hu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junyu Huang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wengui Yu
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
- * E-mail: (DD); (MBW); (BZ)
| | - Ming-Bo Wang
- CSIRO Plant Industry, Canberra, Australia
- * E-mail: (DD); (MBW); (BZ)
| | - Baolong Zhang
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- * E-mail: (DD); (MBW); (BZ)
| |
Collapse
|
88
|
LncRNA expression profile and ceRNA analysis in tomato during flowering. PLoS One 2019; 14:e0210650. [PMID: 30653557 PMCID: PMC6336255 DOI: 10.1371/journal.pone.0210650] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 12/29/2018] [Indexed: 11/19/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs that play essential regulatory roles in various developmental processes and stress responses. However, the functions of lncRNAs during the flowering period of tomato are largely unknown. To explore the lncRNA profiles and functions during flowering in tomato, we performed strand-specific paired-end RNA sequencing of tomato leaves, flowers and roots, with three biological replicates. We identified 10919 lncRNAs including 248 novel lncRNAs, of which 65 novel lncRNAs were significantly differentially expressed (DE) in the flowers, leaves, and roots. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify the cis target gene of DE lncRNAs. The results showed that the lncRNAs might play an important role in the growth, development, and apoptosis of flowering tomato plant by regulating the formation of intima in flower tissues, binding to various molecules, influencing metabolic pathways, and inducing apoptosis. Moreover, we identified the interaction between 32, 78, and 397 kinds of miRNAs, lncRNAs, and mRNAs. The results suggest that the lncRNAs can regulate the expression of mRNA during flowering period in tomato by forming competitive endogenous RNA, and further regulate various biological metabolism pathways in tomato.
Collapse
|
89
|
Wang G, Yin H, Li B, Yu C, Wang F, Xu X, Cao J, Bao Y, Wang L, Abbasi AA, Bajic VB, Ma L, Zhang Z. Characterization and identification of long non-coding RNAs based on feature relationship. Bioinformatics 2019; 35:2949-2956. [DOI: 10.1093/bioinformatics/btz008] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 12/05/2018] [Accepted: 01/07/2019] [Indexed: 01/24/2023] Open
Abstract
Abstract
Motivation
The significance of long non-coding RNAs (lncRNAs) in many biological processes and diseases has gained intense interests over the past several years. However, computational identification of lncRNAs in a wide range of species remains challenging; it requires prior knowledge of well-established sequences and annotations or species-specific training data, but the reality is that only a limited number of species have high-quality sequences and annotations.
Results
Here we first characterize lncRNAs in contrast to protein-coding RNAs based on feature relationship and find that the feature relationship between open reading frame length and guanine-cytosine (GC) content presents universally substantial divergence in lncRNAs and protein-coding RNAs, as observed in a broad variety of species. Based on the feature relationship, accordingly, we further present LGC, a novel algorithm for identifying lncRNAs that is able to accurately distinguish lncRNAs from protein-coding RNAs in a cross-species manner without any prior knowledge. As validated on large-scale empirical datasets, comparative results show that LGC outperforms existing algorithms by achieving higher accuracy, well-balanced sensitivity and specificity, and is robustly effective (>90% accuracy) in discriminating lncRNAs from protein-coding RNAs across diverse species that range from plants to mammals. To our knowledge, this study, for the first time, differentially characterizes lncRNAs and protein-coding RNAs based on feature relationship, which is further applied in computational identification of lncRNAs. Taken together, our study represents a significant advance in characterization and identification of lncRNAs and LGC thus bears broad potential utility for computational analysis of lncRNAs in a wide range of species.
Availability and implementation
LGC web server is publicly available at http://bigd.big.ac.cn/lgc/calculator. The scripts and data can be downloaded at http://bigd.big.ac.cn/biocode/tools/BT000004.
Supplementary information
Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Guangyu Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongyan Yin
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Chunlei Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fan Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xingjian Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiabao Cao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiming Bao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Liguo Wang
- Division of Biomedical Statistics and Informatics, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Amir A Abbasi
- National Center for Bioinformatics, Programme of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Kingdom of Saudi Arabia
| | - Lina Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
90
|
Hisanaga T, Okahashi K, Yamaoka S, Kajiwara T, Nishihama R, Shimamura M, Yamato KT, Bowman JL, Kohchi T, Nakajima K. A cis-acting bidirectional transcription switch controls sexual dimorphism in the liverwort. EMBO J 2019; 38:embj.2018100240. [PMID: 30609993 PMCID: PMC6418429 DOI: 10.15252/embj.2018100240] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/17/2018] [Accepted: 11/27/2018] [Indexed: 01/19/2023] Open
Abstract
Plant life cycles alternate between haploid gametophytes and diploid sporophytes. While regulatory factors determining male and female sexual morphologies have been identified for sporophytic reproductive organs, such as stamens and pistils of angiosperms, those regulating sex‐specific traits in the haploid gametophytes that produce male and female gametes and hence are central to plant sexual reproduction are poorly understood. Here, we identified a MYB‐type transcription factor, MpFGMYB, as a key regulator of female sexual differentiation in the haploid‐dominant dioicous liverwort, Marchantia polymorpha. MpFGMYB is specifically expressed in females and its loss resulted in female‐to‐male sex conversion. Strikingly, MpFGMYB expression is suppressed in males by a cis‐acting antisense gene SUF at the same locus, and loss‐of‐function suf mutations resulted in male‐to‐female sex conversion. Thus, the bidirectional transcription module at the MpFGMYB/SUF locus acts as a toggle between female and male sexual differentiation in M. polymorpha gametophytes. Arabidopsis thaliana MpFGMYB orthologs are known to be expressed in embryo sacs and promote their development. Thus, phylogenetically related MYB transcription factors regulate female gametophyte development across land plants.
Collapse
Affiliation(s)
- Tetsuya Hisanaga
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | | | | | - Masaki Shimamura
- Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
| | - Katsuyuki T Yamato
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Wakayama, Japan
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Keiji Nakajima
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| |
Collapse
|
91
|
Bai L, Chen Q, Jiang L, Lin Y, Ye Y, Liu P, Wang X, Tang H. Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla. HORTICULTURE RESEARCH 2019; 6:42. [PMID: 30854215 PMCID: PMC6397888 DOI: 10.1038/s41438-019-0128-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 05/18/2023]
Abstract
To investigate the molecular mechanism underlying fruit development and color change, comparative transcriptome analysis was employed to generate transcriptome profiles of two typical wild varieties of Fragaria pentaphylla at three fruit developmental stages (green fruit stage, turning stage, and ripe fruit stage). We identified 25,699 long noncoding RNAs (lncRNAs) derived from 25,107 loci in the F. pentaphylla fruit transcriptome, which showed distinct stage- and genotype-specific expression patterns. Time course analysis detected a large number of differentially expressed protein-coding genes and lncRNAs associated with fruit development and ripening in both of the F. pentaphylla varieties. The target genes downregulated in the late stages were enriched in terms of photosynthesis and cell wall organization or biogenesis, suggesting that lncRNAs may act as negative regulators to suppress photosynthesis and cell wall organization or biogenesis during fruit development and ripening of F. pentaphylla. Pairwise comparisons of two varieties at three developmental stages identified 365 differentially expressed lncRNAs in total. Functional annotation of target genes suggested that lncRNAs in F. pentaphylla may play roles in fruit color formation by regulating the expression of structural genes or regulatory factors. Construction of the regulatory network further revealed that the low expression of Fra a and CHS may be the main cause of colorless fruit in F. pentaphylla.
Collapse
Affiliation(s)
- Lijun Bai
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
- Chengdu Life Baseline Technology Co., LTD, Chengdu, China
| | - Qing Chen
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Leiyu Jiang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuanxiu Lin
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Yuntian Ye
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Peng Liu
- Chengdu Life Baseline Technology Co., LTD, Chengdu, China
| | - Xiaorong Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| | - Haoru Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu, 611130 China
| |
Collapse
|
92
|
Li X, Xing X, Xu S, Zhang M, Wang Y, Wu H, Sun Z, Huo Z, Chen F, Yang T. Genome-wide identification and functional prediction of tobacco lncRNAs responsive to root-knot nematode stress. PLoS One 2018; 13:e0204506. [PMID: 30427847 PMCID: PMC6235259 DOI: 10.1371/journal.pone.0204506] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/10/2018] [Indexed: 11/25/2022] Open
Abstract
Root-knot nematodes (RKNs, Meloidogyne spp.) are destructive plant parasites with a wide host range. They severely reduce crop quality and yield worldwide. Tobacco is a versatile model plant organism for studying RKNs-host interactions and a key plant material for molecular research. Long noncoding RNAs (lncRNAs) play critical roles in post transcriptional and transcriptional regulation in a wide range of biological pathways, especially plant development and stress response. In the present study, we obtained 5,206 high-confidence lncRNAs based on RNA sequencing data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed that the target genes of these lncRNAs are mainly involved in plant biotic and abiotic stresses, plant hormone signal transduction, induced systemic resistance, plant-type hypersensitive response, plant-type cell wall organization or biogenesis. The 565 differentially expressed lncRNAs found to be involved in nematode stress response were validated by quantitative PCR using 15 randomly-selected lncRNA genes. Our study provides insights into the molecular mechanisms of RKNs-plant interactions that might help preventing nematode damages to crops.
Collapse
Affiliation(s)
- Xiaohui Li
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Xuexia Xing
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Shixiao Xu
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Mingzhen Zhang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Yuan Wang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Hengyan Wu
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Zhihao Sun
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Zhaoguang Huo
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Fang Chen
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| | - Tiezhao Yang
- College of Tobacco, Henan Agricultural University, Zhengzhou city, Henan province, China
| |
Collapse
|
93
|
Shukla PS, Borza T, Critchley AT, Hiltz D, Norrie J, Prithiviraj B. Ascophyllum nodosum extract mitigates salinity stress in Arabidopsis thaliana by modulating the expression of miRNA involved in stress tolerance and nutrient acquisition. PLoS One 2018; 13:e0206221. [PMID: 30372454 PMCID: PMC6205635 DOI: 10.1371/journal.pone.0206221] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 10/09/2018] [Indexed: 11/25/2022] Open
Abstract
Ascophyllum nodosum extract (ANE) contains bioactive compounds that improve the growth of Arabidopsis in experimentally-induced saline conditions; however, the molecular mechanisms through which ANE elicits tolerance to salinity remain largely unexplored. Micro RNAs (miRNAs) are key regulators of gene expression, playing crucial roles in plant growth, development, and stress tolerance. Next generation sequencing of miRNAs from leaves of control Arabidopsis and from plants subjected to three treatments (ANE, NaCl and ANE+NaCl) was used to identify ANE-responsive miRNA in the absence and presence of saline conditions. Differential gene expression analysis revealed that ANE had a strong effect on miRNAs expression in both conditions. In the presence of salinity, ANE tended to reduce the up-regulation or the down-regulation trend induced caused by NaCl in miRNAs such as ath-miR396a-5p, ath-miR399, ath-miR2111b and ath-miR827. To further uncover the effects of ANE, the expression of several target genes of a number of ANE-responsive miRNAs was analyzed by qPCR. NaCl, but not ANE, down-regulated miR396a-5p, which negatively regulated the expression of AtGRF7 leading to a higher expression of AtDREB2a and AtRD29 in the presence of ANE+NaCl, as compared to ANE alone. ANE+NaCl initially reduced and then enhanced the expression of ath-miR169g-5p, while the expression of the target genes AtNFYA1 and ATNFYA2, known to be involved in the salinity tolerance mechanism, was increased as compared to ANE or to NaCl treatments. ANE and ANE+NaCl modified the expression of ath-miR399, ath-miR827, ath-miR2111b, and their target genes AtUBC24, AtWAK2, AtSYG1 and At3g27150, suggesting a role of ANE in phosphate homeostasis. In vivo and in vitro experiments confirmed the improved growth of Arabidopsis in presence of ANE, in saline conditions and in phosphate-deprived medium, further substantiating the influence of ANE on a variety of essential physiological processes in Arabidopsis including salinity tolerance and phosphate uptake.
Collapse
Affiliation(s)
- Pushp Sheel Shukla
- Marine Bio-products Research Laboratory, Dalhousie University, Department of Plant, Food and Environmental Sciences, Truro, Nova Scotia, Canada
| | - Tudor Borza
- Marine Bio-products Research Laboratory, Dalhousie University, Department of Plant, Food and Environmental Sciences, Truro, Nova Scotia, Canada
| | - Alan T. Critchley
- Research and Development, Acadian Seaplants Limited, Dartmouth, Nova Scotia, Canada
| | - David Hiltz
- Research and Development, Acadian Seaplants Limited, Dartmouth, Nova Scotia, Canada
| | - Jeff Norrie
- Research and Development, Acadian Seaplants Limited, Dartmouth, Nova Scotia, Canada
| | - Balakrishnan Prithiviraj
- Marine Bio-products Research Laboratory, Dalhousie University, Department of Plant, Food and Environmental Sciences, Truro, Nova Scotia, Canada
| |
Collapse
|
94
|
Saha D, Rana RS, Das S, Datta S, Mitra J, Cloutier SJ, You FM. Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes. J Appl Genet 2018; 60:13-25. [PMID: 30368734 DOI: 10.1007/s13353-018-0476-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 01/06/2023]
Abstract
We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions. The panel included 33 accessions from India, including released varieties, dual-purpose lines and landraces, and 60 fiber flax accessions from the global core collection. Thirty-one ReG-SSR markers generated 76 alleles, with an average of 2.5 alleles per primer and a mean allele frequency of 0.77. These markers recorded 0.32 average gene diversity, 0.26 polymorphism information content and 1.35% null alleles. All the 31 ReG-SSR loci were found selectively neutral and showed no evidence of population reduction. A model-based clustering analysis separated the flax accessions into two sub-populations-Indian and global, with some accessions showing admixtures. The distinct clustering pattern of the Indian accessions compared to the global accessions, conforms to the principal coordinate analysis, genetic dissimilarity-based unweighted neighbor-joining tree and analysis of molecular variance. Fourteen flax accessions with 99.3% allelic richness were found optimum to adopt in breeding programs. In summary, the genome-wide ReG-SSR markers will serve as a functional marker resource for genetic and phenotypic relationship studies, marker-assisted selections, and provide a basis for selection of accessions from the Indian and global gene pool in fiber flax breeding programs.
Collapse
Affiliation(s)
- Dipnarayan Saha
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.
| | - Rajeev Singh Rana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Shantanab Das
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India.,School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda University, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, 700103, India
| | - Subhojit Datta
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Jiban Mitra
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700121, India
| | - Sylvie J Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Frank M You
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB, R6M 1Y5, Canada
| |
Collapse
|
95
|
Mancini M, Permingeat H, Colono C, Siena L, Pupilli F, Azzaro C, de Alencar Dusi DM, de Campos Carneiro VT, Podio M, Seijo JG, González AM, Felitti SA, Ortiz JPA, Leblanc O, Pessino SC. The MAP3K-Coding QUI-GON JINN ( QGJ) Gene Is Essential to the Formation of Unreduced Embryo Sacs in Paspalum. FRONTIERS IN PLANT SCIENCE 2018; 9:1547. [PMID: 30405677 PMCID: PMC6207905 DOI: 10.3389/fpls.2018.01547] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/03/2018] [Indexed: 05/20/2023]
Abstract
Apomixis is a clonal mode of reproduction via seeds, which results from the failure of meiosis and fertilization in the sexual female reproductive pathway. In previous transcriptomic surveys, we identified a mitogen-activated protein kinase kinase kinase (N46) displaying differential representation in florets of sexual and apomictic Paspalum notatum genotypes. Here, we retrieved and characterized the N46 full cDNA sequence from sexual and apomictic floral transcriptomes. Phylogenetic analyses showed that N46 was a member of the YODA family, which was re-named QUI-GON JINN (QGJ). Differential expression in florets of sexual and apomictic plants was confirmed by qPCR. In situ hybridization experiments revealed expression in the nucellus of aposporous plants' ovules, which was absent in sexual plants. RNAi inhibition of QGJ expression in two apomictic genotypes resulted in significantly reduced rates of aposporous embryo sac formation, with respect to the level detected in wild type aposporous plants and transformation controls. The QGJ locus segregated independently of apospory. However, a probe derived from a related long non-coding RNA sequence (PN_LNC_QGJ) revealed RFLP bands cosegregating with the Paspalum apospory-controlling region (ACR). PN_LNC_QGJ is expressed in florets of apomictic plants only. Our results indicate that the activity of QGJ in the nucellus of apomictic plants is necessary to form non-reduced embryo sacs and that a long non-coding sequence with regulatory potential is similar to sequences located within the ACR.
Collapse
Affiliation(s)
- Micaela Mancini
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Hugo Permingeat
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Carolina Colono
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Lorena Siena
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Fulvio Pupilli
- Istituto di Bioscienze e BioRisorse, Consiglio Nazionale delle Ricerche, Perugia, Italy
| | - Celeste Azzaro
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | | | | | - Maricel Podio
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - José Guillermo Seijo
- Instituto de Botánica del Nordeste, CONICET-UNNE, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Ana María González
- Instituto de Botánica del Nordeste, CONICET-UNNE, Corrientes, Argentina
- Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Silvina A. Felitti
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | - Juan Pablo A. Ortiz
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| | | | - Silvina C. Pessino
- Instituto de Investigaciones en Ciencias Agrarias de Rosario, CONICET-UNR, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Argentina
| |
Collapse
|
96
|
Danilevicz MF, Moharana KC, Venancio TM, Franco LO, Cardoso SRS, Cardoso M, Thiebaut F, Hemerly AS, Prosdocimi F, Ferreira PCG. Copaifera langsdorffii Novel Putative Long Non-Coding RNAs: Interspecies Conservation Analysis in Adaptive Response to Different Biomes. Noncoding RNA 2018; 4:ncrna4040027. [PMID: 30297664 PMCID: PMC6316758 DOI: 10.3390/ncrna4040027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in multiple regulatory pathways and its versatile form of action has disclosed a new layer in gene regulation. LncRNAs have their expression levels modulated during plant development, and in response to stresses with tissue-specific functions. In this study, we analyzed lncRNA from leaf samples collected from the legume Copaifera langsdorffii Desf. (copaíba) present in two divergent ecosystems: Cerrado (CER; Ecological Station of Botanical Garden in Brasília, Brazil) and Atlantic Rain Forest (ARF; Rio de Janeiro, Brazil). We identified 8020 novel lncRNAs, and they were compared to seven Fabaceae genomes and transcriptomes, to which 1747 and 2194 copaíba lncRNAs were mapped, respectively, to at least one species. The secondary structures of the lncRNAs that were conserved and differentially expressed between the populations were predicted using in silico methods. A few selected lncRNA were confirmed by RT-qPCR in the samples from both biomes; Additionally, the analysis of the lncRNA sequences predicted that some might act as microRNA (miRNA) targets or decoys. The emerging studies involving lncRNAs function and conservation have shown their involvement in several types of biotic and abiotic stresses. Thus, the conservation of lncRNAs among Fabaceae species considering their rapid turnover, suggests they are likely to have been under functional conservation pressure. Our results indicate the potential involvement of lncRNAs in the adaptation of C. langsdorffii in two different biomes.
Collapse
Affiliation(s)
- Monica F Danilevicz
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Kanhu C Moharana
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Rio de Janeiro 28013-602, Brazil.
| | - Luciana O Franco
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Sérgio R S Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Mônica Cardoso
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Diretoria de Pesquisa Científica, Rio de Janeiro 22460-030, Brazil.
| | - Flávia Thiebaut
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Adriana S Hemerly
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Francisco Prosdocimi
- Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| | - Paulo C G Ferreira
- Laboratório de Biologia Molecular de Plantas, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-599, Brazil.
| |
Collapse
|
97
|
Li WQ, Jia YL, Liu FQ, Wang FQ, Fan FJ, Wang J, Zhu JY, Xu Y, Zhong WG, Yang J. Genome-wide identification and characterization of long non-coding RNAs responsive to Dickeya zeae in rice. RSC Adv 2018; 8:34408-34417. [PMID: 35548658 PMCID: PMC9087051 DOI: 10.1039/c8ra04993a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/09/2018] [Indexed: 11/26/2022] Open
Abstract
Plant long non-coding RNA (lncRNA) is a type of newly emerging epigenetic regulator playing a critical role in plant growth, development, and biotic stress responses. However, it is unknown whether lncRNAs are involved in resistance responses between rice and Dickeya zeae, a bacterial agent causing rice foot rot disease. In this study, RNA-seq was performed to uncover the co-expression regulating networks mediated by D. zeae responsive lncRNAs and their candidate target genes. Of the 4709 lncRNAs identified, 2518 and 2191 were up- and down-regulated in response to D. zeae infection, respectively. Expression changes of 17 selected lncRNAs and their predicted targets with a potential role in defense response were investigated by qPCR. The expression levels of five lncRNAs were up-regulated while their cognate candidate target genes were down-regulated upon D. zeae infection. In addition, several lncRNAs were predicted to be target mimics of osa-miR396 and osa-miR156. These results suggest that lncRNAs might play a role in response to D. zeae infection by regulating the transcript levels of their targets and miRNAs in rice.
Collapse
Affiliation(s)
- Wen Qi Li
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Yu Lin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center Stuttgart 72160 USA
| | - Feng Quan Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences Nanjing 210014 China
| | - Fang Quan Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Fang Jun Fan
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jun Wang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jin Yan Zhu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Yang Xu
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Wei Gong Zhong
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| | - Jie Yang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Branch of Chinese National Center for Rice Improvement, Jiangsu High Quality Rice R&D Center Nanjing 210014 China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University Yangzhou 225009 China
| |
Collapse
|
98
|
Huang L, Dong H, Zhou D, Li M, Liu Y, Zhang F, Feng Y, Yu D, Lin S, Cao J. Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:203-222. [PMID: 29975432 DOI: 10.1111/tpj.14016] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/18/2018] [Accepted: 06/26/2018] [Indexed: 05/21/2023]
Abstract
The importance of long non-coding RNAs (lncRNAs) in plant development has been established, but a systematic analysis of lncRNAs expressed during pollen development and fertilization has been elusive. We performed a time series of RNA-seq experiments at five developmental stages during pollen development and three different time points after pollination in Brassica rapa and identified 12 051 putative lncRNAs. A comprehensive view of dynamic lncRNA expression networks underpinning pollen development and fertilization was provided. B. rapa lncRNAs share many common characteristics of lncRNAs: relatively short length, low expression but specific in narrow time windows, and low evolutionary conservation. Gene modules and key lncRNAs regulating reproductive development such as exine formation were uncovered. Forty-seven cis-acting lncRNAs and 451 trans-acting lncRNAs were revealed to be highly coexpressed with their target protein-coding genes. Of particular importance are the discoveries of 14 lncRNAs that were highly coexpressed with 10 function-known pollen-associated coding genes. Fifteen lncRNAs were predicted as endogenous target mimics for 13 miRNAs, and two lncRNAs were proved to be functional target mimics for miR160 after experimental verification and shown to function in pollen development. Our study provides the systematic identification of lncRNAs during pollen development and fertilization in B. rapa and forms the foundation for future genetic, genomic, and evolutionary studies.
Collapse
Affiliation(s)
- Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Heng Dong
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dong Zhou
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Ming Li
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yanhong Liu
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Fang Zhang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Yaoyao Feng
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| | - Dongliang Yu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Sue Lin
- Institute of Life Sciences, Wenzhou University, Wenzhou, 325000, China
| | - Jiashu Cao
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Hangzhou, 310058, China
| |
Collapse
|
99
|
Kirk JM, Kim SO, Inoue K, Smola MJ, Lee DM, Schertzer MD, Wooten JS, Baker AR, Sprague D, Collins DW, Horning CR, Wang S, Chen Q, Weeks KM, Mucha PJ, Calabrese JM. Functional classification of long non-coding RNAs by k-mer content. Nat Genet 2018; 50:1474-1482. [PMID: 30224646 PMCID: PMC6262761 DOI: 10.1038/s41588-018-0207-8] [Citation(s) in RCA: 131] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 07/24/2018] [Indexed: 12/30/2022]
Abstract
The functions of most long non-coding RNAs (lncRNAs) are unknown. In contrast to proteins, lncRNAs with similar functions often lack linear sequence homology; thus, the identification of function in one lncRNA rarely informs the identification of function in others. We developed a sequence comparison method to deconstruct linear sequence relationships in lncRNAs and evaluate similarity based on the abundance of short motifs called kmers. We found that lncRNAs of related function often had similar kmer profiles despite lacking linear homology, and that kmer profiles correlated with protein binding to lncRNAs and with their subcellular localization. Using a novel assay to quantify Xist-like regulatory potential, we directly demonstrated that evolutionarily unrelated lncRNAs can encode similar function through different spatial arrangements of related sequence motifs. Kmer-based classification is a powerful approach to detect recurrent relationships between sequence and function in lncRNAs.
Collapse
Affiliation(s)
- Jessime M Kirk
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan O Kim
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Kaoru Inoue
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
| | - Matthew J Smola
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Ribometrix, Durham, NC, USA
| | - David M Lee
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Megan D Schertzer
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joshua S Wooten
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison R Baker
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Harvard Medical School, Ph.D. Program in Biological and Biomedical Sciences, Boston, MA, USA
| | - Daniel Sprague
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - David W Collins
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Christopher R Horning
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Shuo Wang
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qidi Chen
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - J Mauro Calabrese
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| |
Collapse
|
100
|
Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes (Basel) 2018; 9:E459. [PMID: 30223541 PMCID: PMC6162444 DOI: 10.3390/genes9090459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.
Collapse
Affiliation(s)
- Priyanka Borah
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Antara Das
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Matthew J Milner
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Arif Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Alison R Bentley
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
| |
Collapse
|