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Feng Y, Qi N, Lei P, Wang Y, Xuan Y, Liu X, Fan H, Chen L, Duan Y, Zhu X. Gma-miR408 Enhances Soybean Cyst Nematode Susceptibility by Suppressing Reactive Oxygen Species Accumulation. Int J Mol Sci 2022; 23:ijms232214022. [PMID: 36430501 PMCID: PMC9695887 DOI: 10.3390/ijms232214022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/10/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycine) is a serious damaging disease in soybean worldwide, thus resulting in severe yield losses. MicroRNA408 (miR408) is an ancient and highly conserved miRNA involved in regulating plant growth, development, biotic and abiotic stress response. Here, we analyzed the evolution of miR408 in plants and verified four miR408 members in Glycine max. In the current research, highly upregulated gma-miR408 expressing was detected during nematode migration and syncytium formation response to soybean cyst nematode infection. Overexpressing and silencing miR408 vectors were transformed to soybean to confirm its potential role in plant and nematode interaction. Significant variations were observed in the MAPK signaling pathway with low OXI1, PR1, and wounding of the overexpressing lines. Overexpressing miR408 could negatively regulate soybean resistance to SCN by suppressing reactive oxygen species accumulation. Conversely, silencing miR408 positively regulates soybean resistance to SCN. Overall, gma-miR408 enhances soybean cyst nematode susceptibility by suppressing reactive oxygen species accumulation.
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Affiliation(s)
- Yaxing Feng
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Nawei Qi
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Science, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
- Correspondence:
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Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
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Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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Su H, Fan J, Ma D, Zhu H. Identification and Characterization of Osmoregulation Related MicroRNAs in Gills of Hybrid Tilapia Under Three Types of Osmotic Stress. Front Genet 2021; 12:526277. [PMID: 33889171 PMCID: PMC8056028 DOI: 10.3389/fgene.2021.526277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 02/24/2021] [Indexed: 11/13/2022] Open
Abstract
Researchers have increasingly suggested that microRNAs (miRNAs) are small non-coding RNAs that post-transcriptionally regulate gene expression and protein translation in organs and respond to abiotic and biotic stressors. To understand the function of miRNAs in osmotic stress regulation of the gills of hybrid tilapia (Oreochromis mossambicus ♀ × Oreochromis urolepis hornorum ♂), high-throughput Illumina deep sequencing technology was used to investigate the expression profiles of miRNAs under salinity stress (S, 25‰), alkalinity stress (A, 4‰) and salinity-alkalinity stress (SA, S: 15‰, A: 4‰) challenges. The results showed that 31, 41, and 27 upregulated and 33, 42, and 40 downregulated miRNAs (P < 0.05) were identified in the salt stress, alkali stress, and saline-alkali stress group, respectively, which were compared with those in the control group (C). Fourteen significantly differently expressed miRNAs were selected randomly and then validated by a quantitative polymerase chain reaction. On the basis of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, genes related to osmoregulation and biosynthesis were enriched in the three types of osmotic stress. In addition, three miRNAs and three predicted target genes were chosen to conduct a quantitative polymerase chain reaction in the hybrid tilapia and its parents during 96-h osmotic stress. Differential expression patterns of miRNAs provided the basis for research data to further investigate the miRNA-modulating networks in osmoregulation of teleost.
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Affiliation(s)
- Huanhuan Su
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiajia Fan
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Dongmei Ma
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Huaping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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Zhao T, Tao X, Feng S, Wang L, Hong H, Ma W, Shang G, Guo S, He Y, Zhou B, Guan X. LncRNAs in polyploid cotton interspecific hybrids are derived from transposon neofunctionalization. Genome Biol 2018; 19:195. [PMID: 30419941 PMCID: PMC6233382 DOI: 10.1186/s13059-018-1574-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Interspecific hybridization and whole genome duplication are driving forces of genomic and organism diversification. But the effect of interspecific hybridization and whole genome duplication on the non-coding portion of the genome in particular remains largely unknown. In this study, we examine the profile of long non-coding RNAs (lncRNAs), comparing them with that of coding genes in allotetraploid cotton (Gossypium hirsutum), its putative diploid ancestors (G. arboreum; G. raimondii), and an F1 hybrid (G. arboreum × G. raimondii, AD). RESULTS We find that most lncRNAs (80%) that were allelic expressed in the allotetraploid genome. Moreover, the genome shock of hybridization reprograms the non-coding transcriptome in the F1 hybrid. Interestingly, the activated lncRNAs are predominantly transcribed from demethylated TE regions, especially from long interspersed nuclear elements (LINEs). The DNA methylation dynamics in the interspecies hybridization are predominantly associated with the drastic expression variation of lncRNAs. Similar trends of lncRNA bursting are also observed in the progress of polyploidization. Additionally, we find that a representative novel lncRNA XLOC_409583 activated after polyploidization from a LINE in the A subgenome of allotetraploid cotton was involved in control of cotton seedling height. CONCLUSION Our results reveal that the processes of hybridization and polyploidization enable the neofunctionalization of lncRNA transcripts, acting as important sources of increased plasticity for plants.
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Affiliation(s)
- Ting Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Xiaoyuan Tao
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Shouli Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Luyao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Hui Hong
- National Key Laboratory of Plant Molecular Genetics, National Plant Gene Research Center, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Wei Ma
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China
| | - Guandong Shang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Shisong Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yuxin He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
| | - Xueying Guan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
- College of Agriculture and Biotechnology, Zhejiang University, Zhejiang, 210058, Hangzhou, China.
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Qiang J, Cui YT, Tao FY, Bao WJ, He J, Li XH, Xu P, Sun LY. Physiological response and microRNA expression profiles in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to acute cold stress. Sci Rep 2018; 8:172. [PMID: 29317697 PMCID: PMC5760732 DOI: 10.1038/s41598-017-18512-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022] Open
Abstract
Cold stress has a serious impact on the overwintering survival and yield of genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Understanding the physiological and molecular regulation mechanisms of low-temperature adaptation is necessary to help breed new tolerant strains. The semi-lethal low temperature of juvenile GIFT at 96 h was determined as 9.4 °C. We constructed and sequenced two small RNA libraries from head kidney tissues, one for the control (CO) group and one for the 9.4 °C-stressed (LTS) group, and identified 1736 and 1481 known microRNAs (miRNAs), and 164 and 152 novel miRNAs in the CO and LTS libraries, respectively. We verify the expression of nine up-regulated miRNAs and eight down-regulation miRNAs by qRT-PCR, and found their expression patterns were consistent with the sequencing results. We found that cold stress may have produced dysregulation of free radical and lipid metabolism, decreased superoxide dismutase activity, reduced respiratory burst and phagocytic activity of macrophages, increased malondialdehyde content, and adversely affected the physiological adaptation of GIFT, eventually leading to death. This study revealed interactions among miRNAs and signal regulated pathways in GIFT under cold stress that may help to understand the pathways involved in cold resistance.
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Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Yan T Cui
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Fan Y Tao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Wen J Bao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Xia H Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China. .,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Lan Y Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
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Xu S, Liu N, Mao W, Hu Q, Wang G, Gong Y. Identification of chilling-responsive microRNAs and their targets in vegetable soybean (Glycine max L.). Sci Rep 2016; 6:26619. [PMID: 27216963 PMCID: PMC4877674 DOI: 10.1038/srep26619] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 05/04/2016] [Indexed: 11/09/2022] Open
Abstract
Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. In the present study, systematic identification and functional analysis of miRNAs under chilling stress were carried out to clarify the molecular mechanism of chilling resistance. Two independent small RNA libraries from leaves of soybean were constructed and sequenced with the high-throughput Illumina Solexa system. A total of 434 known miRNAs and 3 novel miRNAs were identified. Thirty-five miRNAs were verified by qRT-PCR analysis. Furthermore, their gene targets were identified via high-throughput degradome sequencing. A total of 898 transcripts were targeted by 54 miRNA families attributed to five categories. More importantly, we identified 51 miRNAs differentially expressed between chilling stress and control conditions. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. Our qRT-PCR analysis confirmed a negative relationship among the miRNAs and their targets under chilling stress. Our work thus provides comprehensive molecular evidence supporting the involvement of miRNAs in chilling-stress responses in vegetable soybean.
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Affiliation(s)
- Shengchun Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Weihua Mao
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, 310058, China
| | - Qizan Hu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Guofu Wang
- Department of Life Science, Yuanpei College, Shaoxing University, Shaoxing 312000, China
| | - Yaming Gong
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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Wang X, Ai G, Zhang C, Cui L, Wang J, Li H, Zhang J, Ye Z. Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. THE NEW PHYTOLOGIST 2016; 209:1442-55. [PMID: 26494192 DOI: 10.1111/nph.13718] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 09/20/2015] [Indexed: 05/20/2023]
Abstract
Long noncoding RNAs (lncRNAs) regulate gene expression and biological processes. With the development of high-throughput RNA sequencing technology, lncRNAs have been extensively studied in recent years. Nevertheless, the expression and evolution of lncRNAs in plants remain poorly understood. Here, we identified 413 and 709 multi-exon noncoding transcripts from 353 and 595 loci of the cultivar tomato Heinz1706 and its wild relative LA1589, respectively. Systematic comparison of the sequence and expression of lncRNAs showed that they are poorly conserved in Solanaceae, with only < 0.4% lncRNAs present in all sequenced genomes of tomato and potato. Sequence analysis of Lycopersicon-specific lncRNA loci in Solanum lycopersicum and S. pennellii showed that the origins of these molecules are associated with transposable elements (TEs). LncRNA-314, a fruit-specific lncRNA expressed in S. lycopersicum and S. pimpinellifolium, but not in S. pennellii, originated through two evolutionary events: speciation of S. pennellii resulted in insertion of a long terminal repeat (LTR) retrotransposon into chromosome 10 and contributed to most of the transcribed region of lncRNA-314; and a large deletion in Lycopersicon generated the promoter region and part of the transcribed region of lncRNA-314. These results provide novel insights into the evolution of lncRNAs in plants.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guo Ai
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Chunli Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Long Cui
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jiafa Wang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hanxia Li
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Junhong Zhang
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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