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Zhao W, Meng X, Xu J, Liu Z, Hu Y, Li B, Chen J, Cao B. Integrated mRNA and Small RNA Sequencing Reveals microRNAs Associated With Xylem Development in Dalbergia odorifera. Front Genet 2022; 13:883422. [PMID: 35547261 PMCID: PMC9081728 DOI: 10.3389/fgene.2022.883422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/23/2022] [Indexed: 11/13/2022] Open
Abstract
Dalbergia odorifera is a rare and precious rosewood specie, whose wood is a very high-quality material for valuable furniture and carving crafts. However, limited information is available about the process of wood formation in D. odorifera. To determine genes that might be closely associated with the xylem differentiation process, we analyzed the differentially expressed genes (DEGs) and microRNAs (miRNAs) from specific xylem tissues of D. odorifera by RNA sequencing (RNA-seq) and small RNA sequencing (small RNA-seq). In total, we obtained 134,221,955 clean reads from RNA-seq and 90,940,761 clean reads from small RNA-seq. By comparing the transition zone (Dotz) and sapwood (Dosw) samples, a total of 395 DEGs were identified. Further analysis revealed that DEGs encoded for WRKY transcription factors (eight genes), lignin synthesis (PER47, COMT, CCR2), cell wall composition (UXS2), gibberellin synthesis (KAO2, GA20OX1), jasmonic acid synthesis (OPR2, CYP74A), and synthesis of flavonoids (PAL2) and terpenoids (CYP71A1). Subsequently, a preliminary analysis by small RNA-seq showed that the expressions of 14 miRNAs (such as miR168a-5p, miR167f-5p, miR167h-5p, miR167e, miR390a, miR156g, novel_52, and novel_9) were significantly different between Dotz and Dosw. Further analysis revealed that the target genes of these differentially expressed miRNAs were enriched in the GO terms "amino acid binding," "cellulase activity," and "DNA beta-glucosyltransferase activity". Further, KEGG pathway annotation showed significant enrichment in "fatty acid elongation" and "biosynthesis of unsaturated fatty acids". These processes might be participating in the xylem differentiation of D. odorifera. Next, expression correlation analysis showed that nine differentially expressed miRNAs were significantly negatively associated with 21 target genes, which encoded for proteins such as pyrH, SPL6, SPL12, GCS1, and ARF8. Overall, this is the first study on miRNAs and their potential functions in the xylem development of D. odorifera, which provides a stepping stone for a detailed functional investigation of D. odorifera miRNAs.
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Affiliation(s)
- Wenxiu Zhao
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiangxu Meng
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jiahong Xu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Zijia Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yangyang Hu
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Bingyu Li
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
| | - Jinhui Chen
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education/Engineering Research Center of Rare and Precious Tree Species in Hainan Province, School of Forestry, Hainan University, Haikou, China
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Bing Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
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Shah SMS, Ullah F. A comprehensive overview of miRNA targeting drought stress resistance in plants. BRAZ J BIOL 2021; 83:e242708. [PMID: 34495144 DOI: 10.1590/1519-6984.242708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/06/2021] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs (miRNAs) are essential nonprotein-coding genes. In a range of organisms, miRNAs has been reported to play an essential role in regulating gene expressions at post-transcriptional level. They participate in most of the stress responsive processes in plants. Drought is an ultimate abiotic stress that affects the crop production. Therefore understanding drought stress responses are essential to improve the production of agricultural crops. Throughout evolution, plants have developed their own defense systems to cope with the adversities of environmental stresses. Among defensive mechanisms include the regulations of gene expression by miRNAs. Drought stress regulates the expression of some of the functionally conserved miRNAs in different plants. The given properties of miRNAs provide an insight to genetic alterations and enhancing drought resistance in cereal crops. The current review gives a summary to regulatory mechanisms in plants as well as miRNAs response to drought stresses in cereal crops. Some possible approaches and guidelines for the exploitation of drought stress miRNA responses to improve cereal crops are also described.
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Affiliation(s)
- S M S Shah
- Chinese Academy of Agricultural Sciences, Institute of Crop Science, National Engineering Laboratory for Crop Molecular Breeding, Beijing, China
| | - F Ullah
- Huazhong Agriculture University, National Key Laboratory of Crop Genetic Improvement, Wuhan, Hubei, China
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Xiao L, Man L, Yang L, Zhang J, Liu B, Quan M, Lu W, Fang Y, Wang D, Du Q, Zhang D. Association Study and Mendelian Randomization Analysis Reveal Effects of the Genetic Interaction Between PtoMIR403b and PtoGT31B-1 on Wood Formation in Populus tomentosa. FRONTIERS IN PLANT SCIENCE 2021; 12:704941. [PMID: 34527007 PMCID: PMC8435637 DOI: 10.3389/fpls.2021.704941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), important posttranscriptional regulators of gene expression, play a crucial role in plant growth and development. A single miRNA can regulate numerous target genes, making the determination of its function and interaction with targets challenging. We identified PtomiR403b target to PtoGT31B-1, which encodes a galactosyltransferase responsible for the biosynthesis of cell wall polysaccharides. We performed an association study and epistasis and Mendelian randomization (MR) analyses to explore how the genetic interaction between PtoMIR403b and its target PtoGT31B-1 underlies wood formation. Single nucleotide polymorphism (SNP)-based association studies identified 25 significant associations (P < 0.01, Q < 0.05), and PtoMIR403b and PtoGT31B-1 were associated with five traits, suggesting a role for PtomiR403b and PtoGT31B-1 in wood formation. Epistasis analysis identified 93 significant pairwise epistatic associations with 10 wood formation traits, and 37.89% of the SNP-SNP pairs indicated interactions between PtoMIR403b and PtoGT31B-1. We performed an MR analysis to demonstrate the causality of the relationships between SNPs in PtoMIR403b and wood property traits and that PtoMIR403b modulates wood formation by regulating expression of PtoGT31B-1. Therefore, our findings will facilitate dissection of the functions and interactions with miRNA-targets.
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Affiliation(s)
- Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Liting Man
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Xining Forestry Science Research Institute, Xining, China
| | - Lina Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinmei Zhang
- Xining Forestry Science Research Institute, Xining, China
| | - Baoyao Liu
- Xining Forestry Science Research Institute, Xining, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Dan Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Wang R, Reng M, Tian S, Liu C, Cheng H, Liu Y, Zhang H, Saqib M, Wei H, Wei Z. Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa. G3 (BETHESDA, MD.) 2021; 11:jkab195. [PMID: 34849817 PMCID: PMC8633455 DOI: 10.1093/g3journal/jkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 05/29/2021] [Indexed: 01/15/2023]
Abstract
We applied miRNA expression profiling method to Populus trichocarpa stems of the three developmental stages, primary stem (PS), transitional stem (TS), and secondary stem (SS), to investigate miRNA species and their regulation on lignocellulosic synthesis and related processes. We obtained 892, 872, and 882 known miRNAs and 1727, 1723, and 1597 novel miRNAs, from PS, TS, and SS, respectively. Comparisons of these miRNA species among different developmental stages led to the identification of 114, 306, and 152 differentially expressed miRNAs (DE-miRNAs), which had 921, 2639, and 2042 candidate target genes (CTGs) in the three respective stages of the same order. Correlation analysis revealed 47, 439, and 71 DE-miRNA-CTG pairs of high negative correlation in PS, TS, and SS, respectively. Through biological process analysis, we finally identified 34, 6, and 76 miRNA-CTG pairs from PS, TS, and SS, respectively, and the miRNA target genes in these pairs regulate or participate lignocellulosic biosynthesis-related biological processes: cell division and differentiation, cell wall modification, secondary cell wall biosynthesis, lignification, and programmed cell death processes. This is the first report on an integrated analysis of genome-wide mRNA and miRNA profilings during multiple phases of poplar stem development. Our analysis results imply that individual miRNAs modulate secondary growth and lignocellulosic biosynthesis through regulating transcription factors and lignocellulosic biosynthetic pathway genes, resulting in more dynamic promotion, suppression, or regulatory circuits. This study advanced our understanding of many individual miRNAs and their essential, diversified roles in the dynamic regulation of secondary growth in woody tree species.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Mengxuan Reng
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Shuanghui Tian
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Cong Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - He Cheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Yingying Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Heilongjiang Harbin 150040, China
| | - Huaxin Zhang
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
| | - Muhammad Saqib
- Institute of Soil and Environmental Sciences, University of Agriculture, Faisalabad 38000, Pakistan
| | - Hairong Wei
- College of Forest Resource and Environmental Science, Michigan Technological University, Houghton MI49931, USA
| | - Zhigang Wei
- Research Center of Saline and Alkali Land of State Forestry and Grassland Administration, Chinese Academy of Forestry, Beijing 100091, China
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5
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Zheng WQ, Zhang Y, Chen B, Wei M, Wang XW, Du L. Identification and Characterization of circRNAs in the Developing Stem Cambium of Poplar Seedlings. Mol Biol 2020. [DOI: 10.1134/s0026893320050131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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Si J, Quan M, Xiao L, Xie J, Du Q, Zhang D. Genetic interactions among Pto-miR319 family members and their targets influence growth and wood properties in Populus tomentosa. Mol Genet Genomics 2020; 295:855-870. [PMID: 32361785 DOI: 10.1007/s00438-020-01667-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/16/2020] [Indexed: 11/25/2022]
Abstract
MicroRNAs (miRNAs) play crucial roles in all aspects of plant growth and development, but the genetic interactions of miRNAs and their target genes in woody plants are largely unknown. Here, we integrated association genetics and expression profiling to decipher the allelic variations and interactions of the Pto-MIR319 family of miRNAs and 12 putative Pto-miR319 target genes related to wood formation in 435 unrelated individuals of Populus tomentosa Carrière (Chinese white poplar). Expression pattern analysis showed that among all pairings between expressions of pre-miRNA of Pto-MIR319 members and targets, 70.0% showed negative correlation of expression levels (r = - 0.944 to 0.674, P < 0.01) in eight tissues and organs of poplar, suggesting that Pto-miR319 may participate in the regulatory network of wood formation. Single SNP-based association studies identified 137 significant associations (P < 0.01, Q < 0.1), representing 126 unique SNPs from Pto-MIR319 members and their targets, with 10 tree growth traits, revealing that these genetic factors have common roles related to wood formation. Epistasis analysis uncovered 105 significant SNP-SNP associations (P < 0.01) influencing the 10 traits, demonstrating the close genetic interactions between Pto-MIR319 family members and the 12 Pto-miR319 target genes. Notably, one common SNP, in the precursor region of Pto-MIR319e, affected the stability of Pto-MIR319e's secondary structure by altering the stem-loop structure and minimum free energy, contributing to variations in the expression of Pto-MIR319e and Pto-miR319e target genes. This study enriches the understanding of the functions of miR319 family miRNAs in poplar and exemplifies a feasible approach to exploring the genetic effects underlying miRNA-mRNA interactions related to complex traits in trees.
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Affiliation(s)
- Jingna Si
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Jianbo Xie
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.,Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. .,Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China. .,Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Forestry University, No. 35, Qinghua East Road, Beijing, 100083, P. R. China.
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7
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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.
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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
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Liu Q, Ding C, Lang X, Guo G, Chen J, Su X. Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. Brief Bioinform 2019; 22:463-473. [PMID: 31885040 PMCID: PMC7820841 DOI: 10.1093/bib/bbz151] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/24/2019] [Accepted: 11/01/2019] [Indexed: 02/05/2023] Open
Abstract
Small noncoding RNAs (sRNA/sncRNAs) are generated from different genomic loci and play important roles in biological processes, such as cell proliferation and the regulation of gene expression. Next-generation sequencing (NGS) has provided an unprecedented opportunity to discover and quantify diverse kinds of sncRNA, such as tRFs (tRNA-derived small RNA fragments), phasiRNAs (phased, secondary, small-interfering RNAs), Piwi-interacting RNA (piRNAs) and plant-specific 24-nt short interfering RNAs (siRNAs). However, currently available web-based tools do not provide approaches to comprehensively analyze all of these diverse sncRNAs. This study presents a novel integrated platform, sRNAtools (https://bioinformatics.caf.ac.cn/sRNAtools), that can be used in conjunction with high-throughput sequencing to identify and functionally annotate sncRNAs, including profiling microRNAss, piRNAs, tRNAs, small nuclear RNAs, small nucleolar RNAs and rRNAs and discovering isomiRs, tRFs, phasiRNAs and plant-specific 24-nt siRNAs for up to 21 model organisms. Different modules, including single case, batch case, group case and target case, are developed to provide users with flexible ways of studying sncRNA. In addition, sRNAtools supports different ways of uploading small RNA sequencing data in a very interactive queue system, while local versions based on the program package/Docker/virtureBox are also available. We believe that sRNAtools will greatly benefit the scientific community as an integrated tool for studying sncRNAs.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaoqiang Lang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Ganggang Guo
- Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China 610041
| | - Jiafei Chen
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Key Laboratory of Tree Breeding and Cultivation of the State Forestry Administration, Beijing 10091, China
| | - Xiaohua Su
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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