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Luo C, He B, Shi P, Xi J, Gui H, Pang B, Cheng J, Hu F, Chen X, Lv Y. Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa. FRONTIERS IN PLANT SCIENCE 2022; 13:988845. [PMID: 36204077 PMCID: PMC9530330 DOI: 10.3389/fpls.2022.988845] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/24/2022] [Indexed: 06/01/2023]
Abstract
Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.
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Affiliation(s)
- Chuping Luo
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Pibiao Shi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jinlong Xi
- Zhejiang Institute of Standardization, Hangzhou, China
| | - Hongbing Gui
- College of Animal Husbandry and Veterinary Medicine, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Bingwen Pang
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junjie Cheng
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xi Chen
- School of Agronomy and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, China
| | - Yuanda Lv
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Yang M, Lu H, Liu J, Wu S, Kim P, Zhou X. lncRNAfunc: a knowledgebase of lncRNA function in human cancer. Nucleic Acids Res 2022; 50:D1295-D1306. [PMID: 34791419 PMCID: PMC8728133 DOI: 10.1093/nar/gkab1035] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 02/05/2023] Open
Abstract
The long non-coding RNAs associating with other molecules can coordinate several physiological processes and their dysfunction can impact diverse human diseases. To date, systematic and intensive annotations on diverse interaction regulations of lncRNAs in human cancer were not available. Here, we built lncRNAfunc, a knowledgebase of lncRNA function in human cancer at https://ccsm.uth.edu/lncRNAfunc, aiming to provide a resource and reference for providing therapeutically targetable lncRNAs and intensive interaction regulations. To do this, we collected 15 900 lncRNAs across 33 cancer types from TCGA. For individual lncRNAs, we performed multiple interaction analyses of different biomolecules including DNA, RNA, and protein levels. Our intensive studies of lncRNAs provide diverse potential mechanisms of lncRNAs that regulate gene expression through binding enhancers and 3'-UTRs of genes, competing for miRNA binding sites with mRNAs, recruiting the transcription factors to gene promoters. Furthermore, we investigated lncRNAs that potentially affect the alternative splicing events through interacting with RNA binding Proteins. We also performed multiple functional annotations including cancer stage-associated lncRNAs, RNA A-to-I editing event-associated lncRNAs, and lncRNA expression quantitative trait loci. lncRNAfunc is a unique resource for cancer research communities to help better understand potential lncRNA regulations and therapeutic lncRNA targets.
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Affiliation(s)
- Mengyuan Yang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Huifen Lu
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Med-X Center for Informatics, Sichuan University, Chengdu 610041, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- College of Electronic and Information Engineering, Tongji University, Shanghai, Shanghai 201804, China
| | - Sijia Wu
- School of Life Sciences and Technology, Xidian University, Xi'an 710126, China
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- School of Dentistry, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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Luo X, Xu L, Liang D, Wang Y, Zhang W, Zhu X, Zhu Y, Jiang H, Tang M, Liu L. Comparative transcriptomics uncovers alternative splicing and molecular marker development in radish (Raphanus sativus L.). BMC Genomics 2017; 18:505. [PMID: 28673249 PMCID: PMC5496183 DOI: 10.1186/s12864-017-3874-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 06/20/2017] [Indexed: 11/17/2022] Open
Abstract
Background Alternative splicing (AS) plays important roles in gene expression and proteome diversity. Single nucleotide polymorphism (SNP) and insertion/deletion (InDel) are abundant polymorphisms and co-dominant inheritance markers, which have been widely used in germplasm identification, genetic mapping and marker-assisted selection in plants. So far, however, little information is available on utilization of AS events and development of SNP and InDel markers from transcriptome in radish. Results In this study, three radish transcriptome datasets were collected and aligned to the reference radish genome. A total of 56,530 AS events were identified from three radish genotypes with intron retention (IR) being the most frequent AS type, which accounted for 59.4% of the total expressed genes in radish. In all, 22,412 SNPs and 9436 InDels were identified with an average frequency of 1 SNP/17.9 kb and 1 InDel/42.5 kb, respectively. A total of 43,680 potential SSRs were identified in 31,604 assembled unigenes with a density of 1 SSR/2.5 kb. The ratio of SNPs with nonsynonymous/synonymous mutations was 1.05:1. Moreover, 35 SNPs and 200 InDels were randomly selected and validated by Sanger sequencing, 83.9% of the SNPs and 70% of the InDels exhibited polymorphism among these three genotypes. In addition, the 15 SNPs and 125 InDels were found to be unevenly distributed on 9 linkage groups. Furthermore, 40 informative InDel markers were successfully used for the genetic diversity analysis on 32 radish accessions. Conclusions These results would not only provide new insights into transcriptome complexity and AS regulation, but also furnish large amount of molecular marker resources for germplasm identification, genetic mapping and further genetic improvement of radish in breeding programs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3874-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liang Xu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Dongyi Liang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Wei Zhang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xianwen Zhu
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Haiyan Jiang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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Cai C, Wu S, Niu E, Cheng C, Guo W. Identification of genes related to salt stress tolerance using intron-length polymorphic markers, association mapping and virus-induced gene silencing in cotton. Sci Rep 2017; 7:528. [PMID: 28373664 PMCID: PMC5428780 DOI: 10.1038/s41598-017-00617-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 03/06/2017] [Indexed: 12/20/2022] Open
Abstract
Intron length polymorphisms (ILPs), a type of gene-based functional marker, could themselves be related to the particular traits. Here, we developed a genome-wide cotton ILPs based on orthologs annotation from two sequenced diploid species, A-genome Gossypium arboreum and D-genome G. raimondii. We identified 10,180 putative ILP markers from 5,021 orthologous genes. Among these, 535 ILP markers from 9 gene families related to stress were selected for experimental verification. Polymorphic rates were 72.71% between G. arboreum and G. raimondii and 36.45% between G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. Furthermore, 14 polymorphic ILP markers were detected in 264 G. hirsutum accessions. Coupled with previous simple sequence repeats (SSRs) evaluations and salt tolerance assays from the same individuals, we found a total of 25 marker-trait associations involved in nine ILPs. The nine genes, temporally named as C1 to C9, showed the various expressions in different organs and tissues, and five genes (C3, C4, C5, C7 and C9) were significantly upregulated after salt treatment. We verified that the five genes play important roles in salt tolerance. Particularly, silencing of C4 (encodes WRKY DNA-binding protein) and C9 (encodes Mitogen-activated protein kinase) can significantly enhance cotton susceptibility to salt stress.
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Affiliation(s)
- Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuang Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Erli Niu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chaoze Cheng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
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Cai C, Zhang X, Niu E, Zhao L, Li N, Wang L, Ding L, Guo W. GhPSY, a phytoene synthase gene, is related to the red plant phenotype in upland cotton (Gossypium hirsutum L.). Mol Biol Rep 2014; 41:4941-52. [DOI: 10.1007/s11033-014-3360-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 03/31/2014] [Indexed: 12/31/2022]
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