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Xiao Q, Lin Y, Li H, Chen Y, Wei W, Li P, Chen L. Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata. BMC Genomics 2022; 23:382. [PMID: 35590244 PMCID: PMC9121591 DOI: 10.1186/s12864-022-08622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 05/10/2022] [Indexed: 11/17/2022] Open
Abstract
Background Tolerance of low temperature has a significant impact on survival and expansion of invasive snail Pomacea canalicuata. Cold acclimation can enhance cold tolerance of Pomacea canalicuata. To elucidate the molecular mechanism of P. canaliculata’s responses to cold acclimation and cold stress, a high-throughput transcriptome analysis of P. canaliculata was performed, and gene expression following artificial cold acclimation and then cold stress at 0 °C for 24 h was compared using RNA sequencing. Results Using the Illumina platform, we obtained 151.59 G subreads. A total of 5,416 novel lncRNAs were identified, and 3166 differentially expressed mRNAs and 211 differentially expressed lncRNAs were screened with stringent thresholds. The potential antisense, cis and trans targets of lncRNAs were predicted. Kyoto Encyclopedia of Genes and Genomes enrichment analysis showed that many target genes were involved in proteasome, linoleic acid metabolism and retinol metabolism under cold acclimation. The lncRNA of P. canaliculata could participate in cold acclimation by regulating the expression of E3 ubiquitin protein ligase, 26S proteasome non-ATPase dependent regulation subunit, glutathione S-transferase, sodium/glucose cotransporter and cytochrome P450. Conclusions These results broaden our understanding of cold acclimation and cold stress associated lncRNAs and mRNAs, and provide new insights into lncRNA mediated regulation of P. canaliculata cold acclimation and cold stress response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08622-5.
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Affiliation(s)
- Qi Xiao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Youfu Lin
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yu Chen
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Wei Wei
- College of Life Sciences, Chemistry and Chemical Engineering, Jiangsu Second Normal University, Nanjing, 210013, China
| | - Peng Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Lian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China.
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Zhang XB, Yang SM. Viewing the current situation of pig model application in China's medical field from the application and funding of NSFC. J Otol 2020; 16:34-39. [PMID: 33505448 PMCID: PMC7814078 DOI: 10.1016/j.joto.2020.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 11/29/2022] Open
Abstract
Background The National Natural Science Foundation of China (NSFC) is an important part of China’s innovation system. In the last decade, the pig has become more and more widely used in the field of medical science, especially in otology research. Objective By analyzing and summarizing the funding information over recent years, we intend to identify the characteristics and trends of funding for research using pig models and provide references for future development. Material and methods This is a comprehensive analysis of features in funding for research projects involving pig models by the NSFC in the past 10 years, with a focus on projects in the field of otolaryngology/head and neck surgery. Results Both the number and amount of funding provided by the NSFC for research involving pig models are on the rise with each passing year. Researchers at the PLA General Hospital have completed a number of studies using miniature pigs in cochlear morphology, electrophysiology, cochlear implantation, cochlear transcription analysis, gene therapy, inner ear disease modeling and Eustachian tube pathology modeling. Conclusion Pigs as an ideal large mammal model are well suited in the current national basic research strategy in China, and can help further strengthen China’s leading position in basic research in the world.
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Affiliation(s)
- Xiao Bin Zhang
- Department of Health Sciences, National Natural Science Foundation of China, China
| | - Shi-Ming Yang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, No. 28 Fuxing Road, Beijing, 100853, China.,National Clinical Research Center for Otolaryngologic Diseases, Beijing, 100853, China.,State Key Lab of Hearing Science, Ministry of Education, Beijing, 100853, China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, 100853, China
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Genome-Wide Identification and Characterization of Fusarium graminearum-Responsive lncRNAs in Triticum aestivum. Genes (Basel) 2020; 11:genes11101135. [PMID: 32992604 PMCID: PMC7601646 DOI: 10.3390/genes11101135] [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: 08/25/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 01/24/2023] Open
Abstract
Although the war between wheat and Fusarium has been widely investigated for years, long noncoding RNAs (lncRNAs), which have been proven to regulate important processes in the development and stress responses of plants, are still poorly known in wheat against Fusarium. Herein, we systematically reveal the roles of wheat lncRNAs in the process of Fusarium graminearum infection by high-throughput RNA sequencing. Well over 4130 of the total 4276 differentially expressed lncRNAs were already specifically expressed at 12 h postinoculation (hpi), but only 89 of these were specifically expressed at 24 hpi, indicating that the initial stage was the crucial stage for lncRNA-mediated gene regulation of wheat defense against F. graminearum. Target analysis showed the lncRNAs participated in various biological stress processes and had exclusive regulation models at different infection stages. Further H2O2 accumulation and protein ubiquitination assays supported this idea. Moreover, two lncRNAs (XLOC_302848 and XLOC_321638) were identified as Fusarium seedling blight resistance candidates by lncRNA-target expression pattern validation, and two lncRNAs (XLOC_113815, XLOC_123624) were Fusarium head blight resistance potential regulators by cross-validating the RNAseq data with the refined meta-QTL of wheat FHB resistance. These findings extend our knowledge on wheat lncRNAs response to F. graminearum attack and provide new insights for the functional and molecular research of future interactions between wheat and Fusarium.
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Zhu Z, Guan Z, Liu G, Wang Y, Zhang Z. SGID: a comprehensive and interactive database of the silkworm. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5677404. [PMID: 31836898 PMCID: PMC6911161 DOI: 10.1093/database/baz134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/27/2019] [Accepted: 11/01/2019] [Indexed: 11/12/2022]
Abstract
Although the domestic silkworm (Bombyx mori) is an important model and economic animal, there is a lack of comprehensive database for this organism. Here, we developed the silkworm genome informatics database (SGID). It aims to bring together all silkworm-related biological data and provide an interactive platform for gene inquiry and analysis. The function annotation in SGID is thorough and covers 98% of the silkworm genes. The annotation details include function description, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, subcellular location, transmembrane topology, protein secondary/tertiary structure, homologous group and transcription factor. SGID provides genome-scale visualization of population genetics test results based on high-depth resequencing data of 158 silkworm samples. It also provides interactive analysis tools of transcriptomic and epigenomic data from 79 NCBI BioProjects. SGID will be extremely useful to silkworm research in the future.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Zhufen Guan
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Gexin Liu
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
| | - Yawang Wang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China.,Khoury College of Computer Sciences, Northeastern University, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Ze Zhang
- School of Life Sciences, Chongqing University, No.55 Daxuecheng South Rd., Shapingba, Chongqing, 401331, China
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Wang J, Lin J, Kan J, Wang H, Li X, Yang Q, Li H, Chang Y. Genome-Wide Identification and Functional Prediction of Novel Drought-Responsive lncRNAs in Pyrus betulifolia. Genes (Basel) 2018; 9:E311. [PMID: 29925818 PMCID: PMC6027255 DOI: 10.3390/genes9060311] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 06/14/2018] [Accepted: 06/14/2018] [Indexed: 11/17/2022] Open
Abstract
Increasing evidence shows that long noncoding RNAs (lncRNAs) play important roles in developmental regulation and many other biological processes in plants. However, identification of lncRNAs in Pyrus betulifolia is limited compared with studies of functional gene expression. Using high-throughput sequencing technology, the transcriptome of P. betulifolia under drought stress was analyzed to identify lncRNAs. A total of 14,478 lncRNAs were identified, of which 251 were found to be drought-responsive. The putative target genes of these differentially expressed lncRNAs were significantly enriched in metabolic processes, organic substance metabolic processes, macromolecule metabolic processes, and heterocyclic compound binding. Real-time quantitative polymerase chain reaction validation suggested that the results of the RNA sequencing data analysis were reliable. This study will provide genetic resources for pear breeding and provide reference to other pomological studies.
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Affiliation(s)
- Jinxing Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jing Lin
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Jialiang Kan
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hong Wang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Xiaogang Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Qingsong Yang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Hui Li
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
| | - Youhong Chang
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 200014, China.
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