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Transcriptional search to identify and assess reference genes for expression analysis in Solanum lycopersicum under stress and hormone treatment conditions

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Journal of Integrative Agriculture 2022年第11期21卷 3216-3229页

作者： DUAN Yao-ke HAN Rong SU Yan WANG Ai-ying LI Shuang SUN Hao GONG Hai-jun Shaanxi Engineering Research Center for Vegetables/College of Horticulture Northwest A&F UniversityYangling 712100ShaanxiP.R.China Henan Key Laboratory of Ion-Beam Bioengineering College of Agricultural SciencesZhengzhou UniversityZhengzhou 450000HenanP.R.China

Tomato(Solanum lycopersicum)is a model plant for research on fruit development and stress response,in which gene expression analysis is frequently *** PCR(qPCR)is a widely used technique for gene expression analysis,and the selection of reference genes may affect the accuracy of results and even *** there have been some frequently used reference genes in tomato,it has been shown that the expressions of some of these genes are not constant in different tissues and environmental ***,little information on genomic identification of reference genes is available in ***,we mined the publicly available transcriptional sequencing data and screened out fifteen candidate reference genes,and the expression stability of these candidate genes and seven traditionally used ones were evaluated under stress and hormone *** results showed that over half of the selected candidate references were housekeeping genes in tomato *** the candidate reference genes and the traditionally used ones,the most stably expressed genes varied under different treatments,and most of these genes were recommended as preferred reference genes at least once except Solyc04g009030 and Solyc07g066610,two traditionally used reference *** study provides some novel reference genes in tomato,and the preferred reference genes under different environmental stimuli,which may be useful for future *** study suggests that excavating stably expressed genes from transcriptome sequencing data is a reliable approach to screening reference genes for qPCR analysis.

关键词： tomato(Solanum lycopersicum) gene expression qPCR reference gene expression stability

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Assessment of internal controls for data normalization of gene expression after different bacterial stimulation by quantitative real-time PCR in golden pompano Trachinotus blochii

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Journal of Oceanology and Limnology 2020年第2期38卷 480-489页

作者： CHEN Xiaojuan ZHANG Xiaoqi SUN Yun TU Zhigang CAO Zhenjie WANG Shifeng ZHOU Yongcan State Key Laboratory of Marine Resource Utilization in South China Sea Hainan UniversityHaikou 570228China Hainan Academy of Ocean and Fisheries Sciences Haikou 570228China

Trachinotus blochii is one of the important commercial fish *** this study,we aim to confirm the reliability reference genes in *** during different bacterial challenge through quantitative real-time PCR(qRT-PCR).The expression of the seven selected genes in four immune organs(i.e.,spleen,kidney,intestine,and gill)stimulated with Vibrio harveyi,Edwardsiella tarda,and Streptococcus agalactiae were determined by *** PCR data was analyzed using the geNorm and NormFinder *** results showed the selection of the internal controls should be tissue specific when studying gene expression in response to bacterial *** 48 h of stimulation with ***,geNorm ranked EF1 A/Actin,18 S rRNA/B2M,UBCE/B2M,and 18 S rRNA/B2M,as the most stably expressed genes in spleen,kidney,intestine,and gill,*** 48 h of stimulation with ***,geNorm ranked 18 S rRNA/EF1 A,18 S rRNA/B2M,B2M/RPL13,and 18 S rRNA/EF1 A,as the most stably expressed genes in spleen,kidney,intestine,and gill,*** 48 h of stimulation with ***,18 S rRNA/EF1 A,18 S rRNA/B2 M,B2 M/Actin,and 18 S rRNA/B2M were ranked as the most stably expressed genes in spleen,kidney,intestine,and gill,*** to the results analyzed by geNorm,reference genes received similar rankings when using NormFinder *** results showed that the reference genes appeared to be not only tissue specific,but also specific to the infecting species of *** one gene is preferred when *** were infected by bacteria,18 S rRNA,B2M,B2M,18 S rRNA may be used in spleen,kidney,intestine,and gill,respectively.

关键词： Trachinotus blochii housekeeping gene expression stability reference gene

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Assessment of suitable reference genes for qRT-PCR analysis in Adelphocoris suturalis

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Journal of Integrative Agriculture 2018年第12期17卷 2745-2757页

作者： LUO Jing MA Chao LI Zhe ZHU Bang-qin ZHANG Jiang LEI Chao-liang JIN Shuang-xia J.Joe Hull CHEN Li-zhen National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research Huazhong Agricultural University Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources College of Life Science Hubei University Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory College of Plant Science and TechnologyHuazhong Agricultural University U.S. Arid Land Agricultural Research Center Agricultural Research Service U.S. Department of Agriculture

Quantitative reverse transcription polymerase chain reaction(qRT-PCR) is the most commonly-used tool for measurement of gene expression, but its accuracy and reliability depend on appropriate data normalization with the use of one or more stable reference genes. Adelphocoris suturalis is one of the most destructive pests of cotton, but until recently knowledge of its underlying molecular physiology had been hindered by a lack of molecular resources. To facilitate research on this pest, we evaluated 12 common housekeeping genes studied in insects(GAPDH, ACT, βACT, TBP, SDH, βTUB, EF1γ, EF1α, EF1δ, RPL32, RPS15, and RPL27) for their expression stability in A. suturalis when subjected to various experimental treatments, including three biotic(developmental stage and sex, tissue type, and metathoracic scent gland for varying developmental stages and sexes) and one abiotic(RNA interference injection) conditions. Four dedicated algorithms(ΔCt method, geNorm, BestKeeper and NormFinder) were used to analyze gene expression stability. In addition, RefFinder provided an overall ranking of the stability/suitability of these candidates. This study is the first to provide a comprehensive list of suitable reference genes for gene expression analyses in A. suturalis, which can serve to facilitate transcript expression study of related biological processes in this and related species.

关键词： Adelphocoris suturalis reference gene qRT-PCR normalization expression stability

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Screening of stable internal reference genes by quantitative real-time PCR in humpback grouper Cromileptes altivelis

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Journal of Oceanology and Limnology 2021年第5期39卷 1985-1999页

作者： Xiaojuan CHEN Yun SUN Panpan ZHANG Jianlong LI Haiping LI Caoying WEI Zhenjie CAO Yongcan ZHOU State Key Laboratory of Marine Resource Utilization in South China Sea Hainan UniversityHaikou 570228China Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan Province Haikou 570228China Department of Aquaculture College of Marine SciencesHainan UniversityHaikou 570228China

Humpback grouper Cromileptes altivelis is one commercial fish with considerable economic *** determine the expression stabilities of six commonly used internal reference genes in *** challenged by Vibrio harveyi and viral nervous necrosis virus(VNNV)through quantitative real-time PCR(qRT-PCR),the expression levels of selected genes in five immune organs stimulated with pathogenic infection were carefully evaluated using algorithms of geNorm,NormFinder,and *** results show that the expre ssion stabilities of the six candidate inte rnal reference genes were diffe re *** no rmal physiological conditions,RPL13 were identified as the most stably expressed genes among five different immune organs(liver,spleen,kidney,intestine,and gill).After *** stimulation,RPL13,RPL13,EF1 A,RPL13,and EF1 A were identified by geNorm,NormFinder,and BestKeeper as the most stable genes in liver,spleen,kidney,intestine,and gill,*** these three algorithms suggested that under stimulation of VNNV,RPL13,EF1 A,Actin,RPL13,and Actin were as the most stable genes in liver,spleen,kidney,intestine,and gill,*** results suggest that specific experiment conditions and tissue types shall be considered when selecting the reference genes in qRT-PCR *** study provided a solid foundation for future studies on gene expression of *** under different conditions.

关键词： Cromileptes altivelis reference gene expression stability pathogenic infection

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