复杂生物样本管家基因研究进展
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摘要
管家基因(HKG)是一类在不同组织中表达稳定,且受环境干扰较小的基因的总称。管家基因检测已被广泛应用于物种进化分析,鉴定以及复杂生物样品的安全监测领域。生物气溶胶成分复杂,管家基因鉴别不同物种的能力为环境气溶胶成分分析提供了新的手段。本文列举了近年来国内外研究中常用的植物、动物和微生物共15种管家基因,总结了其在生物物种鉴定的作用,旨在为环境样本中的复杂生物成分分析提供参考依据。
House-keeping genes(HKGs) are a group of genes that express stably in different tissues,and are less disturbed by external conditions. These genes are widely used in species evolution analysis,identification and safety surveilance of complex biological samples. This review list 15 species of HKGs of plants,animals and microorganisms which commonly used in domestic and international research in recent years,summarized their role in the identification of biological species. It is hope for providing a reference for the follow-up study and application of HKGs in analysis of environmental bioaerosol samples.
House-keeping genes(HKGs) are a group of genes that express stably in different tissues,and are less disturbed by external conditions. These genes are widely used in species evolution analysis,identification and safety surveilance of complex biological samples. This review list 15 species of HKGs of plants,animals and microorganisms which commonly used in domestic and international research in recent years,summarized their role in the identification of biological species. It is hope for providing a reference for the follow-up study and application of HKGs in analysis of environmental bioaerosol samples.
引文
[1] Fowotade A. Normalization of gene expression by quantitative RT-PCR in human cell line:comparison of 12 endogenous reference genes[J]. Ethiop J Health Sci,2018,28(6):741–748.
[2]国家质检总局. SN/T 1204-2016植物及其加工产品中转基因成分实时荧光PCR定性检验方法[S].北京:中国标准出版社出版,2016.
[3]冯海永,韩建林.羊肉产品中若干动物源性成分的七重PCR检测技术应用研究[J].中国畜牧兽医,2010,37(9):85-90.
[4]陈永锋.饲料及动物性食品中山羊源性和绵羊源性成分双重荧光PCR检测方法的建立[J].福建畜牧兽医,2012(3):1-4.
[5]宋丽萍,薛晨玉,路勇,等.应用实时荧光PCR技术定量检测羊肉中的猪肉成分[J].食品科技,2014(10):319-322.
[6]赫晓宇.多重PCR技术在食品中4种肉类成分快速鉴别中的应用[J].中医临床研究,2016,8(25):119-120.
[7] Raupach MJ,Hannig K,Morinière J,et al. A DNA barcode library for ground beetles(Insecta,Coleoptera,Carabidae)of Germany:the genus Bembidion Latreille,1802 and allied taxa[J]. Zookeys,2016(592):121-141.
[8] Coddington JA,Agnarsson I,Cheng RC,et al. DNA barcode data accurately assign higher spider taxa[J]. Peerj,2016,4(1):e2201.
[9] Hebert PDN,Ratnasingham S,Dewaard JR. Barcoding animal life:cytochrome c oxidase subunit I divergences among closely related species[J]. Proc R Soc Lond,2003,270(Suppl 1):96-99.
[10]潘艳仪,邱德义,陈健,等.基于微型DNA条形码的多种动物源性成分的鉴定[J].食品科学,2018,575(10):332-338.
[11] Shah N,Sukumar S. The Hox genes and their roles in oncogenesis[J]. Nature Reviews Cancer,2010,10(5):361-371.
[12] Ruddle FH,Bartels JL,Bentley KL,et al. Evolution of Hox genes[J].Annual Review of Genetics,1994,28(1):423.
[13]丁果,花保祯.同源异形盒基因及其在昆虫幼虫腹足发育生物学研究中的应用[J].昆虫学报,2017,60(5):604-612.
[14]李慧,花保祯.Hox基因及其进化机制的研究进展[J].动物学杂志,2011,46(1):136-142.
[15]杨永存,杨冬燕,李浩,等.实时荧光PCR检测动物源性基因鉴定地沟油[J].中国卫生检验杂志,2013(18):3514-3517.
[16]国家质检总局.GB/T 25165—2010明胶中牛、羊、猪源性成分的定性检测方法实时荧光PCR法[S].北京:中国标准出版社出版,2010.
[17] Wang Y,Duan R,Zhang J. Differentiating collagens based on mitochondrion 12S rRNA gene[J]. Food Chemistry,2017(234):139-143.
[18]张瑞敬.喉鳞状细胞癌中ALDOA、G6PD和PFK1的表达及临床意义[D].石家庄:河北医科大学,2017.
[19] Hollingsworth PM,Li DZ,Michelle VDB,et al. Telling plant species apart with DNA:from barcodes to genomes[J]. Biological Sciences,2016,371(1702):20150338.
[20] Hilu K,Liang H. The matK gene:sequence variation and application in plant systematics[J]. American Journal of Botany,1997,84(6):830.
[21] Braukmann TW,Kuzmina ML,Sills J,et al. Testing the efficacy of DNA barcodes for identifying the vascular plants of Canada[J]. PLoS One,2017,12(1):e0169515.
[22] Dunning LT,Savolainen V. Broad-scale amplification of matK for DNA barcoding plants,a technical note[J]. Botanical Journal of the Linnean Society,2010,164(1):1-9.
[23] Vassou SL,Nithaniyal S,Raju B,et al. Creation of reference DNA barcode library and authentication of medicinal plant raw drugs used in Ayurvedic medicine[J]. BMC complementary and alternative medicine,2016,16(1):186.
[24] Hollingsworth,LL Forrest,JL Spouge,et al. A DNA barcode for land plants[J]. Proceedings of the National Academy of Science,2009,106(31):12794-12797.
[25] Han Q,Zhang Y,Shu Y,et al. Identification of common adulterants in walnut beverage based on plant DNA barcode technology[J]. 2018,doi:dx.doi.org/10.1101/340612.
[26] Giudicelli GC,M?der G,De LF. Efficiency of ITS sequences for DNA barcoding in Passiflora(Passifloraceae).[J]. International Journal of Molecular Sciences,2015,16(4):7289-7303.
[27] Gogoi B,Bhau BS. DNA barcoding of the genus Nepenthes(Pitcher plant):a preliminary assessment towards its identification[J]. BMC Plant Biology,2018,18(1):153-160.
[28] Mishra P,Kumar A,Nagireddy A,et al. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia[J]. PLoS One,2017,12(8):e0182836.
[29] Wang DY,Wang Q,Wang YL,et al. Evaluation of DNA barcodes in Codonopsis(Campanulaceae)and in some large angiosperm plant genera[J]. PLoS One,2017,12(2):e0170286.
[30] Pang X,Liu C,Shi L,et al. Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes:a meta-analysis[J]. PLoS One,2012,7(11):e48833.
[31] Bruni I,Galimberti A,Caridi L,et al. A DNA barcoding approach to identify plant species in multiflower honey[J]. Food Chemistry,2015(170):308-315.
[32] Elizabeth K,Garber PA,Malhi RS. TrnL out performs rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins(Cebus capucinus,Primates)[J]. PLoS One,2018,13(6):e0199556.
[33]粟智平,耿金培,王洪来,等.粉丝中植物源性成分的PCR定性检测方法研究[J].检验检疫学刊,2004,14(5):7-11.
[34]顾晓慧,姚琳,王联珠,等.冷冻鱼糜中植物成分的PCR检测方法[J].中国渔业质量与标准,2014,4(2):44-49.
[35] Gere J,Yessoufou K,Daru,et al. Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae[J]. ZooKeys,2013,365(365):129-147.
[36] Burgess KS,Fazekas AJ,Kesanakurti PR,et al. Discriminating plant species in a local temperate flora using the rbcL+matK,DNA barcode[J]. Methods in Ecology&Evolution,2011,2(4):333-340.
[37] Rocha DJP,Santos CS,Pacheco LGC. Bacterial reference genes for gene expression studies by RT-qPCR:survey and analysis[J]. Antonie Van Leeuwenhoek,2015,108(3):685-693.
[38]刘朝军,沈定霞.16SrDNA序列测定在细菌鉴定中的应用[J].解放军医学院学报,2011,32(7):774-776.
[39] Kumar A,Asthana M,Gupta P,et al. 16S rRNA sequencing of dye decolorizing bacteria isolated from soil[J]. Bioinformation,2015,11(1):1.
[40] Vezzulli L,Pezzati E,Huetestauffer C,et al. 16S rDNA pyrosequencing of the mediterranean gorgonian paramuricea clavata reveals a link among alterations in bacterial holobiont members,anthropogenic influence and disease outbreaks[J]. PLoS One,2013,8(6):e67745.
[41] Zhao MM,Du SS,Li QH,et al. High throughput 16S rRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis[J]. Respiratory research,2017,18(1):28.
[42] Liu Z,Zhu X,Jiang X. Assay of gram-negative bacteria 16S rRNA gene in chronic abacterial prostatitis[J]. Chinese Journal of Urology,2003,24(7):469-471.
[43] Yarza P,Yilmaz P,Pruesse E,et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences[J]. Nature Reviews Microbiology,2014,12(9):635.
[44] Avalos E,Catanzaro D,Catanzaro A,et al. Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates:a systematic review[J]. PLoS One,2015,10(3):e0120470.
[45]肖喻.江西省念珠菌血症致病真菌的鉴定、药物敏感性及多位点序列分型特征[D].南昌:南昌大学,2017.
[46] Schoch CL,Seifert KA,Huhndorf S,et al. Nuclear ribosomal internal transcribed spacer(ITS)region as a universal DNA barcode marker for Fungi[J]. Proceedings of the National Academy of Sciences,2012,109(16):6241-6246.
[47] Duarte S,Batista D,B覿rlocher F,et al. Some new DNA barcodes of aquatic hyphomycete species[J]. Mycoscience,2015,56(1):102-108.
[48] Andreakis N,H覬j L,Kearns P,et al. Diversity of marine-derived fungal cultures exposed by DNA barcodes:the algorithm matters[J]. PLoS One,2015,10(8):e0136130.
[49] Irinyi L,Serena C,Garcia-Hermoso D,et al. International society of human and animal mycology(ISHAM)-ITS reference DNA barcoding database-the quality controlled standard tool for routine identification of human and animal pathogenic fungi[J]. Medical Mycology,2015,53(4):313-337.
[50] Vu D,Groenewald M,de Vries M,et al. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation[J]. Studies in Mycology,2019(92):135-154.
[51]万松华.食品中污染微生物通用型荧光PCR检测方法研究[D].广州:华南理工大学,2015.
[52]江桂斌.快速发展的生物气溶胶学科[J].科学通报,2018,63(10):875.
[2]国家质检总局. SN/T 1204-2016植物及其加工产品中转基因成分实时荧光PCR定性检验方法[S].北京:中国标准出版社出版,2016.
[3]冯海永,韩建林.羊肉产品中若干动物源性成分的七重PCR检测技术应用研究[J].中国畜牧兽医,2010,37(9):85-90.
[4]陈永锋.饲料及动物性食品中山羊源性和绵羊源性成分双重荧光PCR检测方法的建立[J].福建畜牧兽医,2012(3):1-4.
[5]宋丽萍,薛晨玉,路勇,等.应用实时荧光PCR技术定量检测羊肉中的猪肉成分[J].食品科技,2014(10):319-322.
[6]赫晓宇.多重PCR技术在食品中4种肉类成分快速鉴别中的应用[J].中医临床研究,2016,8(25):119-120.
[7] Raupach MJ,Hannig K,Morinière J,et al. A DNA barcode library for ground beetles(Insecta,Coleoptera,Carabidae)of Germany:the genus Bembidion Latreille,1802 and allied taxa[J]. Zookeys,2016(592):121-141.
[8] Coddington JA,Agnarsson I,Cheng RC,et al. DNA barcode data accurately assign higher spider taxa[J]. Peerj,2016,4(1):e2201.
[9] Hebert PDN,Ratnasingham S,Dewaard JR. Barcoding animal life:cytochrome c oxidase subunit I divergences among closely related species[J]. Proc R Soc Lond,2003,270(Suppl 1):96-99.
[10]潘艳仪,邱德义,陈健,等.基于微型DNA条形码的多种动物源性成分的鉴定[J].食品科学,2018,575(10):332-338.
[11] Shah N,Sukumar S. The Hox genes and their roles in oncogenesis[J]. Nature Reviews Cancer,2010,10(5):361-371.
[12] Ruddle FH,Bartels JL,Bentley KL,et al. Evolution of Hox genes[J].Annual Review of Genetics,1994,28(1):423.
[13]丁果,花保祯.同源异形盒基因及其在昆虫幼虫腹足发育生物学研究中的应用[J].昆虫学报,2017,60(5):604-612.
[14]李慧,花保祯.Hox基因及其进化机制的研究进展[J].动物学杂志,2011,46(1):136-142.
[15]杨永存,杨冬燕,李浩,等.实时荧光PCR检测动物源性基因鉴定地沟油[J].中国卫生检验杂志,2013(18):3514-3517.
[16]国家质检总局.GB/T 25165—2010明胶中牛、羊、猪源性成分的定性检测方法实时荧光PCR法[S].北京:中国标准出版社出版,2010.
[17] Wang Y,Duan R,Zhang J. Differentiating collagens based on mitochondrion 12S rRNA gene[J]. Food Chemistry,2017(234):139-143.
[18]张瑞敬.喉鳞状细胞癌中ALDOA、G6PD和PFK1的表达及临床意义[D].石家庄:河北医科大学,2017.
[19] Hollingsworth PM,Li DZ,Michelle VDB,et al. Telling plant species apart with DNA:from barcodes to genomes[J]. Biological Sciences,2016,371(1702):20150338.
[20] Hilu K,Liang H. The matK gene:sequence variation and application in plant systematics[J]. American Journal of Botany,1997,84(6):830.
[21] Braukmann TW,Kuzmina ML,Sills J,et al. Testing the efficacy of DNA barcodes for identifying the vascular plants of Canada[J]. PLoS One,2017,12(1):e0169515.
[22] Dunning LT,Savolainen V. Broad-scale amplification of matK for DNA barcoding plants,a technical note[J]. Botanical Journal of the Linnean Society,2010,164(1):1-9.
[23] Vassou SL,Nithaniyal S,Raju B,et al. Creation of reference DNA barcode library and authentication of medicinal plant raw drugs used in Ayurvedic medicine[J]. BMC complementary and alternative medicine,2016,16(1):186.
[24] Hollingsworth,LL Forrest,JL Spouge,et al. A DNA barcode for land plants[J]. Proceedings of the National Academy of Science,2009,106(31):12794-12797.
[25] Han Q,Zhang Y,Shu Y,et al. Identification of common adulterants in walnut beverage based on plant DNA barcode technology[J]. 2018,doi:dx.doi.org/10.1101/340612.
[26] Giudicelli GC,M?der G,De LF. Efficiency of ITS sequences for DNA barcoding in Passiflora(Passifloraceae).[J]. International Journal of Molecular Sciences,2015,16(4):7289-7303.
[27] Gogoi B,Bhau BS. DNA barcoding of the genus Nepenthes(Pitcher plant):a preliminary assessment towards its identification[J]. BMC Plant Biology,2018,18(1):153-160.
[28] Mishra P,Kumar A,Nagireddy A,et al. Evaluation of single and multilocus DNA barcodes towards species delineation in complex tree genus Terminalia[J]. PLoS One,2017,12(8):e0182836.
[29] Wang DY,Wang Q,Wang YL,et al. Evaluation of DNA barcodes in Codonopsis(Campanulaceae)and in some large angiosperm plant genera[J]. PLoS One,2017,12(2):e0170286.
[30] Pang X,Liu C,Shi L,et al. Utility of the trnH–psbA intergenic spacer region and its combinations as plant DNA barcodes:a meta-analysis[J]. PLoS One,2012,7(11):e48833.
[31] Bruni I,Galimberti A,Caridi L,et al. A DNA barcoding approach to identify plant species in multiflower honey[J]. Food Chemistry,2015(170):308-315.
[32] Elizabeth K,Garber PA,Malhi RS. TrnL out performs rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins(Cebus capucinus,Primates)[J]. PLoS One,2018,13(6):e0199556.
[33]粟智平,耿金培,王洪来,等.粉丝中植物源性成分的PCR定性检测方法研究[J].检验检疫学刊,2004,14(5):7-11.
[34]顾晓慧,姚琳,王联珠,等.冷冻鱼糜中植物成分的PCR检测方法[J].中国渔业质量与标准,2014,4(2):44-49.
[35] Gere J,Yessoufou K,Daru,et al. Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within southern African Combretaceae[J]. ZooKeys,2013,365(365):129-147.
[36] Burgess KS,Fazekas AJ,Kesanakurti PR,et al. Discriminating plant species in a local temperate flora using the rbcL+matK,DNA barcode[J]. Methods in Ecology&Evolution,2011,2(4):333-340.
[37] Rocha DJP,Santos CS,Pacheco LGC. Bacterial reference genes for gene expression studies by RT-qPCR:survey and analysis[J]. Antonie Van Leeuwenhoek,2015,108(3):685-693.
[38]刘朝军,沈定霞.16SrDNA序列测定在细菌鉴定中的应用[J].解放军医学院学报,2011,32(7):774-776.
[39] Kumar A,Asthana M,Gupta P,et al. 16S rRNA sequencing of dye decolorizing bacteria isolated from soil[J]. Bioinformation,2015,11(1):1.
[40] Vezzulli L,Pezzati E,Huetestauffer C,et al. 16S rDNA pyrosequencing of the mediterranean gorgonian paramuricea clavata reveals a link among alterations in bacterial holobiont members,anthropogenic influence and disease outbreaks[J]. PLoS One,2013,8(6):e67745.
[41] Zhao MM,Du SS,Li QH,et al. High throughput 16S rRNA gene sequencing reveals the correlation between Propionibacterium acnes and sarcoidosis[J]. Respiratory research,2017,18(1):28.
[42] Liu Z,Zhu X,Jiang X. Assay of gram-negative bacteria 16S rRNA gene in chronic abacterial prostatitis[J]. Chinese Journal of Urology,2003,24(7):469-471.
[43] Yarza P,Yilmaz P,Pruesse E,et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences[J]. Nature Reviews Microbiology,2014,12(9):635.
[44] Avalos E,Catanzaro D,Catanzaro A,et al. Frequency and geographic distribution of gyrA and gyrB mutations associated with fluoroquinolone resistance in clinical Mycobacterium tuberculosis isolates:a systematic review[J]. PLoS One,2015,10(3):e0120470.
[45]肖喻.江西省念珠菌血症致病真菌的鉴定、药物敏感性及多位点序列分型特征[D].南昌:南昌大学,2017.
[46] Schoch CL,Seifert KA,Huhndorf S,et al. Nuclear ribosomal internal transcribed spacer(ITS)region as a universal DNA barcode marker for Fungi[J]. Proceedings of the National Academy of Sciences,2012,109(16):6241-6246.
[47] Duarte S,Batista D,B覿rlocher F,et al. Some new DNA barcodes of aquatic hyphomycete species[J]. Mycoscience,2015,56(1):102-108.
[48] Andreakis N,H覬j L,Kearns P,et al. Diversity of marine-derived fungal cultures exposed by DNA barcodes:the algorithm matters[J]. PLoS One,2015,10(8):e0136130.
[49] Irinyi L,Serena C,Garcia-Hermoso D,et al. International society of human and animal mycology(ISHAM)-ITS reference DNA barcoding database-the quality controlled standard tool for routine identification of human and animal pathogenic fungi[J]. Medical Mycology,2015,53(4):313-337.
[50] Vu D,Groenewald M,de Vries M,et al. Large-scale generation and analysis of filamentous fungal DNA barcodes boosts coverage for kingdom fungi and reveals thresholds for fungal species and higher taxon delimitation[J]. Studies in Mycology,2019(92):135-154.
[51]万松华.食品中污染微生物通用型荧光PCR检测方法研究[D].广州:华南理工大学,2015.
[52]江桂斌.快速发展的生物气溶胶学科[J].科学通报,2018,63(10):875.