一种用于筛选物种特异性基因组DNA探针以进行物种鉴定的新方法。
A novel method for screening species-specific gDNA probes for species identification.
作者信息
Li Tong Xiang, Wang JinKe, Bai YunFei, Sun XiangDong, Lu ZuHong
机构信息
Chien-Shiung Wu Laboratory, Southeast University, Nanjing 210096, People's Republic of China.
出版信息
Nucleic Acids Res. 2004 Mar 1;32(4):e45. doi: 10.1093/nar/gnh041.
Abstract
We report a method called SSH array which combines the suppression subtraction hybridization (SSH) and DNA array techniques to find species-specific DNA probes from genomic DNA (gDNA) for species identification. The method first obtains the differential gDNA fragments between two species by SSH and then hybridizes the differential gDNA fragments with arrays made of multiple whole genomes from several species to screen the unique gDNA fragments for one species. The screened unique gDNA fragments can be used as species-specific probes to differentiate the species they represent from all other species. We used five species of the genus Dendrobrium, D.aurantiacum Kerr, D.officinale Kimura et Migo, D.nobile Lindl., D.chrysotoxum Lindl. and D.fimbriatum Hook., as experimental materials to study the feasibility of the method. The results showed that the method could efficiently obtain different species-specific probes for each of the five species.
摘要
我们报道了一种名为SSH阵列的方法，该方法结合了抑制消减杂交（SSH）和DNA阵列技术，从基因组DNA（gDNA）中寻找物种特异性DNA探针用于物种鉴定。该方法首先通过SSH获得两个物种之间的差异gDNA片段，然后将差异gDNA片段与由几个物种的多个全基因组制成的阵列进行杂交，以筛选出一个物种的独特gDNA片段。筛选出的独特gDNA片段可作为物种特异性探针，将它们所代表的物种与所有其他物种区分开来。我们使用了石斛属的五个物种，即金钗石斛、铁皮石斛、鼓槌石斛、密花石斛和流苏石斛作为实验材料来研究该方法的可行性。结果表明，该方法可以有效地为这五个物种中的每一个获得不同的物种特异性探针。
相似文献
1
A novel method for screening species-specific gDNA probes for species identification.一种用于筛选物种特异性基因组DNA探针以进行物种鉴定的新方法。
Nucleic Acids Res. 2004 Mar 1;32(4):e45. doi: 10.1093/nar/gnh041.
2
Accurate identification of closely related Dendrobium species with multiple species-specific gDNA probes.使用多种物种特异性基因组DNA探针准确鉴定近缘石斛物种。
J Biochem Biophys Methods. 2005 Feb 28;62(2):111-23. doi: 10.1016/j.jbbm.2004.10.006. Epub 2004 Nov 21.
3
Species identification of Chinese medicinal plant Fallopia multiflora (Thunb.) Haraldson by suppression subtraction hybridization.采用抑制差减杂交技术对中药何首乌进行种属鉴定。
J Nat Med. 2014 Jan;68(1):192-8. doi: 10.1007/s11418-013-0772-1. Epub 2013 Apr 30.
4
SNP, ARMS and SSH authentication of medicinal Dendrobium officinale KIMURA et MIGO and application for identification of Fengdou drugs.药用铁皮石斛的SNP、ARMS和SSH鉴定及其在枫斗药材鉴定中的应用
Biol Pharm Bull. 2008 Apr;31(4):553-7. doi: 10.1248/bpb.31.553.
5
Identification of medicinal plants and plant sequences: multiplexed MLPA assay.
Methods Mol Biol. 2009;547:277-88. doi: 10.1007/978-1-60327-287-2_22.
6
A gDNA microarray for genotyping salvia species.用于鉴定鼠尾草属物种的 gDNA 微阵列。
Mol Biotechnol. 2013 Jul;54(3):770-83. doi: 10.1007/s12033-012-9625-5.
7
[RAPD analysis and construction of specific DNA probes between Pinellia ternata and Typhonium flagelliforme].半夏与水半夏的RAPD分析及特异性DNA探针的构建
Zhong Yao Cai. 2009 Sep;32(9):1374-5.
8
9
The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb.铁皮石斛基因组揭示重要传统中药兰科植物的生物学特性。
Mol Plant. 2015 Jun;8(6):922-34. doi: 10.1016/j.molp.2014.12.011. Epub 2014 Dec 24.
10
Identification of Dendrobium species by dot blot hybridization assay.斑点杂交法鉴定石斛属植物。
Biol Pharm Bull. 2010;33(4):665-8. doi: 10.1248/bpb.33.665.
引用本文的文献
1
Re-Assessment of Strains from Section and Description of Two Unrecorded Species from Korea.对来自某区域菌株的重新评估以及对韩国两种未记录物种的描述。
Mycobiology. 2025 Jun 1;53(4):393-402. doi: 10.1080/12298093.2025.2505300. eCollection 2025.
2
Identification of closely related species in through Analysis of Whole-Genome.通过全基因组分析鉴定密切相关的物种。
Front Microbiol. 2024 Feb 21;15:1323572. doi: 10.3389/fmicb.2024.1323572. eCollection 2024.
3
Development of DNA markers using next-generation sequencing approach for molecular authentication of L. and (Willd.) Miers.利用新一代测序方法开发DNA标记用于对光果甘草（Glycyrrhiza glabra L.）和（Willd.）Miers进行分子鉴定
3 Biotech. 2023 Sep;13(9):304. doi: 10.1007/s13205-023-03732-7. Epub 2023 Aug 15.
4
Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers.利用特异分子标记将斑茅染色质高效导入甘蔗。
Int J Mol Sci. 2022 Aug 21;23(16):9435. doi: 10.3390/ijms23169435.
5
An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex).从菰属（甘蔗复合体）中开发物种特异性重复序列的改良抑制差减杂交技术。
BMC Plant Biol. 2018 Nov 6;18(1):269. doi: 10.1186/s12870-018-1471-6.
6
Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.消减式多样性数组鉴定新型分子标记物，包括用于鉴定紫锥菊属物种的反转录转座子。
PLoS One. 2013 Aug 5;8(8):e70347. doi: 10.1371/journal.pone.0070347. Print 2013.
7
Species identification of Chinese medicinal plant Fallopia multiflora (Thunb.) Haraldson by suppression subtraction hybridization.采用抑制差减杂交技术对中药何首乌进行种属鉴定。
J Nat Med. 2014 Jan;68(1):192-8. doi: 10.1007/s11418-013-0772-1. Epub 2013 Apr 30.
8
Array-based techniques for fingerprinting medicinal herbs.基于阵列的中药材鉴定技术。
Chin Med. 2011 May 18;6(1):18. doi: 10.1186/1749-8546-6-18.
9
Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes.利用从消减抑制杂交中扩增得到的基因作为微阵列探针，生成亚种水平特异性微生物诊断微阵列。
Nucleic Acids Res. 2005 Jul 19;33(13):e113. doi: 10.1093/nar/gni112.
10
Validation of the high-throughput marker technology DArT using the model plant Arabidopsis thaliana.利用模式植物拟南芥对高通量标记技术DArT进行验证。
Mol Genet Genomics. 2005 Aug;274(1):30-9. doi: 10.1007/s00438-005-1145-6. Epub 2005 Jul 16.
本文引用的文献
1
Identification of streptococcus mitis group species by RFLP of the PCR-amplified 16S-23S rDNA intergenic spacer.通过聚合酶链反应扩增的16S-23S核糖体DNA基因间隔区的限制性片段长度多态性鉴定缓症链球菌群菌种
Res Microbiol. 2002 Dec;153(10):687-91. doi: 10.1016/s0923-2508(02)01382-7.
2
Identification of Legionella species by ribotyping and other molecular methods.通过核糖体分型和其他分子方法鉴定军团菌属菌种。
Res Microbiol. 2002 Dec;153(10):679-86. doi: 10.1016/s0923-2508(02)01381-5.
3
Application of species-specific polymerase chain reaction in the forensic identification of tiger species.物种特异性聚合酶链反应在老虎物种法医鉴定中的应用。
Forensic Sci Int. 2003 Jan 9;131(1):75-8. doi: 10.1016/s0379-0738(02)00398-5.
4
A novel multiplex RT-PCR probe capture hybridization (RT-PCR-ELISA) for simultaneous detection of six viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid, and Pospiviroid.一种用于同时检测四个属（苹果锈果类病毒属、霍斯类病毒属、佩拉类病毒属和马铃薯纺锤块茎类病毒属）中六种类病毒的新型多重逆转录聚合酶链反应探针捕获杂交法（逆转录聚合酶链反应 - 酶联免疫吸附测定法）
J Virol Methods. 2002 Aug;105(1):115-21. doi: 10.1016/s0166-0934(02)00090-3.
5
Authentication of stems of Dendrobium officinale by rDNA ITS region sequences.基于rDNA ITS区序列对铁皮石斛茎进行鉴定
Planta Med. 2002 Feb;68(2):191-2. doi: 10.1055/s-2002-20239.
6
Authentication of medicinal Dendrobium species by the internal transcribed spacer of ribosomal DNA.利用核糖体DNA的内部转录间隔区对药用石斛品种进行鉴定。
Planta Med. 2001 Jul;67(5):456-60. doi: 10.1055/s-2001-15818.
7
Diversity arrays: a solid state technology for sequence information independent genotyping.多样性阵列：一种用于独立基因分型的序列信息固态技术。
Nucleic Acids Res. 2001 Feb 15;29(4):E25. doi: 10.1093/nar/29.4.e25.
8
DNA probes specific for the yeast species Debaryomyces hansenii: useful tools for rapid identification.针对汉逊德巴利酵母菌种的DNA探针：快速鉴定的有用工具。
FEMS Microbiol Lett. 2000 Dec 1;193(1):171-7. doi: 10.1111/j.1574-6968.2000.tb09420.x.
9
Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA.使用源自16S - 23S rRNA基因间隔区及其侧翼23S rRNA的组特异性和种特异性引物，通过多重PCR分析快速鉴定11种人类肠道乳酸杆菌。
FEMS Microbiol Lett. 2000 Jun 15;187(2):167-73. doi: 10.1111/j.1574-6968.2000.tb09155.x.
10
Genetic markers in ribosomal DNA for the identification of members of the genus Anisakis (Nematoda: ascaridoidea) defined by polymerase-chain-reaction-based restriction fragment length polymorphism.基于聚合酶链反应的限制性片段长度多态性鉴定异尖线虫属（线虫纲：蛔总科）成员的核糖体DNA中的遗传标记。
Int J Parasitol. 2000 Feb;30(2):223-6. doi: 10.1016/s0020-7519(99)00178-2.
Zotero 插件