A Novel Method for Screening Species-specific GDNA Probes for Species Identification

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Mar 3

PMID 14993468

Citations 9

Authors

Tong Xiang Li

Jinke Wang

Yunfei Bai

Xiangdong Sun

Zuhong Lu

Affiliations

Soon will be listed here.

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.

Citing Articles

Identification of closely related species in through Analysis of Whole-Genome.

Qi G, Hao L, Gan Y, Xin T, Lou Q, Xu W Front Microbiol. 2024; 15:1323572.

PMID: 38450170 PMC: 10915092. DOI: 10.3389/fmicb.2024.1323572.

Development of DNA markers using next-generation sequencing approach for molecular authentication of L. and (Willd.) Miers.

Sharma A, Vohra M, Vinay C, Paul B, Chakrabarty S, Rai P 3 Biotech. 2023; 13(9):304.

PMID: 37593204 PMC: 10427588. DOI: 10.1007/s13205-023-03732-7.

Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers.

Wu J, Zhang M, Liu J, Huang Y, Xu L, Deng Z Int J Mol Sci. 2022; 23(16).

PMID: 36012702 PMC: 9408830. DOI: 10.3390/ijms23169435.

An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex).

Yu F, Huang Y, Luo L, Li X, Wu J, Chen R BMC Plant Biol. 2018; 18(1):269.

PMID: 30400857 PMC: 6220460. DOI: 10.1186/s12870-018-1471-6.

Subtracted diversity array identifies novel molecular markers including retrotransposons for fingerprinting Echinacea species.

Olarte A, Mantri N, Nugent G, Pang E PLoS One. 2013; 8(8):e70347.

PMID: 23940565 PMC: 3734018. DOI: 10.1371/journal.pone.0070347.

References

Rodrigues U, Aguirre M, Facklam R, Collins M . Specific and intraspecific molecular typing of lactococci based on polymorphism of DNA encoding rRNA. J Appl Bacteriol. 1991; 71(6):509-16. DOI: 10.1111/j.1365-2672.1991.tb03825.x. View

Wan Q, Fang S . Application of species-specific polymerase chain reaction in the forensic identification of tiger species. Forensic Sci Int. 2002; 131(1):75-8. DOI: 10.1016/s0379-0738(02)00398-5. View

Ratcliff R, Lanser J, Manning P, Heuzenroeder M . Sequence-based classification scheme for the genus Legionella targeting the mip gene. J Clin Microbiol. 1998; 36(6):1560-7. PMC: 104877. DOI: 10.1128/JCM.36.6.1560-1567.1998. View

Zhong , Millsap , Reid . Differentiation of Lactobacillus Species by Molecular Typing. Appl Environ Microbiol. 1998; 64(7):2418-23. PMC: 106405. DOI: 10.1128/AEM.64.7.2418-2423.1998. View

Lau D, Shaw P, Wang J, But P . Authentication of medicinal Dendrobium species by the internal transcribed spacer of ribosomal DNA. Planta Med. 2001; 67(5):456-60. DOI: 10.1055/s-2001-15818. View

Bansal N, McDonell F . Identification and DNA fingerprinting of Legionella strains by randomly amplified polymorphic DNA analysis. J Clin Microbiol. 1997; 35(9):2310-4. PMC: 229960. DOI: 10.1128/jcm.35.9.2310-2314.1997. View

Ding X, Xu L, Wang Z, Zhou K, Xu H, Wang Y . Authentication of stems of Dendrobium officinale by rDNA ITS region sequences. Planta Med. 2002; 68(2):191-2. DOI: 10.1055/s-2002-20239. View

Salloum G, Meugnier H, Reyrolle M, Grimont F, Grimont P, Etienne J . Identification of Legionella species by ribotyping and other molecular methods. Res Microbiol. 2003; 153(10):679-86. DOI: 10.1016/s0923-2508(02)01381-5. View

Picardeau M, Vincent V . Development of a species-specific probe for Mycobacterium xenopi. Res Microbiol. 1995; 146(3):237-43. DOI: 10.1016/0923-2508(96)80279-8. View

10.

Corredor M, Davila A, Gaillardin C, Casaregola S . DNA probes specific for the yeast species Debaryomyces hansenii: useful tools for rapid identification. FEMS Microbiol Lett. 2000; 193(1):171-7. DOI: 10.1111/j.1574-6968.2000.tb09420.x. View

11.

Lo Presti F, Riffard S, Vandenesch F, Etienne J . Identification of Legionella species by random amplified polymorphic DNA profiles. J Clin Microbiol. 1998; 36(11):3193-7. PMC: 105300. DOI: 10.1128/JCM.36.11.3193-3197.1998. View

12.

Shamloul A, Faggioli F, Keith J, Hadidi A . 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. J Virol Methods. 2002; 105(1):115-21. DOI: 10.1016/s0166-0934(02)00090-3. View

13.

Jaccoud D, Peng K, Feinstein D, Kilian A . Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res. 2001; 29(4):E25. PMC: 29632. DOI: 10.1093/nar/29.4.e25. View

14.

Regnault B, Grimont F, Grimont P . Universal ribotyping method using a chemically labelled oligonucleotide probe mixture. Res Microbiol. 1998; 148(8):649-59. DOI: 10.1016/S0923-2508(99)80064-3. View

15.

Tannock G, Rodtong S, Ng J, Munro K, Alatossava T . Identification of Lactobacillus isolates from the gastrointestinal tract, silage, and yoghurt by 16S-23S rRNA gene intergenic spacer region sequence comparisons. Appl Environ Microbiol. 1999; 65(9):4264-7. PMC: 99775. DOI: 10.1128/AEM.65.9.4264-4267.1999. View

16.

Te Giffel M, Beumer R, Klijn N, Wagendorp A, Rombouts F . Discrimination between Bacillus cereus and Bacillus thuringiensis using specific DNA probes based on variable regions of 16S rRNA. FEMS Microbiol Lett. 1997; 146(1):47-51. DOI: 10.1111/j.1574-6968.1997.tb10169.x. View

17.

Lisitsyn N, Wigler M . Cloning the differences between two complex genomes. Science. 1993; 259(5097):946-51. DOI: 10.1126/science.8438152. View

18.

Song Y, Kato N, Liu C, Matsumiya Y, Kato H, Watanabe K . 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. FEMS Microbiol Lett. 2000; 187(2):167-73. DOI: 10.1111/j.1574-6968.2000.tb09155.x. View

19.

DAmelio S, Mathiopoulos K, Santos C, Pugachev O, Webb S, Picanco M . 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. Int J Parasitol. 2000; 30(2):223-6. DOI: 10.1016/s0020-7519(99)00178-2. View

20.

Barsotti O, Decoret D, Renaud F . Identification of streptococcus mitis group species by RFLP of the PCR-amplified 16S-23S rDNA intergenic spacer. Res Microbiol. 2003; 153(10):687-91. DOI: 10.1016/s0923-2508(02)01382-7. View