1
|
THOMAS R, SAIKIA M, SINGHA S, BARUAH Z, KALITA R, SAHARIA N, RAJKHOWA S. PCR based method for authentication of pork in raw and processed products as well as in binary meat mixtures. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2021. [DOI: 10.56093/ijans.v91i1.113219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
In this study, amplification of species-specific marker of mitochondrial DNA origin was carried out to detect pork in raw, processed and meat mixtures containing varying concentrations of pork, viz. 1, 10, 50, 75 and 100%. The species-specific marker for pork was tested in raw pork from different breeds/varieties of pig such as Hampshire, Yorkshire, Ghungroo, Duroc, Rani, and Asha. The size of the amplified product was 290 bp in all the breeds/ varieties. The results were consistent in processed pork products, viz. frankfurter sausage, salami, cocktail sausage, pork slice, ham, and pork curry which were subjected to different cooking temperatures ranging from 75 to 121°C. In case of all the mixtures with different concentrations of pork, similar results were observed. Subsequently, this marker was tested for cross-amplification by checking them with beef, carabeef, mutton, chevon, chicken, and duck meat and no amplification was observed. The results suggested that the DNA marker used in this study is highly species-specific and reliable to detect pork adulteration, unambiguously, in raw, processed as well as in meat mixtures containing pork. This technique is rapid, simple and economical as compared to other methods of pork adulteration detection.
Collapse
|
2
|
Vozdova M, Kubickova S, Cernohorska H, Fröhlich J, Martínková N, Rubes J. Sequence Analysis and FISH Mapping of Four Satellite DNA Families among Cervidae. Genes (Basel) 2020; 11:genes11050584. [PMID: 32456268 PMCID: PMC7288315 DOI: 10.3390/genes11050584] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/14/2020] [Accepted: 05/20/2020] [Indexed: 01/07/2023] Open
Abstract
Centromeric and pericentromeric chromosome regions are occupied by satellite DNA. Satellite DNAs play essential roles in chromosome segregation, and, thanks to their extensive sequence variability, to some extent, they can also be used as phylogenetic markers. In this paper, we isolated and sequenced satellite DNA I-IV in 11 species of Cervidae. The obtained satellite DNA sequences and their chromosomal distribution were compared among the analysed representatives of cervid subfamilies Cervinae and Capreolinae. Only satI and satII sequences are probably present in all analysed species with high abundance. On the other hand, fluorescence in situ hybridisation (FISH) with satIII and satIV probes showed signals only in a part of the analysed species, indicating interspecies copy number variations. Several indices, including FISH patterns, the high guanine and cytosine (GC) content, and the presence of centromere protein B (CENP-B) binding motif, suggest that the satII DNA may represent the most important satellite DNA family that might be involved in the centromeric function in Cervidae. The absence or low intensity of satellite DNA FISH signals on biarmed chromosomes probably reflects the evolutionary reduction of heterochromatin following the formation of chromosome fusions. The phylogenetic trees constructed on the basis of the satellite I-IV DNA relationships generally support the present cervid taxonomy.
Collapse
Affiliation(s)
- Miluse Vozdova
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
- Correspondence: ; Tel.: +420-533-331-422
| | - Svatava Kubickova
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Halina Cernohorska
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Jan Fröhlich
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| | - Natália Martínková
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, 603 65 Brno, Czech Republic;
| | - Jiri Rubes
- Department of Genetics and Reproduction, Central European Institute of Technology—Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic; (S.K.); (H.C.); (J.F.); (J.R.)
| |
Collapse
|
3
|
Hsieh LJ, Cheng YM, Wang YC, Lin CC, Li YC. Organization and evolution of a novel cervid satellite DNA with yeast CDEI-like repeats. Zool Stud 2014. [DOI: 10.1186/s40555-014-0025-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
It has been proposed that pericentromeric satellite DNA arises from the progressive proximal expansion of ancient centromeric DNA. In an attempt to recover putative ancestral centromeric DNA, we microdissected the pericentromeric/centromeric DNA from the chromosome X + 3 of Indian muntjac (Muntiacus muntjak vaginalis) and constructed a microclone-library of the X + 3 centromeric DNA.
Results
A new cervid satellite DNA element, designated as satellite VI, was isolated from this library. Fluorescence in situ hybridization (FISH) studies revealed that satellite VI is predominately located on the distal pericentromeric region of the Indian muntjac chromosome X + 3 and on the pericentromeres of several Old World deer species studied. Its sequence is organized as 11-bp monomeric (ATCACGTGGGA) tandem repeats. Further sequencing on a BAC clone of Indian muntjac harboring this repeat showed that an array of this repeat stretches over approximately 5 kb followed by approximately 3 kb of interspersed repetitive sequences, such as long interspersed elements (LINEs), short interspersed elements (SINEs), and long terminal repeats (LTRs).
Conclusions
Based on the chromosomal localization, genomic and sequence organization, and copy numbers of satellite VI in deer species studied, we postulate that this newly found satellite DNA could be a putative ancient cervidic centromeric DNA that is still preserved in some Old World deer. Interestingly, the first eight nucleotides of the 11-bp monomeric consensus sequences are highly conserved and identical to the CDEI element in the centromere of the budding yeast Saccharomyces cerevisiae. The centromeric/pericentromeric satellite DNA harboring abundant copies of CDEI sequences is the first found in a mammalian species. Several zipper-like d (GGGA)2 motifs were also found in the (ATCACGTGGGA)n repeat of satellite VI DNA. Whether the satellite VI is structurally and functionally correlated with the CDEI of centromere of budding yeast and whether a zipper-like structure forms in satellite VI require further studies.
Collapse
|
4
|
|
5
|
Haunshi S, Basumatary R, Girish P, Doley S, Bardoloi R, Kumar A. Identification of chicken, duck, pigeon and pig meat by species-specific markers of mitochondrial origin. Meat Sci 2009; 83:454-9. [DOI: 10.1016/j.meatsci.2009.06.026] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 05/02/2009] [Accepted: 06/15/2009] [Indexed: 11/28/2022]
|
6
|
Xiao CT, Zhang MH, Fu Y, Koh HS. Mitochondrial DNA distinction of northeastern China roe deer, Siberian roe deer, and European roe deer, to clarify the taxonomic status of northeastern China roe deer. Biochem Genet 2007; 45:93-102. [PMID: 17219081 DOI: 10.1007/s10528-006-9052-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Partial sequences of the mitochondrial control region of northeastern China roe deer were analyzed to determine the degree of genetic diversity. Fourteen haplotypes were observed. The haplotype diversity was high (h = 0.872), nucleotide diversity was medium (p ( i ) = 0.0108), and the average Tamura-Nei nucleotide distance among them was 1.9%, indicating that genetic diversity of roe deer from northeastern China was relatively high and that the effective population size was large historically. To clarify the northeastern China roe deer's taxonomic status, these 14 haplotypes were compared with 31 haplotypes published in Genbank from Europe, Siberia, and Korea. The average genetic distance between haplogroups of northeastern China and European roe deer (5.8%) was more than twice that between northeastern China and Siberian roe deer (2.7%), indicating sufficient variation to consider roe deer of northeastern China and Siberia as a single species (Capreolus pygargus), distinct from European roe deer (Capreolus capreolus). This is the first presentation of mtDNA data for roe deer in northeastern China, which will be helpful in investigations of genetic diversity and clarifications of the taxonomic status of roe deer in the whole of China.
Collapse
Affiliation(s)
- Chao-Ting Xiao
- College of Animal Sciences, Zhejiang University, Hangzhou 310029, PR China.
| | | | | | | |
Collapse
|
7
|
Lin CC, Li YC. Chromosomal distribution and organization of three cervid satellite DNAs in Chinese water deer (Hydropotes inermis). Cytogenet Genome Res 2006; 114:147-54. [PMID: 16825767 DOI: 10.1159/000093331] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2005] [Accepted: 01/24/2006] [Indexed: 11/19/2022] Open
Abstract
The species-specific profile and centromeric heterochromatin localization of satellite DNA in mammalian genomes imply that satellite DNA may play an important role in mammalian karyotype evolution and speciation. A satellite III DNA family, CCsatIII was thought to be specific to roe deer (Capreolus capreolus). In this study, however, this satellite DNA family was found also to exist in Chinese water deer (Hydropotes inermis) by PCR-Southern screening. A satellite III DNA element of this species was then generated from PCR-cloning by amplifying this satellite element using primer sequences from the roe deer satellite III clone (CCsatIII). The newly generated satellite III DNA along with previously obtained satellite I and II DNA clones were used as probes for FISH studies to investigate the genomic distribution and organization of these three satellite DNA families in centromeric heterochromatin regions of Chinese water deer chromosomes. Satellite I and II DNA were observed in the pericentric/centric regions of all chromosomes, whereas satellite III was distributed on 38 out of 70 chromosomes. The distribution and orientation of satellite DNAs I, II and III in the centromeric heterochromatin regions of the genome were further classified into four different types. The existence of a Capreolus-like satellite III in Chinese water deer implies that satellite III is not specific to the genus Capreolus (Buntjer et al., 1998) and supports the molecular phylogeny classification of Randi et al. (1998) which suggests that Chinese water deer and roe deer are closely related.
Collapse
Affiliation(s)
- C C Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | | |
Collapse
|
8
|
Kuznetsova MV, Kholodova MV, Danilkin AA. Molecular Phylogeny of Deer (Cervidae: Artiodactyla). RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0154-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
9
|
Li YC, Cheng YM, Hsieh LJ, Ryder OA, Yang F, Liao SJ, Hsiao KM, Tsai FJ, Tsai CH, Lin CC. Karyotypic evolution of a novel cervid satellite DNA family isolated by microdissection from the Indian muntjac Y-chromosome. Chromosoma 2005; 114:28-38. [PMID: 15827746 DOI: 10.1007/s00412-005-0335-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2005] [Revised: 02/22/2005] [Accepted: 02/22/2005] [Indexed: 10/25/2022]
Abstract
A minilibrary was constructed from DOP-PCR products using microdissected Y-chromosomes of Indian muntjac as DNA templates. Two microclones designated as IM-Y4-52 and IM-Y5-7 were obtained from negative screening of all three cervid satellite DNAs (satellites I, II, and IV). These two microclones were 295 and 382 bp in size, respectively, and shared approximately 70% sequence homology. Southern blot analysis showed that the IM-Y4-52 clone was repetitive in nature with an approximately 0.32-kb register in HaeIII digest. Sequence comparison revealed no similarities to DNA sequences deposited in the GenBank database, suggesting that the microclone sequences were from a novel satellite DNA family designated as cervid satellite V. A subclone of an Indian muntjac BAC clone which screened positive for IM-Y4-52 had a 3,325-bp insert containing six intact monomers, four deleted monomers, and two partial monomers. The consensus sequence of the monomer was 328 bp in length and shared more than 80% sequence homology with every intact monomer. A zoo blot study using IM-Y4-52 as a probe showed that the strong hybridization with EcoRI digested male genomic DNA of Indian muntjac, Formosan muntjac, Chinese muntjac, sambar deer, and Chinese water deer. Female genomic DNA of Indian muntjac, Chinese water deer, and Formosan muntjac also showed positive hybridization patterns. Satellite V was found to specifically localize to the Y heterochromatin region of the muntjacs, sambar deer, and Chinese water deer and to chromosome 3 of Indian muntjac and the X-chromosome of Chinese water deer.
Collapse
Affiliation(s)
- Y-C Li
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec. 1, Chien Kuo N. Rd., 40203 Taichung, Taiwan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Lin CC, Chiang PY, Hsieh LJ, Liao SJ, Chao MC, Li YC. Cloning, characterization and physical mapping of three cervid satellite DNA families in the genome of the Formosan muntjac (Muntiacus reevesi micrurus). Cytogenet Genome Res 2004; 105:100-6. [PMID: 15218264 DOI: 10.1159/000078015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Accepted: 11/03/2003] [Indexed: 11/19/2022] Open
Abstract
Due to their high sequence diversity even among closely related species, satellite DNA sequences can be a useful molecular marker for phylogenetic and taxonomic analyses. To characterize the satellite DNA in the genome of a native muntjac species of Taiwan, the Formosan muntjac, satellite DNA clones representing three different cervid satellite DNA families from this species were isolated and analyzed. Genomic organization study of these satellite DNAs was also undertaken. Three Formosan muntjac satellite DNA clones were obtained and designated as FM-satI (1,391 bp), FM-satII (1,143 bp) and FM-satIV (1,103 bp), and found to share approximately 82, 81 and 98% sequence homology with the Chinese muntjac satellite I clone (C5), Indian muntjac satellite II clone (Mmv-0.7) and Chinese muntjac satellite IV clone (MR-1.0), respectively. These three satellite DNA families are organized in a pter<--FM-satII-FM-satIV-FM-satI-->qter orientation in the centromeric region with satII closely associated with the telomeric sequences. Satellite DNA sequence comparison, in combination with chromosome data concludes that the Formosan muntjac is likely a subspecies of M. reevesi, closely related to the Chinese muntjac. With the kinetochore satellite II DNA co-localizing with the telomeric sequences, the Formosan muntjac chromosomes could be truly telocentric.
Collapse
Affiliation(s)
- C C Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | | | | | | | | | | |
Collapse
|
11
|
Gallin J, Vogler AP. Evolutionary dynamics of a satellite DNA in the tiger beetle species pair Cicindela campestris and C. maroccana. Genome 2003; 46:213-23. [PMID: 12723037 DOI: 10.1139/g02-126] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Satellite repeat elements are an abundant component of eukaryotic genomes, but not enough is known about their evolutionary dynamics and their involvement in karyotype and species differentiation. We report the nucleotide sequence, chromosomal localization, and evolutionary dynamics of a repetitive DNA element of the tiger beetle species pair Cicindela maroccana and Cicindela campestris. The element was detected after restriction digest of C. maroccana total genomic DNA with EcoRI as a single band and its multimers on agarose gels. Cloning and sequencing of several isolates revealed a consensus sequence of 383 bp with no internal repeat structure and no detectable similarity to any entry in GenBank. Hybridization of the satellite unit to C. maroccana mitotic and meiotic chromosomes revealed the presence of this repetitive DNA in the centromeres of all chromosomes except the Y chromosome, which exhibited only a very weak signal in its short arm. PCR-based tests for this satellite in related species revealed its presence in the sister species C. campestris, but not in other closely related species. Phylogenetic analysis of PCR products revealed well-supported clades that generally separate copies from each species. Because both species exhibit the multiple X chromosome karyotypic system common to Cicindela, but differ in their X chromosome numbers (four in C. maroccana vs. three in C. campestris), structural differences could also be investigated with regard to the position of satellites in a newly arisen X chromosome. We find the satellite in a centromeric position in all X chromosomes of C. maroccana, suggesting that the origin of the additional X chromosome involves multiple karyotypic rearrangements.
Collapse
Affiliation(s)
- José Gallin
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, 3a Planta, Universidad de Murcia, Apdo. 4021, Murcia, 30071, Spain.
| | | |
Collapse
|
12
|
Nijman IJ, Otsen M, Verkaar ELC, de Ruijter C, Hanekamp E, Ochieng JW, Shamshad S, Rege JEO, Hanotte O, Barwegen MW, Sulawati T, Lenstra JA. Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites. Heredity (Edinb) 2003; 90:10-6. [PMID: 12522420 DOI: 10.1038/sj.hdy.6800174] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Hybridization between wild and domestic bovine species occurs worldwide either spontaneously or by organized crossing. We have analysed hybridization of banteng (Bos javanicus) and zebu (Bos indicus) in south-east Asian cattle using mitochondrial DNA (PCR-RFLP and sequencing), AFLP, satellite fragment length polymorphisms (SFLP or PCR-RFLP of satellite DNA) and microsatellite genotyping. The Indonesian Madura zebu breed is reputed to be of hybrid zebu-banteng origin, but this has never been documented and Bali cattle are considered to be a domesticated form of banteng. The banteng mitochondrial type was found in all animals sampled on the isle of Bali, Indonesia, but only in 35% of the animals from a Malaysian Bali-cattle population. The Madura animals also carried mitochondrial DNA of either zebu and banteng origin. In both populations, zebu introgression was confirmed by AFLP and SFLP. Microsatellite analysis of the Malaysian Bali population revealed for 12 out of 15 loci screened, Bali-cattle-specific alleles, several of which were also found in wild banteng animals. The tools we have described are suitable for the detection of species in introgression studies, which are essential for the genetic description of local breeds and the preservation of their economic and cultural value.
Collapse
Affiliation(s)
- I J Nijman
- Institute of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, The Netherlands.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Differentiation of cattle species in beef by PCR-RFLP of mitochondrial and satellite DNA. Meat Sci 2002; 60:365-9. [DOI: 10.1016/s0309-1740(01)00144-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2001] [Revised: 05/17/2001] [Accepted: 06/15/2001] [Indexed: 11/23/2022]
|
14
|
Stitou S, Díaz de la Guardia R, Jiménez R, Burgos M. Isolation of a species-specific satellite DNA with a novel CENP-B-like box from the North African rodent Lemniscomys barbarus. Exp Cell Res 1999; 250:381-6. [PMID: 10413592 DOI: 10.1006/excr.1999.4516] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A species-specific satellite DNA (Lb-MspISAT) was isolated from the North African rodent Lemniscomys barbarus. This DNA is highly homogeneous in the sequence of different repeats and shows no internal repetitions. Filter and in situ hybridizations demonstrated that it is tandemly repeated at the centromeres of all chromosomes of the complement. A 19-bp CENP-B-like motif was found in Lb-MspISAT which conserves 12 of the 17-bp of the human CENP-B box, but only 5 of the 9-bp of the canonical sequence that is necessary to bind the CENP-B protein. Compared with the human CENP-B box, nucleotide substitutions and insertions increase the palindromic structure of this motif. The possibilities that it may be involved in centromeric function or in homogenization of the Lb-MspISAT sequence are discussed.
Collapse
Affiliation(s)
- S Stitou
- Facultad de Ciencias, Universidad de Granada, Granada, 18071, Spain
| | | | | | | |
Collapse
|