scholarly journals CROSS-SPECIES AMPLIFICATION OF MICROSATELLITES AND IDENTIFICATION OF POLYPLOID HYBRIDS BY ALLELE DOSAGE EFFECTS IN COBITIS HANKUGENSIS AND IKSOOKIMIA LONGICORPA HYBRID COMPLEX

2021 ◽  
Author(s):  
Seung-Woon YUN ◽  
Jong-Young PARK ◽  
Karel Janko
Keyword(s):  
Microsatellite Markers ◽  
Mendelian Inheritance ◽  
Molecular Tools ◽  
Genome Composition ◽  
Dosage Effects ◽  
Allele Dosage ◽  
Hybrid Complex ◽  
Specific Amplification ◽  
Reliable Differentiation ◽  
Species Specific

Background. During the course of evolution, numerous taxa abandoned canonical sex and reproduced asexually. Examination of the Cobitis hankugensis - Iksookimia longicorpa asexual complex already revealed important evolutionary discoveries tackling phenomena like interspecific hybridization, non-Mendelian inheritance, polyploidy and asexuality. Yet, as in other similar cases, the investigation is hampered by the lack of easily accessible molecular tools for efficient differentiation among genomotypes. Material and methods. Here, we tested the cross-species amplification of 23 microsatellite markers derived from distantly related species and investigated the extent to which such markers can facilitate the genome identification in non-model hybrid complex. Results. We found that 21 out of 23 microsatellite markers amplified in all genomotypes. Five of them could be used for easy diagnosticity of parental species and their hybrids due to species-specific amplification profiles. We also noted that three markers, i.e. IC654 and IC783 derived from Cobitis choii and Iko_TTA01 from Iksookimia koreensis, had dosage-sensitive amplification efficiencies of species-specific alleles. This could be further used for reliable differentiation of genome composition in polyploids. Conclusions. The present study introduces a noninvasive method applicable for diagnosis of ploidy and genome composition of hybrids, which are not clearly distinguished morphologically. We showed that very detailed information may be obtained even from markers developed in distantly related taxa.

scholarly journals Cross-species amplification of microsatellites and identification of polyploid hybrids by allele dosage effects in Cobitis hankugensis × Iksookimia longicorpa hybrid complex (Actinopterygii: Cypriniformes: Cobitidae)

2021 ◽  
Vol 51 (2) ◽  
pp. 167-174
Author(s):  
Seung-Woon Yun ◽  
Jong-Young Park ◽  
Karel Janko
Keyword(s):  
Microsatellite Markers ◽  
Mendelian Inheritance ◽  
Model Organisms ◽  
Genome Composition ◽  
Allele Dosage ◽  
Hybrid Complex ◽  
Reported Study ◽  
Specific Amplification ◽  
Reliable Differentiation ◽  
Species Specific

During the course of evolution, numerous taxa abandoned canonical sex and reproduced asexually. Examination of the Cobitis hankugensis × Iksookimia longicorpa asexual complex already revealed important evolutionary discoveries tackling phenomena like interspecific hybridization, non-Mendelian inheritance, polyploidy, and asexuality. Yet, as in other similar cases, the investigation is hampered by the lack of easily accessible molecular tools for efficient differentiation among genomotypes. Here, we tested the cross-species amplification of 23 microsatellite markers derived from distantly related species and investigated the extent to which such markers can facilitate the genome identification in the non-model hybrid complex. We found that 21 out of 23 microsatellite markers were amplified in all genomotypes. Five of them could be used for easy diagnostics of parental species and their hybrids due to species-specific amplification profiles. We also noted that three markers, i.e., IC654 and IC783 derived from Cobitis choii Kim et Son, 1984 and Iko_TTA01 from Iksookimia koreensis (Kim, 1975), had dosage-sensitive amplification efficiencies of species-specific alleles. This could be further used for reliable differentiation of genome composition in polyploids. The presently reported study introduces a noninvasive method applicable for the diagnosis of ploidy and genome composition of hybrids, which are not clearly distinguished morphologically. We showed that very detailed information may be obtained even from markers developed in distantly related taxa. Hybridization is being increasingly recognized as a driving force in evolution. Yet, proper detection of hybrids and their ploidy is particularly challenging, especially in non-model organisms. The present paper evaluates the power of microsatellite cross-amplification not only in the identification of hybrid forms but also in estimating their genome dosage on an example of a fish taxon that involves asexuality, hybridization as well as ploidy variation. It thus demonstrates the wide applicability of such cheap and non-invasive tools.

scholarly journals Obtaining microsatellite markers for Pseudoplatystoma reticulatum using heterologous primers

2021 ◽  
Vol 42 (3) ◽  
pp. 1323-1334
Author(s):  
Jefferson Murici Penafort ◽  
◽  
Laís Santana Celestino Mantovani ◽  
Gabriela Hernandes Granzoto ◽  
Pedro Luiz de Castro ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Information Content ◽  
Polymorphic Information Content ◽  
Low Frequency ◽  
Fish Stocks ◽  
Specific Amplification ◽  
Ssrs Markers ◽  
Average Size ◽  
Species Specific ◽  
Future Population

Studies on genetic composition in fish populations contribute to conservationist practices and inbreeding control in fish stocks. To this end, molecular tools such as microsatellite markers (SSRs) are often used, but they are expensive and time-consuming to develop. A species-specific heterologous marker emerges as an alternative, which can be used in taxonomically related species in a fast way. Our goal was to test SSRs markers of Brachyplatystoma rousseauxi and Pseudoplatystoma punctifer in P. reticulatum in an unprecedented way. For this purpose, DNA was extracted from fragments of the caudal fin of 222 P. reticulatum adults, using a NaCl-based method. Then, DNA samples were amplified by Polymerase Chain Reaction (PCR) using six markers, four from B. rousseauxi (BR38, 47, 51, and 61) and two from P. punctifer (PPU13 and PPU15). Two primers showed non-specific amplification and were disregarded (BR38 and PPU13). In the remaining four primers, the number of alleles per locus varied between two (BR47) to sixteen (BR51), and the average size of alleles was between 142 and 400 bp. Mean effective number of alleles per locus ranged from 10,650 (BR51) to 1,784 (BR47), with null or low-frequency alleles in all studied loci. Observed heterozygosity ranged from 0.299 (BR47) to 0.640 (BR51) and was always lower than the expected heterozygosity. Hardy-Weinberg balance was significant (p < 0.05) in all loci, and inbreeding coefficient (FIS) was always positive. Polymorphic Information Content (PIC) confirmed the efficiency of the markers since they had moderate (BR47) to high levels of information (BR51, BR61, and PPU15). Transferability test showed that the heterologous microsatellite molecular markers, originally for B. rousseauxi and P. punctifer, were efficient in P. reticulatum, producing three primers with high information content. Therefore, these markers can be safely used in future population studies of this species.

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

scholarly journals Uneven distribution of cryptic diversity among higher taxa of parasitic worms

2010 ◽  
Vol 7 (2) ◽  
pp. 241-244 ◽  
Author(s):  
Robert Poulin
Keyword(s):  
Cryptic Species ◽  
Zoonotic Diseases ◽  
Helminth Parasites ◽  
Morphological Markers ◽  
Molecular Tools ◽  
Invasive Pathogens ◽  
Higher Taxa ◽  
As Species ◽  
Species Specific ◽  
Parasitic Worms

Cryptic species cause problems for estimates of biodiversity. In the case of parasites, cryptic species also plague efforts to detect potential zoonotic diseases or invasive pathogens. It is crucial to determine whether the likelihood of finding cryptic species differs among higher parasite taxa, to better calibrate estimates of diversity and monitor diseases. Using published reports of cryptic species of helminth parasites identified using molecular tools, I show that the number of species found is strongly related to the number of parasite individuals sequenced, weakly influenced by the number of host species from which parasites were obtained, and unaffected by the genetic markers used. After correction for these factors, more cryptic species of trematodes are found than in other helminth taxa. Although several features distinguish trematodes from other helminths, it is probable that our inability to discriminate among sibling species of trematodes results from their lack of structures serving as species-specific morphological markers. The available data suggest that current estimates of helminth diversity may need to be doubled (tripled for trematodes) to better reflect extant diversity.

scholarly journals Microsatellite loci development and population genetics in Neotropical fish Curimata mivartii (Characiformes: Curimatidae)

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5959 ◽  
Author(s):  
Ricardo M. Landínez-García ◽  
Edna J. Marquez
Keyword(s):  
Population Genetics ◽  
Microsatellite Loci ◽  
Molecular Tools ◽  
Migratory Species ◽  
Lower Section ◽  
Neotropical Fish ◽  
International Union ◽  
Commercially Important ◽  
Species Specific ◽  
Near Threatened

The Curimatidae family plays an ecological role in the recycling and distribution of nutrients and constitutes a major food source for several commercially important fishes. Curimata mivartii, a member of this family, is considered a short-distance migratory species (≤100 km), categorized by the International Union for Conservation of Nature as a near threatened species, based on its declining population densities and habitat disturbance and fragmentation. Since population genetics and species-specific molecular tools remain unknown for all members of the Curimatidae family, this study developed a set of microsatellite loci and studied the population genetics of C. mivartii in the lower section of the Colombian Magdalena-Cauca basin. The results showed high levels of genetic diversity and evidence of gene flow even between locations separated over 350 km. This information provides a baseline for designing conservation and management programs for C.mivartii and constitutes the first study of population genetics in Curimatidae.

Fast identification of scallop adductor muscles using species-specific microsatellite markers

2007 ◽  
Vol 227 (2) ◽  
pp. 353-359 ◽  
Author(s):  
Aibin Zhan ◽  
Jingjie Hu ◽  
Xiaoli Hu ◽  
Wei Lu ◽  
Mingling Wang ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Fast Identification ◽  
Adductor Muscles ◽  
Species Specific

Species-specific amplification by PCR of ribosomal DNA from some equine strongyles

Parasitology ◽  
1999 ◽  
Vol 119 (1) ◽  
pp. 69-80 ◽  
Author(s):  
G.-C. HUNG ◽  
R. B. GASSER ◽  
I. BEVERIDGE ◽  
N. B. CHILTON
Keyword(s):  
Ribosomal Dna ◽  
Anthelmintic Resistance ◽  
Pcr Assay ◽  
Strongylus Vulgaris ◽  
Faecal Samples ◽  
Faecal Egg Count ◽  
Specific Amplification ◽  
Internal Transcribed Spacer Sequences ◽  
Second Internal Transcribed Spacer ◽  
Species Specific

The first and second internal transcribed spacer sequences of 28 morphologically-defined species of horse strongyle were characterized, and specific oligonucleotide primers were designed for some species based on the nucleotide differences. Utilizing these primers, a PCR approach was developed for the specific amplification of ribosomal DNA of Strongylus vulgaris, Cyathostomum catinatum, Cylicocyclus nassatus, Cylicostephanus longibursatus or Cylicostephanus goldi. The method allowed the species-specific amplification of parasite DNA derived from faecal samples and/or copro-cultures, demonstrating the potential of the approach for the diagnosis of equine strongyloidosis. The establishment of this PCR assay also has implications for studying the biology and epidemiology of equine strongyles and anthelmintic resistance using faecal egg count reduction tests.

Low-copy microsatellite markers for Pinus taeda L.

Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 550-555 ◽  
Author(s):  
Christine G Elsik ◽  
Virginia T Minihan ◽  
Sarah E Hall ◽  
Ann M Scarpa ◽  
Claire G Williams
Keyword(s):  
Microsatellite Markers ◽  
Pinus Taeda ◽  
Loblolly Pine ◽  
Trinucleotide Repeat ◽  
Polymorphic Information Content ◽  
Mendelian Inheritance ◽  
Multiple Alleles ◽  
Pcr Products ◽  
Pinus Taeda L ◽  
Specific Priming

Eighteen low-copy and genomic microsatellite markers were tested for Mendelian inheritance and then assayed in 41 Pinus taeda L. samples drawn from five regions in the southern United States. The PCR products had multiple alleles, high levels of polymorphism, and little non-specific priming. Fifteen of the 18 markers were informative for a P. taeda three-generation RFLP (restriction fragment length polymorphism) pedigree, and a P. taeda population survey revealed three to 28 alleles per locus. The highest allele numbers and polymorphic information content (PIC) values were associated with complex repeat sequences and (or) with sequences consisting of the longer strings of perfect repeats. The abundance of low- to rare-frequency alleles also accounted for high PIC values in both types of markers. Low-copy microsatellites are useful for the large, complex pine genome, especially in the absence of entire gene sequences in public databases and with the low levels of polymorphism in markers developed from expressed sequence tags (ESTs).Key words: loblolly pine, conifers, gymnosperms, trinucleotide repeat motifs.

Evaluation of maize microsatellite markers for genetic diversity analysis and fingerprinting in sugarcane

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 394-403 ◽  
Author(s):  
A Selvi ◽  
N V Nair ◽  
N Balasundaram ◽  
T Mohapatra
Keyword(s):  
Microsatellite Markers ◽  
Cost Effective ◽  
Diversity Analysis ◽  
Phenetic Analysis ◽  
Potential Cost ◽  
Banding Patterns ◽  
Genomic Libraries ◽  
Cost Effective Method ◽  
Low Diversity ◽  
Species Specific

The use of maize microsatellite markers as a potential cost-effective method for molecular analysis of sugarcane was evaluated. Of the 34 primer pairs obtained from maize genomic libraries, 14 showed repeatable amplifications in Saccharum species clones, commercial hybrids, and the related genera Erianthus, accounting for 41.17% cross transferability. Complex banding patterns were encountered in sugarcane with the number of amplified fragments ranging from 7 to 14 with an average of 10 per primer, indicating the high polyploidy and heterozygosity existing in sugarcane. Phenetic analysis of the SSR polymorphisms produced by nine primers could clearly differentiate the different species of Saccharum and Erianthus and revealed the relationships that existed between them. Genetic similarity co-efficient indicated low diversity existing among the S. officinarum clones (82%) and a relatively higher level of diversity in the S. spontaneum clones (69.7%). Higher level of divergence of Erianthus from Saccharum was also clearly estabilished. Five primers produced genus- and species-specific fragments for Erianthus, S. spontaneum, S. officinarum, and S. barberi. The polymorphic primers, when tested on a panel of 30 commercial sugarcane cultivars, revealed a broad range (32.4–83.3%) of pair-wise similarity values, indicating their ability to detect high levels of polymorphism. A combination of two primers could differentiate all the varieties, further emphasizing their potential in fingerprinting and varietal identification.Key words: maize microsatellites, Saccharum, Erianthus, diversity analysis, fingerprinting.

Sign in / Sign up

Export Citation Format

Share Document