scholarly journals Isolation and identification of a new set of microsatellite loci from Ucides cordatus genome

2015 ◽  
Vol 67 (4) ◽  
pp. 1369-1376 ◽  
Author(s):  
Erlane Araújo ◽  
Fábio Britto ◽  
Adriana Carvalho ◽  
Gleice Orasmo ◽  
Fábio Diniz
Keyword(s):  
Microsatellite Loci ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Magnetic Bead ◽  
Isolation And Identification ◽  
Tetranucleotide Repeat ◽  
Mangrove Species ◽  
Ucides Cordatus ◽  
Microsatellite Isolation ◽  
Mangrove Crab

A new set of microsatellite loci (simple sequence repeats, SSRs) from the overexploited mangrove crab Ucides cordatus is described in this study. Microsatellite isolation used a highly simplified and inexpensive protocol based on (i) multiple enzyme digestion/ligation; (ii) mixed biotin-labeled probes and streptavidin-coated magnetic bead hybridization capture strategy, and (iii) a double-repeat-enrichment procedure. A genomic library, double-enriched for inserts containing tetranucleotide repeat motifs [(GACA)6, (GATA)7, (GGAT)5 and (GTAT)5], was constructed to increase the chance of recovering SSR-containing sequences within DNA fragments. Amplified enriched DNA was cloned and transformed into competent E. coli. Then, positive clones were identified by 'white/blue plaque selection?. One hundred and five colonies were PCR-screened for sequencing, and 72 of these were found to have unique SSR inserts. Microsatellite motifs contained more than five repeats, and most loci were found to have perfect tandem repeats (51.4%), of which 94.4% were dinucleotide and 5.5% trinucleotide. Only 20% of all loci were compound and 28.6% were imperfect repeats containing di-, tri- and/or tetranucleotides. The high frequency of perfect repeat motifs after enrichment is additional evidence of the importance of adopting this procedure for the isolation of SSR. The novel 34 SSRs described in this study are expected to be highly polymorphic and, therefore, useful in population/stocks discrimination of this valuable mangrove species throughout its range, currently subjected to excessive fishing efforts.

scholarly journals Development of Microsatellites: A Powerful Genetic Marker

2016 ◽  
Vol 13 (1) ◽  
pp. 152-172 ◽  
Author(s):  
M Moniruzzaman ◽  
R Khatun ◽  
Zahira Yaakob ◽  
M S Khan ◽  
A A Mintoo
Keyword(s):  
Tandem Repeats ◽  
Genomic Library ◽  
De Novo ◽  
Genome Mapping ◽  
Variable Number ◽  
Genomic Libraries ◽  
Microsatellite Isolation ◽  
Major Disadvantage ◽  
A Genome ◽  
Variable Number Tandem Repeats

The tandem repeats, conserved short segments of DNA, which are found in all prokaryotic and eukaryotic genomes, are called microsatellites. It is also known as variable number tandem repeats (VNTRs), simple sequence repeats (SSRs) and short tandem repeats (STRs). Microsatellites present in both coding and non-coding regions of a genome. The high polymorphism of microsatellites makes them powerful genetic markers for genome mapping of many organisms. It is also suitable for ancient and forensic DNA studies for population genetics and conservation of biological resources. The major disadvantage of microsatellites is that for the first time they need to be isolated de novo from most species being examined. The task of microsatellite isolation is quite cumbersome involving in terms of effort and time, because it traditionally involves screening of genomic libraries. Cross-species amplification, Mining microsatellites from nucleotide sequenced data and Genomic library- based method are general methods of microsatellite isolation.  Cross-species method may not effective for all species, Data mining is not applicable if there is no or limited data of DNA sequence. Genomic library based method is the best choice. Traditional protocol, primer extension protocol, selective hybridization, and Fast Isolation by AFLP of Sequences containing repeats (FIASCO) are the protocols of microsatellite development based on genomic library.  FIASCO is the best protocol ever developed.The Agriculturists 2015; 13(1) 152-172

Isolation and characterization of 11 microsatellite loci in the mangrove crab, Ucides cordatus (Ocypodidae: Ucidinae)

2009 ◽  
Vol 9 (5) ◽  
pp. 1395-1397 ◽  
Author(s):  
EDUARDO SOUSA VARELA ◽  
EVONNILDO DA COSTA GONÇALVES ◽  
MELISSA DE OLIVEIRA SANTOS ◽  
IRACILDA SAMPAIO ◽  
HORACIO SCHNEIDER
Keyword(s):  
Microsatellite Loci ◽  
Ucides Cordatus ◽  
Isolation And Characterization ◽  
Mangrove Crab

scholarly journals Acute toxicity of sodium metabisulphite on mangrove crab Ucides cordatus (Decapoda, Ucididae)

2012 ◽  
Vol 84 (4) ◽  
pp. 1009-1014
Author(s):  
Adriana B. Pedale ◽  
Rodrigo Y. Fujimoto ◽  
Rudã F.B. Santos ◽  
Fernando A. Abrunhosa
Keyword(s):  
Black Spot ◽  
Preliminary Test ◽  
Control Group ◽  
Mangrove Species ◽  
Shrimp Culture ◽  
Ucides Cordatus ◽  
Toxicological Effect ◽  
Sodium Metabisulphite ◽  
Mangrove Crab ◽  
Mortality Index

The sodium metabisulphite salt is usually used in shrimp culture to prevent black spot. Unfortunately the toxicological effect of this xenobiotic in decapod crabs is unknown. Thus, the present study aims to investigate the sodium metabisulphite LC50 - 96 h in the mangrove species Ucides cordatus. Crabs were collected in the tidal creek margins in Bragança estuarine and were submitted to preliminary test (screening) and posterior definitive test. Crabs were exposed in five different concentrations and a control group in five replicates, two crabs per recipient (5 L) during 96 hours. A negative correlation was observed to sodium metabisulphite concentration in relation to dissolved oxygen and pH. At the end of the experiment were obtained the following mortality index in relation to sodium metabisulphite concentrations: 100% in 86.0 mg.L-1, 74% in 62.0 mg.L-1, 52% in 52.0 mg.L-1, 44% in 38.0 mg.L-1. The value of LC50 - 96 h for U. cordatus was determinate at 42.58 mg.L-1/Na2S2O5. The results strongly indicate that sodium metabisulphite is toxic for U. cordatus, and this crab could be used for biomonitoring the environmental impact.

Temporal variation in the weight-size relationship of the mangrove crab Ucides cordatus L. (Decapoda: Ucididae) in relation to its life cycle phases

2014 ◽  
Vol 64 (4) ◽  
pp. 333-342 ◽  
Author(s):  
Marcos de Miranda Leão Leite ◽  
Cynthia Yuri Ogawa ◽  
Carla Ferreira Rezende ◽  
José Roberto Feitosa Silva
Keyword(s):  
Life Cycle ◽  
Condition Factor ◽  
River Estuary ◽  
Total Weight ◽  
Northeastern Brazil ◽  
Annual Life Cycle ◽  
Ucides Cordatus ◽  
Mangrove Crab ◽  
Significant Difference ◽  
The Relationship

The relationship between weight and size of individuals can be used to evaluate the status of a population, which is particularly useful for natural populations that are being exploited. Ucides cordatus occurs on the Atlantic coast of the American continent, from Florida (USA) to Santa Catarina (Brazil). This species is economically very important, most of all in the Northeastern area of Brazil, as well as in the Dominican Republic and Suriname. The objective of this study was to analyze life phases (‘fattening’, ‘matumba’, ‘milk-crab’, ‘maturation’ and ‘walking’) by use of the weight-length relationships, as well as temporal variations in this condition factor for each sex of U. cordatus. For this purpose, individuals were sampled monthly for twenty-four months at the Jaguaribe River estuary, Ceará State, Northeastern Brazil. The relationship between total weight and cephalothorax width was established using regression analysis, adjusted by a power equation. The dynamics of the condition factor were analyzed for each sex using the variation of its averages related to annual life cycle; this was done for each of the previously-mentioned phases. The relationship between total weight and cephalothorax width showed an isometric growth in males and negative allometric growth in females suggesting that, for the same reference size, males are heavier than females. When considering the average of the female condition factors, these were greater than those for males during the annual life cycle, except during the ‘maturation’ phase, which is the phase with a higher demand of energetic reserves for males. Annual variation of the condition factor in females presented no significant difference.

Influence of seasonality on the natural modulation of oxidative stress biomarkers in mangrove crab Ucides cordatus (Brachyura, Ucididae)

2019 ◽  
Vol 227 ◽  
pp. 146-153 ◽  
Author(s):  
Carla Carolina Miranda dos Santos ◽  
Jorge Felippe Medeiros da Costa ◽  
Cléverson Rannieri Meira dos Santos ◽  
Lílian Lund Amado
Keyword(s):  
Oxidative Stress ◽  
Oxidative Stress Biomarkers ◽  
Ucides Cordatus ◽  
Stress Biomarkers ◽  
Mangrove Crab

Molecular and cytogenetic analysis of repetitive DNA in pea (Pisum sativum L.)

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 716-728 ◽  
Author(s):  
Pavel Neumann ◽  
Marcela Nouzová ◽  
Jirí Macas
Keyword(s):  
Pisum Sativum ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Genomic Library ◽  
Chromosome Morphology ◽  
Plant Genome ◽  
Genomic Repeats ◽  
Dispersed Repeats

A set of pea DNA sequences representing the most abundant genomic repeats was obtained by combining several approaches. Dispersed repeats were isolated by screening a short-insert genomic library using genomic DNA as a probe. Thirty-two clones ranging from 149 to 2961 bp in size and from 1000 to 39 000/1C in their copy number were sequenced and further characterized. Fourteen clones were identified as retrotransposon-like sequences, based on their homologies to known elements. Fluorescence in situ hybridization using clones of reverse transcriptase and integrase coding sequences as probes revealed that corresponding retroelements were scattered along all pea chromosomes. Two novel families of tandem repeats, named PisTR-A and PisTR-B, were isolated by screening a genomic DNA library with Cot-1 DNA and by employing genomic self-priming PCR, respectively. PisTR-A repeats are 211–212 bp long, their abundance is 2 × 104 copies/1C, and they are partially clustered in a secondary constriction of one chromosome pair with the rest of their copies dispersed on all chromosomes. PisTR-B sequences are of similar abundance (104 copies/1C) but differ from the "A" family in their monomer length (50 bp), high A/T content, and chromosomal localization in a limited number of discrete bands. These bands are located mainly in (sub)telomeric and pericentromeric regions, and their patterns, together with chromosome morphology, allow discrimination of all chromosome types within the pea karyotype. Whereas both tandem repeat families are mostly specific to the genus Pisum, many of the dispersed repeats were detected in other legume species, mainly those in the genus Vicia.Key words: repetitive DNA, plant genome, retroelements, satellite DNA, Pisum sativum.

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