Microsatellite loci from the pink shrimp <i>Farfantenaeus notialis</i> (Crustacea, Decapoda)

Robainas, A.; Monnerot, Monique; Solignac, Michel; Dennebouy, N.; Espinosa, Georgina; García‐Machado, Erik

doi:10.1046/j.1471-8286.2002.00241.x

Cited by 7 publications

(6 citation statements)

References 7 publications

(7 reference statements)

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“…Despite the observed exceptions, similar to those reported for other crustaceans and insects (Robainas et al, 2003), microsatellites containing dinucleotide repetitions seem to be the most frequent among penaeid shrimp, followed by microsatellites containing trinucleotides. Moreover, even though a few motifs of all the analyzed classes may appear at greater abundance, there is a pronounced variability within and between species, indicating the high differentiation dynamism of these repetitions within this animal group.…”

Section: Introductionsupporting

confidence: 84%

“…However, the motifs TA (24%) in L. vannamei and TC and CA that appeared in equal proportion (6%) in P. monodon were the most abundant, differing from those observed when the set of all species is considered. The tetranucleotides were also abundant in the compound microsatellites of both species, corroborating the results that considered the entire penaeid set.Despite the observed exceptions, similar to those reported for other crustaceans and insects (Robainas et al, 2003), microsatellites containing dinucleotide repetitions seem to be the most frequent among penaeid shrimp, followed by microsatellites containing trinucleotides. Moreover, even though a few motifs of all the analyzed classes may appear at greater abundance, there is a pronounced variability within and between species, indicating the high differentiation dynamism of these repetitions within this animal group.…”

supporting

confidence: 84%

“…; (7) number and size of alleles per locus; and (8) results generated by the TRF program during the analysis, including any inconsistencies with the literature concerning the locus in question. Among the main observed inconsistencies in the sequences analyzed were the presence of microsatellites which were not flanked by one or both of the described primers, partially or totally absent repeats in the sequence described, microsatellites described with different motifs than those found by the TRF program and microsatellites with more than one GenBank ID or for which the ID numbers were different to those described in the paper in which it was cited.Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed: Farfantepenaeus notialis (Robainas et al, 2002;Robainas et al, 2003) (Espinosa et al, 2001;Maggioni et al, 2003; Borrel et al, 2004), Litopenaeus setiferus (Ball et al, 1998), Litopenaeus stylirostris (Vonau et al, 1999;Bierne et al, 2000), Litopenaeus vannamei (Wolfus et al, 1997;Cruz et al, 2002;Meehan et al, 2003;Pérez et al, 2005), Marsupenaeus japonicus (Moore et al, 1999), Penaeus esculentus (Meadows et al, 2003) and Penaeus monodon (Xu et al, 1999;Pongsomboon et al, 2000;Brooker et al, 2000;Xu et al, 2001;Wuthisuthimethavee et al, 2003;Pan et al, 2004). Cross-species amplification results are practically inexistent, being limited to a few loci described for L. vannamei that were also efficient in Rimapenaeus byrdi (= Trachypenaeus byrdi) and L. stylirostris (Pérez et al 2005).…”

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confidence: 99%

“…Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed: Farfantepenaeus notialis (Robainas et al, 2002;Robainas et al, 2003), Farfantepenaeus paulensis and Farfantepenaeus subtilis (Maggioni and Rogers 2002), Fenneropenaeus chinensis (Wang et al, 2005), Fenneropenaeus merguiensis (Wanna et al, 2004), Litopenaeus schmitti (Espinosa et al, 2001;Maggioni et al, 2003;Borrel et al, 2004), Litopenaeus setiferus (Ball et al, 1998), Litopenaeus stylirostris (Vonau et al, 1999;Bierne et al, 2000), Litopenaeus vannamei (Wolfus et al, 1997;Cruz et al, 2002;Meehan et al, 2003;Pérez et al, 2005), Marsupenaeus japonicus (Moore et al, 1999), Penaeus esculentus (Meadows et al, 2003) and Penaeus monodon (Xu et al, 1999;Pongsomboon et al, 2000;Brooker et al, 2000;Xu et al, 2001;Wuthisuthimethavee et al, 2003;Pan et al, 2004). Cross-species amplification results are practically inexistent, being limited to a few loci described for L. vannamei that were also efficient in Rimapenaeus byrdi (= Trachypenaeus byrdi) and L. stylirostris (Pérez et al 2005).…”

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confidence: 99%

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In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

et al. 2007

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We performed an in silico analysis of all microsatellites so far described for penaeid shrimp and for which the polymorphic behavior has previously been analyzed. The objective of the study was to evaluate the structural characteristics of these microsatellites and identifying patterns which allow the characterization of the nature of these sequences in the penaeid genome. All data were compiled in a free-access database specially constructed for this study. Three hundred non-mononucleotide polymorphic microsatellite loci described for 12 shrimp species belonging to the family Penaeidae were analyzed and simple and compound microsatellites with di-, tri-, tetra-, penta-and hexanucleotide motifs were found. Dinucleotides and trinucleotides were the most frequent motifs among both the simple and the compound microsatellites. Although a certain bias related to different microsatellite isolation methodology could not be discarded, it is possible that part of this microsatellite abundance reflects some degree of conservation of microsatellite motifs among the different species. There was a pronounced motif variability within and between species, indicating high differentiation dynamism of these repetitions in this animal group. This study not only sheds light on the structure of the microsatellites present in the penaeid shrimp genome but also resulted in the free-access Penaeid Shrimp Microsatellite Database (available at http://www.shrimp.ufscar.br) which may be very useful for optimizing the use of these microsatellites.Key words: Crustacea, microsatellite structure, Penaeidae, SSR.Received: September 19, 2006; Accepted: May 7, 2007. Over the last few decades, microsatellite sequences have been widely used in many animal groups, including shrimp, and principally in economically important species (Wolfus et al., 1997;Bierne et al., 2000;Xu et al., 2001). Due to their high level of allelic variation and codominant nature, microsatellite loci have been extremely useful for the determination of genetic diversity, stock discrimination, identification of lineages and individuals, the establishment of pedigrees, the development of breeding programs, linkage map studies and the identification of loci related to commercially important characteristics (Moore et al., 1999;Ozaki et al., 2000).In the past half decade, different research groups have been striving to characterize microsatellite markers in the genome of a number of penaeid shrimp species (Cruz et al., 2002;Meehan et al., 2003;Pérez et al., 2005). However, the validation of these sequences has generally not been easy. The penaeid genome seems to contain very long microsatellite repetitions, hindering the cloning and sequencing of microsatellites containing both flanking regions. A few comparisons demonstrate that the microsatellites found in penaeids (Tassanakajon et al., 1998;Cruz et al., 2002) are approximately twice the size of the sequences found in other animal groups (Estoup et al., 1993;Brooker et al., 1994), being four or five times larger in so...

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Section: Introductionsupporting

confidence: 84%

supporting

confidence: 84%

mentioning

confidence: 99%

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confidence: 99%

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In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

et al. 2007

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“…In the present study, all five studied microsatellite loci revealed the varied degree of polymorphism, significant differences in the genetic heterogeneity and allele frequencies. Also, Robainas, Monnerot, Solignac, Dennebouy, and Espinosa (2002) by evaluation the genetic variability from the pink shrimp Farfantenaeus notialis (Crustacea, Decapoda) in Cuba reported seven pairs of their primers showed reliable amplification products and five of them was polymorphic. The maximum of heterozygosity was found in white shrimp samples from Lifeh-Boosif populations that indicated, the studied populations have rich genetic diversity based on allelic variation.…”

Section: Discussionmentioning

confidence: 99%

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Shokoohmand¹,

Zolgharnein²,

Mashjoor³

et al. 2018

Turk. J. Fish. Aquat. Sci.

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We investigated the genetic structure of Metapenaeus affinis population from the northern coasts (Khuzestan Province: Bahrakan and Lifeh-Boosiaf region) of the Persian Gulf, using five microsatellite markers. The samples of pleopods tissue of shrimp were taken, DNA extracted and PCR was performed on microsatellite primers. The results revealed that all five microsatellite loci were polymorphic, the number of alleles (Na) ranged from 5 to 12 per locus, and the observed and effective number was 7 and 3.67, respectively, also the observed and expected heterozygosis was ranged from 0.1 to 0.77 and 0.1 and 0.83, respectively, which indicated that the two populations of M. affinis possessed a rich genetic diversity. The deviation from Hardy-Weinberg equilibrium (P<0.05) was observed that due to the heterozygote deficiency in populations. Based on the analysis of molecular variance (AMOVA), the genetic variation among stocks (17%) was much lower than that within stocks (83%), and Fst, Rst, and Nm were 0.107, 0.372 and 2.092, respectively. The highest genetic distance was 0.571 and the lowest was 0.561. Genetic distance and cluster analysis using UPGMA divided the two stocks into two groups. The present study showed that two different populations of M. affinis had a certain genetic diversity.

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Isolation and Mapping of Telomeric Pentanucleotide (TAACC) n Repeats of the Pacific Whiteleg Shrimp, Penaeus vannamei, Using Fluorescence In Situ Hybridization

et al. 2006

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To develop genetic and physical maps for shrimp, accurate information on the actual number of chromosomes and a large number of genetic markers is needed. Previous reports have shown two different chromosome numbers for the Pacific whiteleg shrimp, Penaeus vannamei, the most important penaeid shrimp species cultured in the Western hemisphere. Preliminary results obtained by direct sequencing of clones from a Sau3A-digested genomic library of P. vannamei ovary identified a large number of (TAACC/GGTTA)-containing SSRs. The objectives of this study were to (1) examine the frequency of (TAACC)n repeats in 662 P. vannamei genomic clones that were directly sequenced, and perform homology searches of these clones, (2) confirm the number of chromosomes in testis of P. vannamei, and (3) localize the TAACC repeats in P. vannamei chromosome spreads using fluorescence in situ hybridization (FISH). Results for objective 1 showed that 395 out of the 662 clones sequenced contained single or multiple SSRs with three or more repeat motifs, 199 of which contained variable tandem repeats of the pentanucleotide (TAACC/GGTTA)n, with 3 to 14 copies per sequence. The frequency of (TAACC)n repeats in P. vannamei is 4.68 kb for SSRs with five or more repeat motifs. Sequence comparisons using the BLASTN nonredundant and expressed sequence tag (EST) databases indicated that most of the TAACC-containing clones were similar to either the core pentanucleotide repeat in PVPENTREP locus (GenBank accession no. X82619) or portions of 28S rRNA. Transposable elements (transposase for Tn1000 and reverse transcriptase family members), hypothetical or unnamed protein products, and genes of known function such as 18S and 28S rRNAs, heat shock protein 70, and thrombospondin were identified in non-TAACC-containing clones. For objective 2, the meiotic chromosome number of P. vannamei was confirmed as N = 44. For objective 3, four FISH probes (P1 to P4) containing different numbers of TAACC repeats produced positive signals on telomeres of P. vannamei chromosomes. A few chromosomes had positive signals interstitially. Probe signal strength and chromosome coverage differed in the general order of P1>P2>P3>P4, which correlated with the length of TAACC repeats within the probes: 83, 66, 35, and 30 bp, respectively, suggesting that the TAACC repeats, and not the flanking sequences, produced the TAACC signals at chromosome ends and TAACC is likely the telomere sequence for P. vannamei.

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Microsatellite loci from the pink shrimp Farfantenaeus notialis (Crustacea, Decapoda)

Cited by 7 publications

References 7 publications

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

In silico analysis of polymorphic microsatellites in penaeid shrimp and construction of a free-access database

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Isolation and Mapping of Telomeric Pentanucleotide (TAACC) n Repeats of the Pacific Whiteleg Shrimp, Penaeus vannamei, Using Fluorescence In Situ Hybridization

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