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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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An Erratum to this article was published on 19 December 2006

Abstract

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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Acknowledgments

We thank Dr. Brad Argue for technical assistance with preparation of chromosome spreads, Drs. Jurgenne Primavera and Leobert de la Pena of Southeast Asian Fisheries Development Center, Iloilo, Philippines for access to wild P. monodon DNA, Mr. Johnny Alcivar for assistance with homology searches, and Mr. Freddy Aveiga for comments on a first draft of the manuscript. This research was supported in part by grant 98-38808-1424 from the U.S. Department of Agriculture to the U.S. Marine Shrimp Farming Program. Partial support was received from NOAA National Sea Grant College Program Office, U.S. Department of Commerce (grant NA90-AA-D-SG480), and Department of Environmental and Population Health, Cummings School of Veterinary Medicine at Tufts University. FISH work was supported by grants from Sea Grant (B/T-9801 and ODRP-29) and New Jersey Commission on Science and Technology (02-2042-007-11) to X.G. Y.P.W. was partly supported by National Natural Science Foundation of China (Award No. 2001AA628150 and 39825121).

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Correspondence to Acacia Alcivar-Warren.

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An erratum to this article is available at http://dx.doi.org/10.1007/s10126-006-6802-1.

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Alcivar-Warren, A., Meehan-Meola, D., Wang, Y. et al. Isolation and Mapping of Telomeric Pentanucleotide (TAACC) n Repeats of the Pacific Whiteleg Shrimp, Penaeus vannamei, Using Fluorescence In Situ Hybridization. Mar Biotechnol 8, 467–480 (2006). https://doi.org/10.1007/s10126-005-6031-z

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