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Evidence of multiple retrotransposons in two litopenaeid species.
Anim Genet. 2008 Aug; 39(4):363-73.AG

Abstract

Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon.

Authors+Show Affiliations

Department of Biological Sciences, California State University, San Marcos, CA 920296, USA.No affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural

Language

eng

PubMed ID

18557973

Citation

Hizer, S E., et al. "Evidence of Multiple Retrotransposons in Two Litopenaeid Species." Animal Genetics, vol. 39, no. 4, 2008, pp. 363-73.
Hizer SE, Tamulis WG, Robertson LM, et al. Evidence of multiple retrotransposons in two litopenaeid species. Anim Genet. 2008;39(4):363-73.
Hizer, S. E., Tamulis, W. G., Robertson, L. M., & Garcia, D. K. (2008). Evidence of multiple retrotransposons in two litopenaeid species. Animal Genetics, 39(4), 363-73. https://doi.org/10.1111/j.1365-2052.2008.01739.x
Hizer SE, et al. Evidence of Multiple Retrotransposons in Two Litopenaeid Species. Anim Genet. 2008;39(4):363-73. PubMed PMID: 18557973.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Evidence of multiple retrotransposons in two litopenaeid species. AU - Hizer,S E, AU - Tamulis,W G, AU - Robertson,L M, AU - Garcia,D K, Y1 - 2008/06/28/ PY - 2008/6/19/pubmed PY - 2008/9/5/medline PY - 2008/6/19/entrez SP - 363 EP - 73 JF - Animal genetics JO - Anim. Genet. VL - 39 IS - 4 N2 - Retrotransposons encompass a specific class of mobile genetic elements that are widespread across eukaryotic genomes. The impact of the varied types of retrotransposons on these genomes is just beginning to be deciphered. In a step towards understanding their role in litopenaeid shrimp, we have herein identified nine non-LTR retrotransposons, among which several appear to exist outside the standard defined clades. Two Litopenaeus stylirostris elements were discovered through degenerate PCR amplification using previously defined non-LTR degenerate primers, and through primers designed from a RAPD-derived sequence. A third genomic L. stylirostris element was identified using specific priming from an amplification protocol. These three PCR-derived sequences showed conserved domains of the non-LTR reverse transcriptase gene. In silico searching of genome databases and subsequent contig construction yielded six non-LTR retrotransposons (both genomic and expressed) in the Litopenaeus vannamei genome that also exhibited the highly conserved domains found in our PCR-derived sequences. Phylogenetic placement among representatives from all non-LTR clades showed a possibly novel monophyletic group that included five of our nine sequences. This group, which included elements from both L. stylirostris and L. vannamei, appeared most closely related to the highly active RTE clade. Our remaining four sequences placed in the CR1 and I clades of retrotransposons, with one showing strong similarity to ancient Penelope elements. This research describes three newly discovered retrotransposons in the L. stylirostris genome. Phylogenetic analysis clusters these in a monophyletic grouping with retrotransposons previously described from two closely related species, L. vannamei and Penaeus monodon. SN - 1365-2052 UR - https://www.unboundmedicine.com/medline/citation/18557973/Evidence_of_multiple_retrotransposons_in_two_litopenaeid_species_ L2 - https://doi.org/10.1111/j.1365-2052.2008.01739.x DB - PRIME DP - Unbound Medicine ER -