PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

Bae, Young-An; Ahn, Jong-Sook; Kim, Seon Hee; Rhyu, Mun-Gan; Kong, Yoon; Cho, Seung Yull

doi:10.1186/1471-2164-9-482

Cited by 13 publications

(7 citation statements)

References 42 publications

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“…A number of families of retrotransposons have been characterized from trematode genomes including CsRn1, PwRn1, Gulliver , the LTR retrotransposons from C. sinensis (Bae et al, 2001), Paragonimus westermani (Bae et al, 2008) and S. japonicum (Laha et al, 2001), respectively. Moreover, numerous non-LTR retrotransposons have been characterized from schistosome genomes (Brindley et al, 2003; Drew et al, 1999; Laha et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: Potential target for DNA-based diagnosis

Phung

Loukas

Brindley

et al. 2014

Infection, Genetics and Evolution

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Infections by the fish-borne liver flukes Opisthorchis viverrini and Clonorchis sinensis can lead to bile duct cancer. These neglected tropical disease pathogens occur in East Asia, with O. viverrini primarily in Thailand and Laos and C. sinensis in Cambodia, Vietnam, and China. Genomic information about these pathogens holds the potential to improve disease treatment and control. Transcriptome analysis indicates that mobile genetic elements are active in O. viverrini, including a novel non-Long Terminal Repeat (LTR) retrotransposon. A consensus sequence of this element, termed OV-RTE-1, was assembled from expressed sequence tags and PCR amplified genomic DNA. OV-RTE-1 was 3,330 bp in length, encoded 1,101 amino acid residues and exhibited hallmark structures and sequences of non-LTR retrotransposons including a single open reading frame encoding apurinic-apyrimidinic endonuclease (EN) and reverse transcriptase (RT). Phylogenetic analyses confirmed that OV-RTE-1 was member of the RTE clade of non-LTR retrotransposons. OV-RTE-1 is the first non-LTR retrotransposon characterized from the trematode family Opisthorchiidae. Sequences of OV-RTE-1 were targeted to develop a diagnostic tool for detection of infection by O. viverrini. PCR specific primers for detection of O. viverrini DNA showed 100% specificity and sensitivity for detection of as little as five femtograms of O. viverrini DNA whereas the PCR based approach showed 62% sensitivity and 100% specificity with clinical stool samples. The OV-RTE-1 specific PCR could be developed as a molecular diagnostic for Opisthorchis infection targeting parasite eggs in stool samples, especially in regions of mixed infection of O. viverrini and/or C. sinensis and minute intestinal flukes.

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Section: Discussionmentioning

confidence: 99%

Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: Potential target for DNA-based diagnosis

Phung

Loukas

Brindley

et al. 2014

Infection, Genetics and Evolution

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“…These amino acid sequences were aligned with those of other LTR retrotransposons representing each of the distinct clades of the Ty3 / gypsy family (Malik and Eickbush, 1999; Bae et al . 2001, 2008; DeMarco et al . 2004) using the ClustalX program (Thompson et al .…”

Section: Methodsmentioning

confidence: 99%

“…Multiple scaffolds retrieved by a single query were compared with one another and then, a common genetic element was isolated from them by BL2Seq at NCBI, as described previously (Bae et al . 2008). Terminal repeats flanking a protein-encoding internal region were determined similarly by the program.…”

Section: Methodsmentioning

confidence: 99%

“…Amino acids of the RT domain that were tightly conserved in diverse retroelements (Xiong and Eickbush, 1990), were extracted by homology-based matching of these polypeptides against the CsRn1 Pol sequence. These amino acid sequences were aligned with those of other LTR retrotransposons representing each of the distinct clades of the Ty3/gypsy family (Malik and Eickbush, 1999;Bae et al 2001Bae et al , 2008DeMarco et al 2004) using the ClustalX program (Thompson et al 1997). LTR retrotransposons of parasitic platyhelminths including S. mansoni were also included in the structural comparison.…”

Section: Sequence Analysesmentioning

confidence: 99%

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Evolutionary characterization ofTy3/gypsy-like LTR retrotransposons in the parasitic cestodeEchinococcus granulosus

Bae

2016

Parasitology

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Cyclophyllidean cestodes including Echinococcus granulosus have a smaller genome and show characteristics such as loss of the gut, a segmented body plan, and accelerated growth rate in hosts compared with other tissue-invading helminths. In an effort to address the molecular mechanism relevant to genome shrinkage, the evolutionary status of long-terminal-repeat (LTR) retrotransposons, which are known as the most potent genomic modulators, was investigated in the E. granulosus draft genome. A majority of the E. granulosus LTR retrotransposons were classified into a novel characteristic clade, named Saci-2, of the Ty3/gypsy family, while the remaining elements belonged to the CsRn1 clade of identical family. Their nucleotide sequences were heavily corrupted by frequent base substitutions and segmental losses. The ceased mobile activity of the major retrotransposons and the following intrinsic DNA loss in their inactive progenies might have contributed to decrease in genome size. Apart from the degenerate copies, a gag gene originating from a CsRn1-like element exhibited substantial evidences suggesting its domestication including a preserved coding profile and transcriptional activity, the presence of syntenic orthologues in cestodes, and selective pressure acting on the gene. To my knowledge, the endogenized gag gene is reported for the first time in invertebrates, though its biological function remains elusive.

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“…Tetraploid forms, which might produce viable gametes, have been found in China [ 91 ]. Research on relationships and origins of the polyploid forms is likely to continue for some time [ 92 ].…”

Section: Taxonomy Of Paragonimus Speciesmentioning

confidence: 99%

Paragonimiasis

Blair

2014

Advances in Experimental Medicine and Biology

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PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy

Cited by 13 publications

References 42 publications

Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: Potential target for DNA-based diagnosis

Retrotransposon OV-RTE-1 from the carcinogenic liver fluke Opisthorchis viverrini: Potential target for DNA-based diagnosis

Evolutionary characterization ofTy3/gypsy-like LTR retrotransposons in the parasitic cestodeEchinococcus granulosus

Paragonimiasis

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