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LTR retroelements in the genome of Daphnia pulex.
BMC Genomics. 2010 Jul 09; 11:425.BG

Abstract

BACKGROUND

Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex.

RESULTS

We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed.

CONCLUSIONS

Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century.

Authors+Show Affiliations

School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

20618961

Citation

Rho, Mina, et al. "LTR Retroelements in the Genome of Daphnia Pulex." BMC Genomics, vol. 11, 2010, p. 425.
Rho M, Schaack S, Gao X, et al. LTR retroelements in the genome of Daphnia pulex. BMC Genomics. 2010;11:425.
Rho, M., Schaack, S., Gao, X., Kim, S., Lynch, M., & Tang, H. (2010). LTR retroelements in the genome of Daphnia pulex. BMC Genomics, 11, 425. https://doi.org/10.1186/1471-2164-11-425
Rho M, et al. LTR Retroelements in the Genome of Daphnia Pulex. BMC Genomics. 2010 Jul 9;11:425. PubMed PMID: 20618961.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - LTR retroelements in the genome of Daphnia pulex. AU - Rho,Mina, AU - Schaack,Sarah, AU - Gao,Xiang, AU - Kim,Sun, AU - Lynch,Michael, AU - Tang,Haixu, Y1 - 2010/07/09/ PY - 2009/06/29/received PY - 2010/07/09/accepted PY - 2010/7/13/entrez PY - 2010/7/14/pubmed PY - 2010/9/4/medline SP - 425 EP - 425 JF - BMC genomics JO - BMC Genomics VL - 11 N2 - BACKGROUND: Long terminal repeat (LTR) retroelements represent a successful group of transposable elements (TEs) that have played an important role in shaping the structure of many eukaryotic genomes. Here, we present a genome-wide analysis of LTR retroelements in Daphnia pulex, a cyclical parthenogen and the first crustacean for which the whole genomic sequence is available. In addition, we analyze transcriptional data and perform transposon display assays of lab-reared lineages and natural isolates to identify potential influences on TE mobility and differences in LTR retroelements loads among individuals reproducing with and without sex. RESULTS: We conducted a comprehensive de novo search for LTR retroelements and identified 333 intact LTR retroelements representing 142 families in the D. pulex genome. While nearly half of the identified LTR retroelements belong to the gypsy group, we also found copia (95), BEL/Pao (66) and DIRS (19) retroelements. Phylogenetic analysis of reverse transcriptase sequences showed that LTR retroelements in the D. pulex genome form many lineages distinct from known families, suggesting that the majority are novel. Our investigation of transcriptional activity of LTR retroelements using tiling array data obtained from three different experimental conditions found that 71 LTR retroelements are actively transcribed. Transposon display assays of mutation-accumulation lines showed evidence for putative somatic insertions for two DIRS retroelement families. Losses of presumably heterozygous insertions were observed in lineages in which selfing occurred, but never in asexuals, highlighting the potential impact of reproductive mode on TE abundance and distribution over time. The same two families were also assayed across natural isolates (both cyclical parthenogens and obligate asexuals) and there were more retroelements in populations capable of reproducing sexually for one of the two families assayed. CONCLUSIONS: Given the importance of LTR retroelements activity in the evolution of other genomes, this comprehensive survey provides insight into the potential impact of LTR retroelements on the genome of D. pulex, a cyclically parthenogenetic microcrustacean that has served as an ecological model for over a century. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/20618961/LTR_retroelements_in_the_genome_of_Daphnia_pulex_ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-11-425 DB - PRIME DP - Unbound Medicine ER -