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Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome.
Genome Res. 2009 Feb; 19(2):243-54.GR

Abstract

Although the proliferation of LTR retrotransposons can cause major genomic modification and reorganization, the evolutionary dynamics that affect their frequency in host genomes are poorly understood. We analyzed patterns of genetic variation among LTR retrotransposons from Oryza sativa to investigate the type of selective forces that potentially limit their amplification and subsequent population of a nuclear genome. We performed both intra- and interfamily analyses of patterns of molecular sequence variation across multiple LTR retrotransposon genes. This analysis involved more than 1000 LTR retrotransposon sequences from 14 separate families that varied in both their insertion dates and full-length copy numbers. We uncovered evidence of strong purifying selection across all gene regions, but also indications that rare episodes of positive selection and adaptation to the host genome occur. Furthermore, our results indicate that LTR retrotransposons exhibit different but predictable patterns of sequence variation depending on their date of transposition, suggesting that LTR retrotransposons, regardless of superfamily and family classifications, show similar "life-histories."

Authors+Show Affiliations

Department of Genetics, University of Georgia, Athens, Georgia 30602-7223, USA. gbaucom@uga.eduNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

19029538

Citation

Baucom, Regina S., et al. "Natural Selection On Gene Function Drives the Evolution of LTR Retrotransposon Families in the Rice Genome." Genome Research, vol. 19, no. 2, 2009, pp. 243-54.
Baucom RS, Estill JC, Leebens-Mack J, et al. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Res. 2009;19(2):243-54.
Baucom, R. S., Estill, J. C., Leebens-Mack, J., & Bennetzen, J. L. (2009). Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Genome Research, 19(2), 243-54. https://doi.org/10.1101/gr.083360.108
Baucom RS, et al. Natural Selection On Gene Function Drives the Evolution of LTR Retrotransposon Families in the Rice Genome. Genome Res. 2009;19(2):243-54. PubMed PMID: 19029538.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. AU - Baucom,Regina S, AU - Estill,James C, AU - Leebens-Mack,Jim, AU - Bennetzen,Jeffrey L, Y1 - 2008/11/24/ PY - 2008/11/26/pubmed PY - 2009/4/3/medline PY - 2008/11/26/entrez SP - 243 EP - 54 JF - Genome research JO - Genome Res. VL - 19 IS - 2 N2 - Although the proliferation of LTR retrotransposons can cause major genomic modification and reorganization, the evolutionary dynamics that affect their frequency in host genomes are poorly understood. We analyzed patterns of genetic variation among LTR retrotransposons from Oryza sativa to investigate the type of selective forces that potentially limit their amplification and subsequent population of a nuclear genome. We performed both intra- and interfamily analyses of patterns of molecular sequence variation across multiple LTR retrotransposon genes. This analysis involved more than 1000 LTR retrotransposon sequences from 14 separate families that varied in both their insertion dates and full-length copy numbers. We uncovered evidence of strong purifying selection across all gene regions, but also indications that rare episodes of positive selection and adaptation to the host genome occur. Furthermore, our results indicate that LTR retrotransposons exhibit different but predictable patterns of sequence variation depending on their date of transposition, suggesting that LTR retrotransposons, regardless of superfamily and family classifications, show similar "life-histories." SN - 1088-9051 UR - https://www.unboundmedicine.com/medline/citation/19029538/Natural_selection_on_gene_function_drives_the_evolution_of_LTR_retrotransposon_families_in_the_rice_genome_ L2 - http://genome.cshlp.org/cgi/pmidlookup?view=long&pmid=19029538 DB - PRIME DP - Unbound Medicine ER -