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Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.
PLoS Genet. 2009 Nov; 5(11):e1000732.PG

Abstract

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.

Authors+Show Affiliations

Department of Genetics, University of Georgia, Athens, Georgia, United States of America.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

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

Language

eng

PubMed ID

19936065

Citation

Baucom, Regina S., et al. "Exceptional Diversity, Non-random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome." PLoS Genetics, vol. 5, no. 11, 2009, pp. e1000732.
Baucom RS, Estill JC, Chaparro C, et al. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet. 2009;5(11):e1000732.
Baucom, R. S., Estill, J. C., Chaparro, C., Upshaw, N., Jogi, A., Deragon, J. M., Westerman, R. P., Sanmiguel, P. J., & Bennetzen, J. L. (2009). Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genetics, 5(11), e1000732. https://doi.org/10.1371/journal.pgen.1000732
Baucom RS, et al. Exceptional Diversity, Non-random Distribution, and Rapid Evolution of Retroelements in the B73 Maize Genome. PLoS Genet. 2009;5(11):e1000732. PubMed PMID: 19936065.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. AU - Baucom,Regina S, AU - Estill,James C, AU - Chaparro,Cristian, AU - Upshaw,Naadira, AU - Jogi,Ansuya, AU - Deragon,Jean-Marc, AU - Westerman,Richard P, AU - Sanmiguel,Phillip J, AU - Bennetzen,Jeffrey L, Y1 - 2009/11/20/ PY - 2009/08/25/received PY - 2009/10/19/accepted PY - 2009/11/26/entrez PY - 2009/11/26/pubmed PY - 2010/3/3/medline SP - e1000732 EP - e1000732 JF - PLoS genetics JO - PLoS Genet VL - 5 IS - 11 N2 - Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity. SN - 1553-7404 UR - https://www.unboundmedicine.com/medline/citation/19936065/Exceptional_diversity_non_random_distribution_and_rapid_evolution_of_retroelements_in_the_B73_maize_genome_ L2 - https://dx.plos.org/10.1371/journal.pgen.1000732 DB - PRIME DP - Unbound Medicine ER -