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Retrotranspositions in orthologous regions of closely related grass species.
BMC Evol Biol. 2006 Aug 16; 6:62.BE

Abstract

BACKGROUND

Retrotransposons are commonly occurring eukaryotic transposable elements (TEs). Among these, long terminal repeat (LTR) retrotransposons are the most abundant TEs and can comprise 50-90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail.

RESULTS

Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons.

CONCLUSION

Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb) is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially providing an important role for retrotransposons in the evolution of gene function.

Authors+Show Affiliations

Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA. chunguan@waksman.rutgers.eduNo 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

16914031

Citation

Du, Chunguang, et al. "Retrotranspositions in Orthologous Regions of Closely Related Grass Species." BMC Evolutionary Biology, vol. 6, 2006, p. 62.
Du C, Swigonová Z, Messing J. Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol. 2006;6:62.
Du, C., Swigonová, Z., & Messing, J. (2006). Retrotranspositions in orthologous regions of closely related grass species. BMC Evolutionary Biology, 6, 62.
Du C, Swigonová Z, Messing J. Retrotranspositions in Orthologous Regions of Closely Related Grass Species. BMC Evol Biol. 2006 Aug 16;6:62. PubMed PMID: 16914031.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Retrotranspositions in orthologous regions of closely related grass species. AU - Du,Chunguang, AU - Swigonová,Zuzana, AU - Messing,Joachim, Y1 - 2006/08/16/ PY - 2006/03/08/received PY - 2006/08/16/accepted PY - 2006/8/18/pubmed PY - 2006/9/28/medline PY - 2006/8/18/entrez SP - 62 EP - 62 JF - BMC evolutionary biology JO - BMC Evol. Biol. VL - 6 N2 - BACKGROUND: Retrotransposons are commonly occurring eukaryotic transposable elements (TEs). Among these, long terminal repeat (LTR) retrotransposons are the most abundant TEs and can comprise 50-90% of the genome in higher plants. By comparing the orthologous chromosomal regions of closely related species, the effects of TEs on the evolution of plant genomes can be studied in detail. RESULTS: Here, we compared the composition and organization of TEs within five orthologous chromosomal regions among three grass species: maize, sorghum, and rice. We identified a total of 132 full or fragmented LTR retrotransposons in these regions. As a percentage of the total cumulative sequence in each species, LTR retrotransposons occupy 45.1% of the maize, 21.1% of the rice, and 3.7% of the sorghum regions. The most common elements in the maize retrotransposon-rich regions are the copia-like retrotransposons with 39% and the gypsy-like retrotransposons with 37%. Using the contiguous sequence of the orthologous regions, we detected 108 retrotransposons with intact target duplication sites and both LTR termini. Here, we show that 74% of these elements inserted into their host genome less than 1 million years ago and that many retroelements expanded in size by the insertion of other sequences. These inserts were predominantly other retroelements, however, several of them were also fragmented genes. Unforeseen was the finding of intact genes embedded within LTR retrotransposons. CONCLUSION: Although the abundance of retroelements between maize and rice is consistent with their different genome sizes of 2,364 and 389 Mb respectively, the content of retrotransposons in sorghum (790 Mb) is surprisingly low. In all three species, retrotransposition is a very recent activity relative to their speciation. While it was known that genes re-insert into non-orthologous positions of plant genomes, they appear to re-insert also within retrotransposons, potentially providing an important role for retrotransposons in the evolution of gene function. SN - 1471-2148 UR - https://www.unboundmedicine.com/medline/citation/16914031/Retrotranspositions_in_orthologous_regions_of_closely_related_grass_species_ L2 - https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-6-62 DB - PRIME DP - Unbound Medicine ER -