Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza

Andrea Zuccolo; Jetty S.S. Ammiraju; Hye Ran Kim; Abhijit Sanyal; Scott Jackson; Rod A. Wing

doi:10.1007/s12284-008-9002-y

Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza

Andrea Zuccolo, Jetty S.S. Ammiraju, Hye Ran Kim, Abhijit Sanyal, Scott Jackson, Rod A. Wing

Research output: Contribution to journal › Article › peer-review

6 Scopus citations

Abstract

Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The proliferation of Atlantys elements, in many cases, took place after respective speciation events occurred. Most of the retrotranspositional events occurred within the last three million years. Atlantys is an ancient and ubiquitous component of the genus Oryza and has made significant contributions to genome size variation across the genus. Its structure is unusual when compared to other Ty3-Gypsy elements and its proliferation in the different Oryza species has been rapid and differential.

Original language	English (US)
Pages (from-to)	85-99
Number of pages	15
Journal	Rice
Volume	1
Issue number	1
DOIs	https://doi.org/10.1007/s12284-008-9002-y
State	Published - Sep 2008

Keywords

Genome size
LTR retrotransposon
Officinalis complex
Oryza
Ty3-gypsy

ASJC Scopus subject areas

Agronomy and Crop Science
Soil Science
Plant Science

Access to Document

10.1007/s12284-008-9002-y

Cite this

@article{0570d693715f42aa82e328f45f2dbac2,

title = "Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza",

abstract = "Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The proliferation of Atlantys elements, in many cases, took place after respective speciation events occurred. Most of the retrotranspositional events occurred within the last three million years. Atlantys is an ancient and ubiquitous component of the genus Oryza and has made significant contributions to genome size variation across the genus. Its structure is unusual when compared to other Ty3-Gypsy elements and its proliferation in the different Oryza species has been rapid and differential.",

keywords = "Genome size, LTR retrotransposon, Officinalis complex, Oryza, Ty3-gypsy",

author = "Andrea Zuccolo and Ammiraju, {Jetty S.S.} and Kim, {Hye Ran} and Abhijit Sanyal and Scott Jackson and Wing, {Rod A.}",

note = "Funding Information: Acknowledgements This work was funded by the NSF Plant Genome Program award #DBI-0321678 and the Bud Antle Endowed Chair to RAW. We also thank the AGI technical staff that supported this project, especially members of the BAC/EST Resource, Sequencing, and Bioinformatics Centers.",

year = "2008",

month = sep,

doi = "10.1007/s12284-008-9002-y",

language = "English (US)",

volume = "1",

pages = "85--99",

journal = "Rice",

issn = "1939-8425",

publisher = "Springer",

number = "1",

}

TY - JOUR

T1 - Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza

AU - Zuccolo, Andrea

AU - Ammiraju, Jetty S.S.

AU - Kim, Hye Ran

AU - Sanyal, Abhijit

AU - Jackson, Scott

AU - Wing, Rod A.

N1 - Funding Information: Acknowledgements This work was funded by the NSF Plant Genome Program award #DBI-0321678 and the Bud Antle Endowed Chair to RAW. We also thank the AGI technical staff that supported this project, especially members of the BAC/EST Resource, Sequencing, and Bioinformatics Centers.

PY - 2008/9

Y1 - 2008/9

N2 - Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The proliferation of Atlantys elements, in many cases, took place after respective speciation events occurred. Most of the retrotranspositional events occurred within the last three million years. Atlantys is an ancient and ubiquitous component of the genus Oryza and has made significant contributions to genome size variation across the genus. Its structure is unusual when compared to other Ty3-Gypsy elements and its proliferation in the different Oryza species has been rapid and differential.

AB - Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The proliferation of Atlantys elements, in many cases, took place after respective speciation events occurred. Most of the retrotranspositional events occurred within the last three million years. Atlantys is an ancient and ubiquitous component of the genus Oryza and has made significant contributions to genome size variation across the genus. Its structure is unusual when compared to other Ty3-Gypsy elements and its proliferation in the different Oryza species has been rapid and differential.

KW - Genome size

KW - LTR retrotransposon

KW - Officinalis complex

KW - Oryza

KW - Ty3-gypsy

UR - http://www.scopus.com/inward/record.url?scp=84863012703&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84863012703&partnerID=8YFLogxK

U2 - 10.1007/s12284-008-9002-y

DO - 10.1007/s12284-008-9002-y

M3 - Article

AN - SCOPUS:84863012703

SN - 1939-8425

VL - 1

SP - 85

EP - 99

JO - Rice

JF - Rice

IS - 1

ER -

Rapid and differential proliferation of the Ty3-Gypsy LTR retrotransposon Atlantys in the genus Oryza

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this