Genomics of Transposable Elements in the Triticeae

Francois Sabot, Alan Schulman

Research output: Book/ReportAnthology or special issueScientificpeer-review

Abstract

Triticeae genomes are structured as blocks of relatively gene-dense “islands” surrounded by long expanses of repetitive DNA. Most of the repetitive DNA is comprised of transposable elements; the greatest bulk of these are the Class I, or retrotransposons, which transpose via an RNA intermediate. The remainder is Class II DNA transposons, which move by a “cut-and-paste” mechanism. The LTR retrotransposons, which is the most abundant group of retrotransposons in the Triticeae genomes, compose 55–70 % of the genome. The precise numbers and insertion sites of members of the various families of transposons and retrotransposons in Triticeae genomes vary, which is a result of continual insertion and loss of individual copies at particular chromosomal locations. Among both the transposons and retrotransposons, non-autonomous forms are quite prevalent, among them the MITEs, SINEs, LARDs, and TRIMs. These require the proteins of autonomous forms for their mobility. Hence, the genome contains a mixture of autonomous elements, some of which contain stop codons or frameshifts inactivating translation, nonautonomous elements, and various deletion derivatives of both. The cell employs many regulatory mechanisms, including transcriptional silencing by DNA methylation and RNAi post-transcriptional silencing, to reduce transposable element propagation. Nevertheless, transposable elements have effects on Triticeae plants and their genomes over various time frames, ranging from read-through modulation of gene expression following stress activation to gene mutagenesis and growth in genome size. Genomic diversification driven by transposable element activity has made possible the exploitation of these elements as molecular markers for the Triticeae, complementing genic markers such as SNPs. With the emergence of genome sequences for members of the Triticeae and for related species such Brachypodium distachyon, a picture of the role of transposable elements in the evolution of genomes in the Triticeae is now emerging.
Original languageEnglish
PublisherSpringer-Verlag
ISBN (Print)ISBN 978-0-387-77488-6
Publication statusPublished - 2009
MoE publication typeC2 Edited book

Publication series

NamePlant Genetics and Genomics: Crops and Models
Volume7

Cite this

Sabot, F., & Schulman, A. (2009). Genomics of Transposable Elements in the Triticeae. (Plant Genetics and Genomics: Crops and Models; Vol. 7). Springer-Verlag.
Sabot, Francois ; Schulman, Alan. / Genomics of Transposable Elements in the Triticeae. Springer-Verlag, 2009. (Plant Genetics and Genomics: Crops and Models).
@book{5f042603b4bd46f99d0f10ec3fa888b0,
title = "Genomics of Transposable Elements in the Triticeae",
abstract = "Triticeae genomes are structured as blocks of relatively gene-dense “islands” surrounded by long expanses of repetitive DNA. Most of the repetitive DNA is comprised of transposable elements; the greatest bulk of these are the Class I, or retrotransposons, which transpose via an RNA intermediate. The remainder is Class II DNA transposons, which move by a “cut-and-paste” mechanism. The LTR retrotransposons, which is the most abundant group of retrotransposons in the Triticeae genomes, compose 55–70 {\%} of the genome. The precise numbers and insertion sites of members of the various families of transposons and retrotransposons in Triticeae genomes vary, which is a result of continual insertion and loss of individual copies at particular chromosomal locations. Among both the transposons and retrotransposons, non-autonomous forms are quite prevalent, among them the MITEs, SINEs, LARDs, and TRIMs. These require the proteins of autonomous forms for their mobility. Hence, the genome contains a mixture of autonomous elements, some of which contain stop codons or frameshifts inactivating translation, nonautonomous elements, and various deletion derivatives of both. The cell employs many regulatory mechanisms, including transcriptional silencing by DNA methylation and RNAi post-transcriptional silencing, to reduce transposable element propagation. Nevertheless, transposable elements have effects on Triticeae plants and their genomes over various time frames, ranging from read-through modulation of gene expression following stress activation to gene mutagenesis and growth in genome size. Genomic diversification driven by transposable element activity has made possible the exploitation of these elements as molecular markers for the Triticeae, complementing genic markers such as SNPs. With the emergence of genome sequences for members of the Triticeae and for related species such Brachypodium distachyon, a picture of the role of transposable elements in the evolution of genomes in the Triticeae is now emerging.",
author = "Francois Sabot and Alan Schulman",
year = "2009",
language = "English",
isbn = "ISBN 978-0-387-77488-6",
series = "Plant Genetics and Genomics: Crops and Models",
publisher = "Springer-Verlag",
address = "Germany",

}

Sabot, F & Schulman, A 2009, Genomics of Transposable Elements in the Triticeae. Plant Genetics and Genomics: Crops and Models, vol. 7, Springer-Verlag.

Genomics of Transposable Elements in the Triticeae. / Sabot, Francois; Schulman, Alan.

Springer-Verlag, 2009. (Plant Genetics and Genomics: Crops and Models; Vol. 7).

Research output: Book/ReportAnthology or special issueScientificpeer-review

TY - BOOK

T1 - Genomics of Transposable Elements in the Triticeae

AU - Sabot, Francois

AU - Schulman, Alan

PY - 2009

Y1 - 2009

N2 - Triticeae genomes are structured as blocks of relatively gene-dense “islands” surrounded by long expanses of repetitive DNA. Most of the repetitive DNA is comprised of transposable elements; the greatest bulk of these are the Class I, or retrotransposons, which transpose via an RNA intermediate. The remainder is Class II DNA transposons, which move by a “cut-and-paste” mechanism. The LTR retrotransposons, which is the most abundant group of retrotransposons in the Triticeae genomes, compose 55–70 % of the genome. The precise numbers and insertion sites of members of the various families of transposons and retrotransposons in Triticeae genomes vary, which is a result of continual insertion and loss of individual copies at particular chromosomal locations. Among both the transposons and retrotransposons, non-autonomous forms are quite prevalent, among them the MITEs, SINEs, LARDs, and TRIMs. These require the proteins of autonomous forms for their mobility. Hence, the genome contains a mixture of autonomous elements, some of which contain stop codons or frameshifts inactivating translation, nonautonomous elements, and various deletion derivatives of both. The cell employs many regulatory mechanisms, including transcriptional silencing by DNA methylation and RNAi post-transcriptional silencing, to reduce transposable element propagation. Nevertheless, transposable elements have effects on Triticeae plants and their genomes over various time frames, ranging from read-through modulation of gene expression following stress activation to gene mutagenesis and growth in genome size. Genomic diversification driven by transposable element activity has made possible the exploitation of these elements as molecular markers for the Triticeae, complementing genic markers such as SNPs. With the emergence of genome sequences for members of the Triticeae and for related species such Brachypodium distachyon, a picture of the role of transposable elements in the evolution of genomes in the Triticeae is now emerging.

AB - Triticeae genomes are structured as blocks of relatively gene-dense “islands” surrounded by long expanses of repetitive DNA. Most of the repetitive DNA is comprised of transposable elements; the greatest bulk of these are the Class I, or retrotransposons, which transpose via an RNA intermediate. The remainder is Class II DNA transposons, which move by a “cut-and-paste” mechanism. The LTR retrotransposons, which is the most abundant group of retrotransposons in the Triticeae genomes, compose 55–70 % of the genome. The precise numbers and insertion sites of members of the various families of transposons and retrotransposons in Triticeae genomes vary, which is a result of continual insertion and loss of individual copies at particular chromosomal locations. Among both the transposons and retrotransposons, non-autonomous forms are quite prevalent, among them the MITEs, SINEs, LARDs, and TRIMs. These require the proteins of autonomous forms for their mobility. Hence, the genome contains a mixture of autonomous elements, some of which contain stop codons or frameshifts inactivating translation, nonautonomous elements, and various deletion derivatives of both. The cell employs many regulatory mechanisms, including transcriptional silencing by DNA methylation and RNAi post-transcriptional silencing, to reduce transposable element propagation. Nevertheless, transposable elements have effects on Triticeae plants and their genomes over various time frames, ranging from read-through modulation of gene expression following stress activation to gene mutagenesis and growth in genome size. Genomic diversification driven by transposable element activity has made possible the exploitation of these elements as molecular markers for the Triticeae, complementing genic markers such as SNPs. With the emergence of genome sequences for members of the Triticeae and for related species such Brachypodium distachyon, a picture of the role of transposable elements in the evolution of genomes in the Triticeae is now emerging.

M3 - Anthology or special issue

SN - ISBN 978-0-387-77488-6

T3 - Plant Genetics and Genomics: Crops and Models

BT - Genomics of Transposable Elements in the Triticeae

PB - Springer-Verlag

ER -

Sabot F, Schulman A. Genomics of Transposable Elements in the Triticeae. Springer-Verlag, 2009. (Plant Genetics and Genomics: Crops and Models).