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. 2013;5(5):1010-20.
doi: 10.1093/gbe/evt064.

Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat

Natacha Senerchia  1 , Thomas Wicker, François Felber, Christian Parisod
Affiliations

Evolutionary dynamics of retrotransposons assessed by high-throughput sequencing in wild relatives of wheat

Natacha Senerchia et al. Genome Biol Evol. 2013.

Abstract

Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindrica and Ae. geniculata using 454 identified more than 70% of the sequences as known TEs, mainly long terminal repeat (LTR) retrotransposons. Comparing the abundance of reads as well as patterns of sequence diversity and divergence within and among genomes assessed the dynamics of 44 major LTR retrotransposon families of the 165 identified. In particular, molecular population genetics on individual TE copies distinguished recently active from quiescent families and highlighted different evolutionary trajectories of retrotransposons among related species. This work presents a suite of tools suitable for current sequencing data, allowing to address the genome-wide evolutionary dynamics of TEs at the family level and advancing our understanding of the evolution of nonmodel genomes.

Keywords: 454 pyrosequencing; Aegilops; molecular population genetics; repetitive fraction composition; transposable elements; whole-genome snapshot.

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Figures

F<sc>ig</sc>. 1.—
Fig. 1.—
Overview of the approach used here to identify and classify 454 reads into families of TEs, and then investigate their evolutionary dynamics through molecular population genetics.
F<sc>ig</sc>. 2.—
Fig. 2.—
Contribution of 44 major LTR retrotransposon families to 454 reads in Aegilops cylindrica (CY, dark gray) and Ae. geniculata (GE, light gray) with 95% confidence interval estimated by resampling. Families are grouped according to their superfamilies: CO, copia; GY, gypsy; X, unclassified retrotransposon. *,†mark TE families making at least 50% of the genome complement of Ae. cylindrica and Ae. geniculata, respectively. Proportions for BARE1, Fatima, and Sabrina are not at scale and are indicated by values.
F<sc>ig</sc>. 3.—
Fig. 3.—
Examples of phylogenetic relationships among copies of LTR retrotransposon families in Aegilops cylindrica (green) and Ae. geniculata (orange). Unrooted accelerated maximum likelihood trees distinguish four main topologies: (a) trees with only few species-specific clades of insertions as shown by the Lila family (referred as Tree I), (b) Tree II is composed of several species-specific clades of insertions, such as the family BARE1, (c) Tree III with only few species-specific clades but preponderant mixed-species clades of insertions, as shown by the Maximus family, and (d) families such as Hawi showing only mixed-species clades of insertions (Tree IV). Scale bar represents the branch lengths. In each panel, the distribution of distances among sequences from species-specific alignments (i.e., mismatch distribution) is shown using blue and red for significantly positive and negative slopes respectively.
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