Sample Sequence Analysis Uncovers Recurrent Horizontal Transfers of Transposable Elements among Grasses.

Minkyu Park,Jeffrey L Bennetzen,Pascal-Antoine Christin

doi:10.1093/molbev/msab133

Minkyu Park, Jeffrey L Bennetzen + Show 1 more

Open Access

https://doi.org/10.1093/molbev/msab133

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Abstract

Limited genome resources are a bottleneck in the study of horizontal transfer (HT) of DNA in plants. To solve this issue, we tested the usefulness of low-depth sequencing data generated from 19 previously uncharacterized panicoid grasses for HT investigation. We initially searched for horizontally transferred LTR-retrotransposons by comparing the 19 sample sequences to 115 angiosperm genome sequences. Frequent HTs of LTR-retrotransposons were identified solely between panicoids and rice (Oryza sativa). We consequently focused on additional Oryza species and conducted a nontargeted investigation of HT involving the panicoid genus Echinochloa, which showed the most HTs in the first set of analyses. The comparison of nine Echinochloa samples and ten Oryza species identified recurrent HTs of diverse transposable element (TE) types at different points in Oryza history, but no confirmed cases of HT for sequences other than TEs. One case of HT was observed from one Echinochloa species into one Oryza species with overlapping geographic distributions. Variation among species and data sets highlights difficulties in identifying all HT, but our investigations showed that sample sequence analyses can reveal the importance of HT for the diversification of the TE repertoire of plants.

Highlights

Evolution results from selection and drift controlling the fate of modifications of the genetic material of organisms
We show that low-depth sample sequence analyses can solve the genome sequence shortage by generating data that can be used to detect horizontal transfer (HT) for large numbers of species
Despite the large number of species, putative HTs were initially detected only to O. sativa. These results suggest that HT happens frequently only between some groups of plants

Summary

Introduction

Evolution results from selection and drift controlling the fate of modifications of the genetic material of organisms. Transposable elements (TEs) are the major components of many plant genomes (Bennetzen 2000; Schnable et al 2009; Kim et al 2014), only three studies have focused on their HT among plants (Diao et al 2006; Roulin et al 2008; El Baidouri et al 2014), and have suggested that HT of LTR-retrotransposons in particular is widespread and Lisch 2000), and horizontal transfer (HT) of DNA (Schaack across diverse plant lineages (El Baidouri et al 2014). As more genome sequences become available, we more studies in plants are required to understand the role of are able to gain new insights into these processes and their horizontally transferred TEs in plant genome evolution.

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