Site-Specific Insertion Polymorphism of the MITE Alex-1 in the Genus Coffea Suggests Interspecific Gene Flow

Christine Dubreuil-Tranchant,Romain Guyot,Perla Hamon,Norosoa Razafinarivo,Serge Hamon,Alexandre De Kochko,Valérie Poncet,Amira Guellim,Marion De La Mare,Caroline Duret

doi:10.4061/2011/358412

Abstract

Miniature Inverted-repeat Transposable Elements (MITEs) are small nonautonomous class-II transposable elements distributed throughout eukaryotic genomes. We identified a novel family of MITEs (named Alex) in the Coffea canephora genome often associated with expressed sequences. The Alex-1 element is inserted in an intron of a gene at the CcEIN4 locus. Its mobility was demonstrated by sequencing the insertion site in C. canephora accessions and Coffea species. Analysis of the insertion polymorphism of Alex-1 at this locus in Coffea species and in C. canephora showed that there was no relationship between the geographical distribution of the species, their phylogenetic relationships, and insertion polymorphism. The intraspecific distribution of C. canephora revealed an original situation within the E diversity group. These results suggest possibly greater gene flow between species than previously thought. This MITE family will enable the study of the C. canephora genome evolution, phylogenetic relationships, and possible gene flows within the Coffea genus.

Highlights

A new type of molecular marker based on the insertion polymorphism of transposable elements (TEs) was shown to be effective for plant diversity studies [1,2,3,4]
We identified a novel family of Miniature Inverted-repeat Transposable Elements (MITEs) in the Coffea canephora genome often associated with expressed sequences
We report the results of a study on the insertion polymorphism of the MITE Alex1 at the g3 locus using PCR approaches on a representative set of Coffea species and a representative set of C. canephora diversity groups [18,19,20,21]

Summary

Introduction

A new type of molecular marker based on the insertion polymorphism of transposable elements (TEs) was shown to be effective for plant diversity studies [1,2,3,4] Because of their repeated nature and, in some cases, their great number [5, 6], these mobile genetic elements may be inserted at different loci in the genome where they lead to mutations or chromosomal rearrangements. Their activity is responsible for considerable natural polymorphism that can be used to study within and between species diversity and to identify possible population genetic structure and phylogenetic relationships [7, 8]. Their even distribution throughout plant genomes makes them an ideal tool for the study of genome evolution and genetic relationships [10,11,12]

Methods

Discussion

Conclusion