The Subtelomeric khipu Satellite Repeat from Phaseolus vulgaris: Lessons Learned from the Genome Analysis of the Andean Genotype G19833.

Manon M S Richard,Vincent Thareau,Sophie Blanchet,Andrea Pedrosa-Harand,Valérie Geffroy,Scott A Jackson,Nicolas W G Chen,Stéphanie Pflieger,Carolina Chavarro,Aiko Iwata

doi:10.3389/fpls.2013.00109

Abstract

Subtelomeric regions in eukaryotic organisms are known for harboring species-specific tandemly repeated satellite sequences. However, studies on the molecular organization and evolution of subtelomeric repeats are scarce, especially in plants. Khipu is a satellite DNA of 528-bp repeat unit, specific of the Phaseolus genus, with a subtelomeric distribution in common bean, P. vulgaris. To investigate the genomic organization and the evolution of khipu, we performed genome-wide analysis on the complete genome sequence of the common bean genotype G19833. We identified 2,460 khipu units located at most distal ends of the sequenced regions. Khipu units are arranged in discrete blocks of 2–55 copies and are heterogeneously distributed among the different chromosome ends of G19833 (from 0 to 555 khipus units per chromosome arm). Phylogenetically related khipu units are spread between numerous chromosome ends, suggesting frequent exchanges between non-homologous subtelomeres. However, most subclades contain numerous khipu units from only one or few chromosome ends indicating that local duplication is also driving khipu expansion. Unexpectedly, we also identified 81 khipu units located at centromeres. All the centromeric khipu units belong to a single divergent clade also comprised of a few units from several subtelomeres, suggesting that a few sequence exchanges between centromeres and subtelomeres took place in the common bean genome. The divergence and low copy number of these centromeric units from the subtelomeric units could explain why they were not detected by FISH (Fluorescence in situ Hybridization) although it can not be excluded that these centromeric units may have resulted from errors in the pseudomolecule assembly. Altogether our data highlight extensive sequence exchanges in subtelomeres between non-homologous chromosomes in common bean and confirm that subtelomeres represent one of the most dynamic and rapidly evolving regions in eukaryotic genomes.

Highlights

Common bean (Phaseolus vulgaris) is a major source of protein for human consumption in many parts of the world (FAO 1980), especially in developing countries such as tropical areas of Latin America and Eastern Africa where common bean is one of the major staple crops (Pastor-Corrales and Tu, 1989; Broughton et al, 2003)
DATA SOURCES We used the “Phaseolus vulgaris v1.0” genome sequence of the Andean common bean genotype G198332 and sequenced BAC clones from G19833 reported in Innes et al (2008) that correspond to ∼1 Mb of the Co-2 cluster, located at the end of the long arm of chromosome 11, and from Chen et al (2010), corresponding to 239 kb located at one end of chromosome 5, referred to as PvA05A
Each khipu sequence extracted from the genome of G19833 was named Pvxxyk#####, with Pv referring to Phaseolus vulgaris, “xx” referring to pseudomolecule (01–11), “y” corresponding to the location on the chromosome (S for short arm, C for centromere, and L for long arm), “k” referring to “khipu,” and a 5-digit number referring to the khipu order on the pseudomolecules from the start (5 ) to the end (3 ). khipu elements on each pseudomolecule were sequentially numbered in increments of 10

Summary

INTRODUCTION

Common bean (Phaseolus vulgaris) is a major source of protein for human consumption in many parts of the world (FAO 1980), especially in developing countries such as tropical areas of Latin America and Eastern Africa where common bean is one of the major staple crops (Pastor-Corrales and Tu, 1989; Broughton et al, 2003). Satellite DNA can be defined as highly reiterated non-coding DNA sequences, organized as long arrays of head-to-tail linked repeats located in the constitutive heterochromatin (Plohl et al, 2008). Despite their ubiquity in eukaryotic genomes, the function of such repeats is poorly understood. A 528-bp subtelomeric satellite repeat, referred to as khipu, has been identified (David et al, 2009). We conducted genome-wide analysis to investigate the physical organization and the evolution of khipu sequence based on the complete genome sequence of common bean genotype G19833

MATERIALS AND METHODS

RESULTS AND DISCUSSION

CONCLUSION