title: Evolutionary dynamics of satellite DNA repeats from Phaseolus beans.
abstract: Common bean (Phaseolus vulgaris) subtelomeres are highly enriched for khipu, the main satellite DNA identified so far in this genome. Here, we comparatively investigate khipu genomic organization in Phaseolus species from different clades. Additionally, we identified and characterized another satellite repeat, named jumper, associated to khipu. A mixture of P. vulgaris khipu clones hybridized in situ confirmed the presence of khipu-like sequences on subterminal chromosome regions in all Phaseolus species, with differences in the number and intensity of signals between species and when species-specific clones were used. Khipu is present as multimers of ∼500 bp and sequence analyses of cloned fragments revealed close relationship among khipu repeats. The new repeat, named jumper, is a 170-bp satellite sequence present in all Phaseolus species and inserted into the nontranscribed spacer (NTS) of the 5S rDNA in the P. vulgaris genome. Nevertheless, jumper was found as a high-copy repeat at subtelomeres and/or pericentromeres in the Phaseolus microcarpus lineage only. Our data argue for khipu as an important subtelomeric satellite DNA in the genus and for a complex satellite repeat composition of P. microcarpus subtelomeres, which also contain jumper. Furthermore, the differential amplification of these repeats in subtelomeres or pericentromeres reinforces the presence of a dynamic satellite DNA library in Phaseolus.
authors.affiliation: Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil.
authors.forename: Tiago
authors.initials: T
authors.lastname: Ribeiro
authors.affiliation: Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil.
authors.forename: Karla G B
authors.initials: KG
authors.lastname: Dos Santos
authors.affiliation: Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.
authors.forename: Manon M S
authors.initials: MM
authors.lastname: Richard
authors.affiliation: Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.
authors.forename: Mireille
authors.initials: M
authors.lastname: Sévignac
authors.affiliation: Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.
authors.forename: Vincent
authors.initials: V
authors.lastname: Thareau
authors.affiliation: Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Bâtiment 630, 91405, Orsay, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Geffroy
authors.affiliation: Laboratório de Citogenética e Evolução Vegetal, Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil. andrea.pedrosaharand@pesquisador.cnpq.br.
authors.forename: Andrea
authors.identifier: http://orcid.org/0000-0001-5213-4770
authors.initials: A
authors.lastname: Pedrosa-Harand
mesh_terms: D001483:Base Sequence; D015139:Blotting, Southern; D032461:Chromosomes, Plant / Q000235:genetics; D002999:Clone Cells; D018744:DNA, Plant / Q000235:genetics*; D004276:DNA, Satellite / Q000235:genetics*; D019143:Evolution, Molecular; D017404:In Situ Hybridization, Fluorescence; D027805:Phaseolus / Q000235:genetics*; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D004276:DNA, Satellite
keywords: 5S rRNA; Differential amplification; Pericentromeres; Phaseolus; Satellite DNA; Subtelomeres