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First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species

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Abstract

Peanut is an allotetraploid (2n = 2x = 40, AABB) of recent origin. Arachis duranensis and A. ipaënsis, the most probable diploid ancestors of the cultigen, and several other wild diploid species with different genomes (A, B, D, F and K) are used in peanut breeding programs. However, the genomic relationships and the evolutionary pathways of genome differentiation of these species are poorly understood. We performed a sequence-based phylogenetic analysis of the L1 reverse transcriptase and estimated its representation and chromosome distribution in species of five genomes and three karyotype groups with the aim of contributing to the knowledge of the genomic structure and evolution of peanut and wild diploid relatives. All the isolated rt fragments were found to belong to plant L1 lineage and were named ALI. The best supported phylogenetic groups were not concordant with the genomes or karyotype groups. The copy number of ALI sequences was higher than the expected one for plants and directly related to genome size. FISH experiments revealed that ALI is mainly located on the euchromatin of interstitial and distal regions of most chromosome arms. Divergence of ALI sequences would have occurred before the differentiation of the genomes and karyotype groups of Arachis. The representation and chromosome distribution of ALI in peanut was almost additive of those of the parental species suggesting that the spontaneous hybridization of the two parental species of peanut followed by chromosome doubling would not have induced a significant burst of ALI transposition.

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Abbreviations

LINEs:

Long interspersed nuclear elements

rt :

Reverse transcriptase

GSS:

Genomic survey sequences

ESTs:

Expressed sequence tags

FISH:

Fluorescent in situ hybridization

LTR:

Long terminal repeats

SINEs:

Short interspersed nuclear elements

NJ:

Neighbor joining

GISH:

Genome in situ hybridization

ORFs:

Open reading frames

PCR:

Polymerase chain reaction

dNTPs:

Deoxynucleotide triphosphates

CSPD:

Disodium 3-(4-methoxyspiro {1,2-dioxetane-3,2′-(5′-chloro)tricyclo [3.3.1.13,7]decan}-4-yl)phenyl phosphate

DAPI:

4,6-Diamidino-2-phenylindole

TE:

Transposable element

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Acknowledgments

This work is part of S. Samoluk Doctoral Thesis that will be presented in the Facultad de Ciencias Agrarias, Universidad Nacional de Rosario (Santa Fe, Argentina). It was supported by the Agencia Nacional de Promoción Científica y Tecnológica (ANPCyT), Argentina, Project PICT 2007-1356 and PICT 2012-1875, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina, Project PIP No 11220090100613 and Universidad Nacional del Nordeste, PI No 189. S. Samoluk, M. Podio and L. Chalup received fellowships from CONICET. G. Robledo, S. Pessino, J.P.A. Ortiz and J. G. Seijo are research staff members of CONICET. We would like to thank INTA Manfredi Station, Córdoba, Argentina and the Texas Agriculture Experimental Station, Stephenville, Texas, for providing seeds of some accessions.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Instituto de Botánica del Nordeste (Facultad de Ciencias Agrarias, UNNE-CONICET), Casilla de Correo 209, 3400, Corrientes, Argentina

    Sergio Sebastián Samoluk, Germán Robledo, Laura Chalup & José Guillermo Seijo

  2. Facultad de Ciencias Exactas y Naturales y Agrimensura Universidad Nacional del Nordeste, Av. Libertad 5460, 3400, Corrientes, Argentina

    Germán Robledo & José Guillermo Seijo

  3. Laboratorio de Biología Molecular, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Campo Experimental J. Villarino CC 14, S2125ZAA, Zavalla, Santa Fe, Argentina

    Maricel Podio, Juan Pablo A. Ortiz & Silvina Claudia Pessino

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  1. Sergio Sebastián Samoluk
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  2. Germán Robledo
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  3. Maricel Podio
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  4. Laura Chalup
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  6. Silvina Claudia Pessino
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  7. José Guillermo Seijo
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Correspondence to Sergio Sebastián Samoluk.

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10709_2015_9820_MOESM1_ESM.pdf

Alignments of deduced amino acid rt sequences used for construction of NJ trees of ALI elements and LINEs from other species. Arabidopsis thaliana Ta11-1 (L47193), Beta vulgaris BvL2 (FM993987), Zea mays Cin4 (Y00086), Hordeum vulgare BLIN (AJ270056), Cannabis sativa LINE-CS (AB013908), Rattus norvegicus L1 rat (U83119), Homo sapiens L1 hs (U93574), Drosophila melanogaster I (M14954), Drosophila melanogaster Jockey (M22874), Gallus gallus CR1 (U88211). The symbols “-, ? and *” indicates gaps, incomplete codons and stop codons, respectively. (PDF 140 kb)

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Samoluk, S.S., Robledo, G., Podio, M. et al. First insight into divergence, representation and chromosome distribution of reverse transcriptase fragments from L1 retrotransposons in peanut and wild relative species. Genetica 143, 113–125 (2015). https://doi.org/10.1007/s10709-015-9820-y

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