HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.) M. Buti, T. Giordani, M. Vukich, L. Gentzbittel, L. Pistelli, F. Cattonaro, M. Morgante, A. Cavallini, and L. Natali Abstract: In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotrans- poson of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 (Helianthus annuus copia- like retroelement 1). HACRE1 carries 5’ and 3’ long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5’ LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last *84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high se- quence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under dif- ferent light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions. Key words: copia, Helianthus annuus, retrotransposon, sunflower. Re ´sume ´: Dans ce travail, les auteurs de ´crivent pour la premie `re fois l’isolement et la caracte ´risation d’un re ´trotransposon complet, long de 6511 pb, chez le tournesol. En fonction de l’ordre des domaines prote ´iques et de la similarite ´ nucle ´oti- dique avec d’autres e ´le ´ments copia chez les dicotyle ´dones, ce re ´trotransposon a e ´te ´ assigne ´a ` la superfamille copia de re ´- trotransposons et nomme ´ HACRE1 (« Helianthus annuus copia-like retroelement 1 »). HACRE1 porte de longues re ´pe ´titions terminales (LTR) en 5’ et 3’, lesquelles bordent un segment interne de 4661 pb. Les LTR sont identiques en ce qui a trait a ` leur se ´quence a ` l’exception de deux de ´le ´tions, de 7 et 5 nucle ´otides, au sein du 5’ LTR. En raison de l’identite ´ des se ´quences LTR, les auteurs estiment que l’e ´le ´ment HACRE1 se serait inse ´re ´ depuis moins de *84 000 ans. La se ´- quence isole ´e contient un cadre de lecture ouvert complet, avec un seul cadre de lecture complet. L’absence de mutations non-sens, tout comme la tre `s grande similarite ´ des LTR, confirme que l’insertion de HACRE1 serait re ´cente. Le ge ´nome haploı ¨de du tournesol (ligne ´e fixe ´e HCM) compte environ 160 copies de l’e ´le ´ment HACRE1. Ce re ´trotransposon est ex- prime ´ dans les jeunes feuilles chez des plantules de 7 jours dans diverses conditions d’e ´clairage, phe ´nome `ne qui s’explique vraisemblablement par la pre ´sence, au sein des LTR, de plusieurs putatifs e ´le ´ments cis re ´gule ´s par la lumie `re. Cependant, les ADNc se ´quence ´s affichent moins de variabilite ´ nucle ´otidique que les copies ge ´nomiques, ce qui sugge `re que seul un sous-ensemble des e ´le ´ments de cette famille est exprime ´ dans ces conditions. Mots-cle ´s : copia, Helianthus annuus, re ´trotransposon, tournesol. [Traduit par la Re ´daction] Introduction The repetitive component of the eukaryotic genome is largely composed of class I transposons or retroelements (REs). REs propagate via a ‘‘copy and paste’’ mechanism in which autonomously produced enzymes (protease, integrase, reverse transcriptase, and RNase H) process retrotransposon transcripts to synthesize double-stranded DNA copies to be integrated back into the host genome. This mechanism re- sembles the replication cycle of retroviruses (Wicker et al. 2007). Class I elements can be divided into LTR and non-LTR Received 13 April 2009. Accepted 29 July 2009. Published on the NRC Research Press Web site at genome.nrc.ca on 20 October 2009. Corresponding Editor: T. Bureau. M. Buti, T. Giordani, M. Vukich, L. Pistelli, A. Cavallini, and L. Natali. 1 Dipartimento di Biologia delle Piante Agrarie, Universita ` di Pisa, I-56124 Pisa, Italy. L. Gentzbittel. INP–ENSAT, Unite ´ Symbiose et Pathologie des Plantes, Toulouse, France. F. Cattonaro. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, I-33100 Udine, Italy. M. Morgante. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, I-33100 Udine, Italy; Dipartimento di Scienze Agrarie e Ambientali, Universita ` di Udine, I-33100 Udine, Italy. 1 Corresponding author (e-mail: lnatali@agr.unipi.it). 904 Genome 52: 904–911 (2009) doi:10.1139/G09-064 Published by NRC Research Press