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Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions.
Theor Appl Genet 2011; 123(5):779-91TA

Abstract

Improved knowledge of genome composition, especially of its repetitive component, generates important informations in both theoretical and applied research. In this study, we provide the first insight into the local organization of the sunflower genome by sequencing and annotating 349,380 bp from 3 BAC clones, each including one single-copy gene. These analyses resulted in the identification of 11 putative gene sequences, 18 full-length LTR retrotransposons, 6 incomplete LTR retrotransposons, 2 non-autonomous LTR-retroelements (LINEs), 2 putative DNA transposons fragments and one putative helitron. Among LTR-retrotransposons, non-autonomous elements (the so-called LARDs), which do not carry any protein-encoding sequence, were discovered for the first time in the sunflower. The insertion time of intact retroelements was measured, based on sister LTRs divergence. All isolated elements were inserted relatively recently, especially those belonging to the Gypsy superfamily. Retrotransposon families related to those identified in the BAC clones are present also in other species of Helianthus, both annual and perennial, and even in other Asteraceae. In one of the three BAC clones, we found five copies of a lipid transfer protein (LTP) encoding gene within less than 100,000 bp, four of which are potentially functional. Two of these are interrupted by LTR retrotransposons, in the intron and in the coding sequence, respectively. The divergence between sister LTRs of the retrotransposons inserted within the genes indicates that LTP gene duplication started earlier than 1.749 MYRS ago. On the whole, the results reported in this study confirm that the sunflower is an excellent system to study transposons dynamics and evolution.

Authors+Show Affiliations

Department of Crop Plant Biology, University of Pisa, Pisa, Italy.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

21647740

Citation

Buti, M, et al. "Temporal Dynamics in the Evolution of the Sunflower Genome as Revealed By Sequencing and Annotation of Three Large Genomic Regions." TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, vol. 123, no. 5, 2011, pp. 779-91.
Buti M, Giordani T, Cattonaro F, et al. Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. Theor Appl Genet. 2011;123(5):779-91.
Buti, M., Giordani, T., Cattonaro, F., Cossu, R. M., Pistelli, L., Vukich, M., ... Natali, L. (2011). Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik, 123(5), pp. 779-91. doi:10.1007/s00122-011-1626-4.
Buti M, et al. Temporal Dynamics in the Evolution of the Sunflower Genome as Revealed By Sequencing and Annotation of Three Large Genomic Regions. Theor Appl Genet. 2011;123(5):779-91. PubMed PMID: 21647740.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Temporal dynamics in the evolution of the sunflower genome as revealed by sequencing and annotation of three large genomic regions. AU - Buti,M, AU - Giordani,T, AU - Cattonaro,F, AU - Cossu,R M, AU - Pistelli,L, AU - Vukich,M, AU - Morgante,M, AU - Cavallini,A, AU - Natali,L, Y1 - 2011/06/07/ PY - 2011/02/12/received PY - 2011/05/09/accepted PY - 2011/6/8/entrez PY - 2011/6/8/pubmed PY - 2011/12/23/medline SP - 779 EP - 91 JF - TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik JO - Theor. Appl. Genet. VL - 123 IS - 5 N2 - Improved knowledge of genome composition, especially of its repetitive component, generates important informations in both theoretical and applied research. In this study, we provide the first insight into the local organization of the sunflower genome by sequencing and annotating 349,380 bp from 3 BAC clones, each including one single-copy gene. These analyses resulted in the identification of 11 putative gene sequences, 18 full-length LTR retrotransposons, 6 incomplete LTR retrotransposons, 2 non-autonomous LTR-retroelements (LINEs), 2 putative DNA transposons fragments and one putative helitron. Among LTR-retrotransposons, non-autonomous elements (the so-called LARDs), which do not carry any protein-encoding sequence, were discovered for the first time in the sunflower. The insertion time of intact retroelements was measured, based on sister LTRs divergence. All isolated elements were inserted relatively recently, especially those belonging to the Gypsy superfamily. Retrotransposon families related to those identified in the BAC clones are present also in other species of Helianthus, both annual and perennial, and even in other Asteraceae. In one of the three BAC clones, we found five copies of a lipid transfer protein (LTP) encoding gene within less than 100,000 bp, four of which are potentially functional. Two of these are interrupted by LTR retrotransposons, in the intron and in the coding sequence, respectively. The divergence between sister LTRs of the retrotransposons inserted within the genes indicates that LTP gene duplication started earlier than 1.749 MYRS ago. On the whole, the results reported in this study confirm that the sunflower is an excellent system to study transposons dynamics and evolution. SN - 1432-2242 UR - https://www.unboundmedicine.com/medline/citation/21647740/Temporal_dynamics_in_the_evolution_of_the_sunflower_genome_as_revealed_by_sequencing_and_annotation_of_three_large_genomic_regions_ L2 - https://dx.doi.org/10.1007/s00122-011-1626-4 DB - PRIME DP - Unbound Medicine ER -