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Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).
BMC Genomics 2017; 18(1):634BG

Abstract

BACKGROUND

Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels.

RESULTS

After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species.

CONCLUSIONS

This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species.

Authors+Show Affiliations

Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123, Perugia, Italy.Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy.Department of Agriculture, Food and Environment, University of Pisa, 56124, Pisa, Italy. lucia.natali@unipi.it.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28821238

Citation

Mascagni, Flavia, et al. "Genome-wide Analysis of LTR-retrotransposon Diversity and Its Impact On the Evolution of the Genus Helianthus (L.)." BMC Genomics, vol. 18, no. 1, 2017, p. 634.
Mascagni F, Giordani T, Ceccarelli M, et al. Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.). BMC Genomics. 2017;18(1):634.
Mascagni, F., Giordani, T., Ceccarelli, M., Cavallini, A., & Natali, L. (2017). Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.). BMC Genomics, 18(1), p. 634. doi:10.1186/s12864-017-4050-6.
Mascagni F, et al. Genome-wide Analysis of LTR-retrotransposon Diversity and Its Impact On the Evolution of the Genus Helianthus (L.). BMC Genomics. 2017 Aug 18;18(1):634. PubMed PMID: 28821238.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.). AU - Mascagni,Flavia, AU - Giordani,Tommaso, AU - Ceccarelli,Marilena, AU - Cavallini,Andrea, AU - Natali,Lucia, Y1 - 2017/08/18/ PY - 2017/04/05/received PY - 2017/08/10/accepted PY - 2017/8/20/entrez PY - 2017/8/20/pubmed PY - 2018/4/3/medline KW - Annual and perennial habit KW - Comparative genomics KW - Helianthus KW - LTR-retrotransposons KW - Plant genome evolution KW - Repetitive DNA SP - 634 EP - 634 JF - BMC genomics JO - BMC Genomics VL - 18 IS - 1 N2 - BACKGROUND: Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. RESULTS: After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. CONCLUSIONS: This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species. SN - 1471-2164 UR - https://www.unboundmedicine.com/medline/citation/28821238/Genome_wide_analysis_of_LTR_retrotransposon_diversity_and_its_impact_on_the_evolution_of_the_genus_Helianthus__L___ L2 - https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4050-6 DB - PRIME DP - Unbound Medicine ER -