ArticleBMC genomics2013
The repetitive component of the sunflower genome as shown by different procedures for assembling next generation sequencing reads.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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30 citing papers in PubMed, 55 citations in OpenAlex.
- Genome evolution of Mediterranean olives following DNA repeats diversification.The plant genome · 2026Article
- Connecting Epigenetic and Genetic Diversity of LTR Retrotransposons in Sunflower (Plants (Basel, Switzerland) · 2026Article
- Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.Plants (Basel, Switzerland) · 2023Article
- Characterisation of LTR-Retrotransposons ofInternational journal of molecular sciences · 2022Article
- In Silico Genome-Wide Characterisation of the Lipid Transfer Protein Multigenic Family in Sunflower (Plants (Basel, Switzerland) · 2022Article
- De novo whole-genome assembly of Chrysanthemum makinoi, a key wild chrysanthemum.G3 (Bethesda, Md.) · 2022Article
- The Singular Evolution ofFrontiers in plant science · 2022Article
- K-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.The plant genome · 2021Article
- Article
- On the Trail ofInternational journal of molecular sciences · 2020Article
- A computational genome-wide analysis of long terminal repeats retrotransposon expression in sunflower roots (Helianthus annuus L.).Genetica · 2020Article
- Differential Genome Size and Repetitive DNA Evolution in Diploid Species ofFrontiers in plant science · 2020Article
- Retrotransposons in Plant Genomes: Structure, Identification, and Classification through Bioinformatics and Machine Learning.International journal of molecular sciences · 2019Review
- Arbuscular mycorrhizal fungi induce the expression of specific retrotransposons in roots of sunflower (Helianthus annuus L.).PloS one · 2019Article
- Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers.Genes · 2018Article
- Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots.Scientific reports · 2018Article
- Genomic abundance and transcriptional activity of diverse gypsy and copia long terminal repeat retrotransposons in three wild sunflower species.BMC plant biology · 2018Article
- Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).BMC genomics · 2017Article
- Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome.Molecular genetics and genomics : MGG · 2017Article
- Recent and dynamic transposable elements contribute to genomic divergence under asexuality.BMC genomics · 2016Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNext generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage Illumina or 454 libraries.
resultsBy varying sequencing technology (Illumina or 454), coverage (0.55 x-1.25 x), assemblers and assembly procedures, six different genomic databases were produced. The annotation of these databases showed that they were composed of different proportions of repetitive DNA families. The final assembly of the sequences belonging to the six databases produced a whole genome set of 283,800 contigs. The redundancy of each contig was estimated by mapping the whole genome set with a large Illumina read set and measuring the number of matched Illumina reads. The repetitive component amounted to 81% of the sunflower genome, that is composed mainly of numerous families of Gypsy and Copia retrotransposons. Also many families of non autonomous retrotransposons and DNA transposons (especially of the Helitron superfamily) were identified.
conclusionsThe results substantially matched those previously obtained by using a Sanger-sequenced shotgun library and a standard 454 whole-genome-shotgun approach, indicating the reliability of the proposed procedures also for other species. The repetitive sequences were collected to produce a database, SUNREP, that will be useful for the annotation of the sunflower genome sequence and for studying the genome evolution in dicotyledons.
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