Specific LTR-Retrotransposons Show Copy Number Variations between Wild and Cultivated Sunflowers

Abstract

The relationship between variation of the repetitive component of the genome and domestication in plant species is not fully understood. In previous work, variations in the abundance and proximity to genes of long terminal repeats (LTR)-retrotransposons of sunflower (Helianthus annuus L.) were investigated by Illumina DNA sequencingtocompare cultivars and wild accessions. In this study, we annotated and characterized 22 specific retrotransposon families whose abundance varies between domesticated and wild genotypes. These families mostly belonged to the Chromovirus lineage of the Gypsy superfamily and were distributed overall chromosomes. They were also analyzed in respect to their proximity to genes. Genes close to retrotransposon were classified according to biochemical pathways, and differences between domesticated and wild genotypes are shown. These data suggest that structural variations related to retrotransposons might have occurred to produce phenotypic variation between wild and domesticated genotypes, possibly by affecting the expression of genes that lie close to inserted or deleted retrotransposons and belong to specific biochemical pathways as those involved in plant stress responses.

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

“…The sample for genome sequencing was collected from young leaf tissue (0.5-1 cm in diameter) obtained from a single female plant of the Italian F. carica cultivar Dottato. Genomic DNA was isolated using the CTAB method as modified by Mascagni et al (2017Mascagni et al ( , 2018. For gel electrophoresis we used a Lambda Eco/Hind marker to size the linear double-stranded DNA and isolate only fragments with a molecular weight greater than 20 000 bp.…”

Sunflower Genetics from Ancestors to Modern Hybrids—A Review

“…Genetic studies of sunflower domestication revealed that contrary to findings in other plant species, where it was found that the phenotypic differences caused by domestication are due to a smaller number of genes with a strong effect [ 14 , 15 ], in sunflower, there is a larger number of genes involved in domestication, with the majority of genes showing small or moderate phenotypic effect [ 6 , 8 ]. Another difference between wild and cultivated sunflowers is the copy number of long terminal repeats (LTR) retrotransposons and splicing divergence [ 16 ]. A detailed list of domestication related quantitative trait loci (QTL) mapped in different crosses between cultivated and wild sunflower and primitive and wild sunflower is given in Table A1 .…”

On the Trail of Tetu1: Genome-Wide Discovery of CACTA Transposable Elements in Sunflower Genome

“…For each CACTA sequence, the genomic abundance was first assessed by mapping DNA reads of the sunflower genome, downloaded from NCBI (SRR5004633), according to the strategy already used for repetitive sequences in Mascagni et al [41,42]. Illumina HiSeq 2000 reads were preprocessed to remove Illumina adapters, then quality-trimmed using the default settings, and the lengths of reads were defined at 90 nt.…”