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

Genes
Flavia MascagniL Natali

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.

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Citations

Dec 7, 2019·The Plant Journal : for Cell and Molecular Biology·Gabriele UsaiLucia Natali
Mar 20, 2020·International Journal of Molecular Sciences·Maria VentimigliaFlavia Mascagni
Aug 9, 2019·International Journal of Molecular Sciences·Simon Orozco-AriasRomain Guyot
Nov 2, 2018·Genes·Aleksandra RadanovićSiniša Jocić
May 19, 2021·BMC Plant Biology·Alberto VangelistiTommaso Giordani
Jun 12, 2021·Molecular Biology and Evolution·Claudine Bleykasten-GrosshansJoseph Schacherer

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Datasets Mentioned

BETA
PRJNA302358

Software Mentioned

BWA
house R script
R package vegan
R FactoMineR
RepeatExplorer
CLC
SAMtools
RepeatMasker
in
house Perl script

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