Repetitive DNA landscape in essential A and supernumerary B chromosomes of Festuca pratensis Huds

Rahman Ebrahimzadegan,Ghader Mirzaghaderi,Andreas Houben

doi:10.1038/s41598-019-56383-1

Rahman Ebrahimzadegan, Ghader Mirzaghaderi + Show 1 more

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https://doi.org/10.1038/s41598-019-56383-1

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Abstract

Here, we characterized the basic properties of repetitive sequences in essential A and supernumerary B chromosomes of Festuca pratensis Huds. This was performed by comparative analysis of low-pass Illumina sequence reads of B chromosome lacking (−B) and B chromosome containing (+B) individuals of F. pratensis. 61% of the nuclear genome is composed of repetitive sequences. 43.1% of the genome are transposons of which DNA transposons and retrotransposons made up 2.3% and 40.8%, respectively. LTR retrotransposons are the most abundant mobile elements and contribute to 40.7% of the genome and divided into Ty3-gypsy and Ty1-copia super families with 32.97% and 7.78% of the genome, respectively. Eighteen different satellite repeats were identified making up 3.9% of the genome. Five satellite repeats were used as cytological markers for chromosome identification and genome analysis in the genus Festuca. Four satellite repeats were identified on B chromosomes among which Fp-Sat48 and Fp-Sat253 were specific to the B chromosome of F. pratensis.

Highlights

The genus Festuca consists of more than 450 species[1] and is one of the largest genera in the Poaceae
Physical mapping of ribosomal DNA sites in some Festuca species revealed that 5S and 45S ribosomal loci in F. pratensis have been localized on the short arms of chromosomes 2 and 3, respectively[36]
Low-pass Illumina sequencing of the genomic −B chromosomes (Bs)/+B DNA followed by the repeat characterization from the sequence reads using RepeatExplorer[41] and TAREAN42 pipelines provided a comprehensive view about the types, abundance and organization of repetitive DNA sequences in F. pratensis

Summary

Introduction

The genus Festuca consists of more than 450 species[1] and is one of the largest genera in the Poaceae. (Meadow fescue) is a diploid species in the genus Festuca with 2n = 2x = 14 standard (A) chromosomes (Fp genome). Transposons and satellites (satDNA) are two major groups of repetitive sequence in eukaryotic genomes and have diverse sequence and distribution patterns[21,22,23,24,25]. The rapid evolution of satellite repeats in plant genomes, has led to their intraspecific homogenization and fixation of species-specific polymorphisms, making satDNA families unique source of molecular and cytogenetic markers to analyze genetic diversity and genome evolution[28,29,30,31,32]. FISH using BAC clones[37] and sequencing of chromosome 4F38 have identified some repetitive DNA sequences in the meadow fescue genome. Et al.[40] identified an A chromosome-specific repetitive sequence in this species

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