Abstract
Hippodamia variegata is one of the most commercialized ladybirds used for the biological control of aphid pest species in many economically important crops. This species is the first Coccinellidae whose satellitome has been studied by applying new sequencing technologies and bioinformatics tools. We found that 47% of the H. variegata genome is composed of repeated sequences. We identified 30 satellite DNA (satDNA) families with a median intragenomic divergence of 5.75% and A+T content between 45.6% and 74.7%. This species shows satDNA families with highly variable sizes although the most common size is 100–200 bp. However, we highlight the existence of a satDNA family with a repeat unit of 2 kb, the largest repeat unit described in Coleoptera. PCR amplifications for fluorescence in situ hybridization (FISH) probe generation were performed for the four most abundant satDNA families. FISH with the most abundant satDNA family as a probe shows its pericentromeric location on all chromosomes. This location is coincident with the heterochromatin revealed by C-banding and DAPI staining, also analyzed in this work. Hybridization signals for other satDNA families were located only on certain bivalents and the X chromosome. These satDNAs could be very useful as chromosomal markers due to their reduced location.
Highlights
Eukaryotic genomes are composed of single copy sequences and repetitive sequences that are mainly responsible for the structure, size and genome diversity [1]
The most significant portion in a eukaryotic genome is composed of repetitive DNA sequences tandemly repeated among the genome, known as satellite
We examined the contigs assembled by RepeatExplorer to search tandem repeated structures using the Dotmatcher tool and identify the monomer sequence for each satellite
Summary
Eukaryotic genomes are composed of single copy sequences and repetitive sequences that are mainly responsible for the structure, size and genome diversity [1]. The mean size of the monomer among satDNA families can vary between 100 and 1000 bp, it changes widely [4] These repeated sequences are typically found in the heterochromatin [5], being part of chromosome structures, such as telomeres [6] and pericentromeric and centromeric regions [1]. The evolution rate of repetitive sequences is very fast and they can vary in nucleotide composition, chromosomal distribution or genome representation These factors can affect the genome structure or they can affect the genome size between species [12]. This species is native in the Palearctic area but currently has spread to other regions through introduction to control crop pests [42] In spite of their ecological and economic importance, the data about repetitive DNA in Coccinelids are scarce. This study may be a first step that could help in the future to obtain the complete assembled genome of this important species
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