Abstract
BackgroundClementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine.ResultsA graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)3 was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin.ConclusionsThe composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.
Highlights
Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide
The bioinformatics analysis data revealed that the Clementine genome, like other higher eukaryotic plant genomes, contained a large proportion of different families of repetitive DNA elements
The observed proportions of each family of repetitive DNAs in the Clementine genome are summarized in Table 1, and the specific information is listed in Additional file 1
Summary
Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosomespecific. To date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine. Ex Tan.) (2n = 2x = 18) [1], belonging to the Rutaceae family [2], is one of the most famous commercial citrus cultivars worldwide [3, 4]. Repetitive DNA sequences represent a large proportion of the genome in higher eukaryotes [7], reaching 20% or, in some cases, up to 90% of the genome size [8], and they comprise tandem repeat sequences (satellites, minisatellites and microsatellites) and dispersed transposable elements (transposons and retrotransposons) [9]. Many recent studies have emphasized the important role of repetitive DNAs in determining the size, composition and evolution of genomes. Repeats have always presented technical challenges for sequence alignment and genome assembly programs [12]
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