Background 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 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. Results A 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. Conclusions The 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. Electronic supplementary material The online version of this article (10.1186/s12870-019-1676-3) contains supplementary material, which is available to authorized users.

Blood orange [ Citrus sinensis (L.) Osbeck] has been increasingly appreciated by consumers worldwide owing to its brilliant red color, abundant anthocyanin and other health-promoting compounds. However, there is still relatively little known about its cytogenetic characteristics, probably because of the small size and similar morphology of metaphase chromosomes and the paucity of chromosomal landmarks. In our previous study, a naturally occurring tetraploid blood orange plant was obtained via seedling screening. Before this tetraploid germplasm can be manipulated into a citrus triploid seedless breeding program, it is of great importance to determine its chromosome characterization and composition. In the present study, an integrated karyotype of blood orange was constructed using sequential multicolor fluorescence in situ hybridization (FISH) with four satellite repeats, two ribosomal DNAs (rDNAs), a centromere-like repeat and an oligonucleotide of telomere repeat (TTTAGGG) 3 as probes. Satellite repeats were preferentially located at the terminal regions of the chromosomes of blood orange. Individual somatic chromosome pairs of blood orange were unambiguously identified by repetitive DNA-based multicolor FISH. These probes proved to be effective chromosomal landmarks. The karyotype was formulated as 2 n = 2 x = 18 = 16m+2sm (1sat) with the karyotype asymmetry degree belonging to 2B. The chromosomal distribution pattern of these repetitive DNAs in this spontaneously occurring tetraploid was identical to that of the diploid, but the tetraploid carried twice the number of hybridization sites as the diploid, indicating a possible pathway involving the spontaneous duplication of chromosome sets in nucellar cells. Our work may facilitate the molecular cytogenetic study of blood orange and provide chromosomal characterization for the future utilization of this tetraploid germplasm in the service of seedless breeding programs.

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Aroma differences are generally sensed in white-and red-fleshed loquats. Here, volatile compounds in four white-and three red-fleshed loquat varieties were investigated by headspace solid-phase microextraction and combined analysis of electronic nose (e-nose) and gas chromatography-mass spectrometry (GC-MS). On total, 83 volatile compounds were identified, and 33 were common in all of the cultivars. D-limonene, hexanal, (E)-2-hexenal, octanal and nonanal were the most abundant volatile compounds. β-cyclocitral and β-ionone were only detected in red-fleshed varieties. Furthermore, Huayu Seedless 1 (triploid white-fleshed loquats) with low levels of terpenoid compounds detected by GC-MS were clearly differentiated from the other cultivars tested by principal component analysis (PCA), which was consistent with the e-nose results. PCA analysis showed that Huabai 1(white flesh cultivar)had a prominent volatile profile characterized by higher concentrations of C6 aldehydes and alcohols, (E)-2-hexanal, (Z)-3-hexenal and hexanal, (Z)-3-hexenol, (E)-2-hexenol and hexanol. On comparison with red-fleshed loquats, white-fleshed loquats were characterized by high aldehydes content. These volatile compounds served to recognize and classify all of the analysed varieties.