Molecular cytogenetic analysis of genome-specific repetitive elements in Citrus clementina Hort. Ex Tan. and its taxonomic implications

Abstract

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.

Distinguishing Sichuan Walnut Cultivars and Examining Their Relationships with Juglans regia and J. sigillata by FISH, Early-Fruiting Gene Analysis, and SSR Analysis

“…The FISH 5S rDNA oligonucleotide with two signals and (AG 3 T 3 ) 3 with an end signal on every chromosome showed almost no differences among the four walnut cultivars in this study. Similar distribution patterns have also been observed in Citrus species (Deng et al, 2019); Berberis species (Liu and Luo, 2019); and Fraxinus, Syringa, and Ligustrum species (Luo and Liu, 2019a). FISH probes (AG 3 T 3 ) 3 located at chromosome ends ensure accurate chromosome counts (Pereira et al, 2018), although (AG 3 T 3 ) 3 is also occasionally observed in the internal positions of chromosomes (Murray et al, 2002;Majerová et al, 2014;Vasconcelos et al, 2018).…”

“…At least five molecular genetic linkage maps for walnut have been established (Fjellstrom and Parfitt, 1994;Woeste et al, 1996;Malvolti et al, 2001;Luo et al, 2015;Zhu et al, 2015). Fluorescence in situ hybridization (FISH) with probe-labeled chromosome ends enables accurate counting of small walnut chromosomes (Deng et al, 2019;Liu and Luo, 2019;Luo and Liu, 2019a). Karyotype analysis aids in chromosome physical map construction and chromosome assembly (Hizume et al, 2002;Luo et al, 2017;Luo et al, 2018;Pereira et al, 2018), thereby providing a guide for distinguishing Sichuan walnut cultivars to a certain degree.…”

Integrated Karyotypes of Diploid and Tetraploid Carrizo Citrange (Citrus sinensis L. Osbeck × Poncirus trifoliata L. Raf.) as Determined by Sequential Multicolor Fluorescence in situ Hybridization With Tandemly Repeated DNA Sequences

“…Karyotypic features have greatly facilitated taxonomic and systematic studies, and they have also provided important insight into genome size estimations as well as genome structure and organization at the chromosomal level in numerous plant species (Chèvre et al, 2018), including radish (Raphanus sativus L.) (He et al, 2015), Coix lacryma-jobi L. and Coix aquatica Roxb. (Cai et al, 2014), peanut (Arachis hypogaea) (Zhang et al, 2016), sweet potato (Sun et al, 2019), Oleaceae plants (Luo and Liu, 2019), Clementine mandarin (Deng et al, 2019b), and blood orange [C. sinensis (L.) Osb.] (Deng et al, 2019a).…”

“…As sequencing technology and associated bioinformatics tools have advanced, citrus genomics have followed suit. Recently, we analyzed the repeat sequence composition in the Clementine mandarin genome and successfully developed a set of FISH probes, encompassing a centromeric-like repeat (CL17), four major satellite repeats (CL1, CL2, CL3, and CL4), two rDNAs (45S and 5S rDNA), and a telomeric repeat (TTTAGGG) n (Deng et al, 2019b). In that study, the physical distribution of these repetitive DNAs on the same somatic metaphase chromosomes of Clementine mandarin and other several citrus cultivars were also analyzed (Deng et al, 2019b).…”

“…Recently, we analyzed the repeat sequence composition in the Clementine mandarin genome and successfully developed a set of FISH probes, encompassing a centromeric-like repeat (CL17), four major satellite repeats (CL1, CL2, CL3, and CL4), two rDNAs (45S and 5S rDNA), and a telomeric repeat (TTTAGGG) n (Deng et al, 2019b). In that study, the physical distribution of these repetitive DNAs on the same somatic metaphase chromosomes of Clementine mandarin and other several citrus cultivars were also analyzed (Deng et al, 2019b). Subsequently, a detailed karyotype of diploid blood orange was established by multicolor FISH with these excellent probes, and we did the same for its spontaneously occurring tetraploid plant (Deng et al, 2019a).…”