Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species
Abstract The centromere plays a pivotal role in the karyotype of citrus chromosomes. However, the development of markers capable of distinguishing individual chromosomes remains a challenge. Oligo-FISH provides an efficient method for generating citrus centromere-specific markers. Accurate identific...
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Springer
2025-07-01
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| Series: | Horticulture Advances |
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| Online Access: | https://doi.org/10.1007/s44281-025-00076-5 |
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| author | Gong-Ao Xiao Qiang-Ming Xia Jia-Qin Ren Yao-Yuan Duan Xiao-Meng Wu Wen-Wu Guo Kai-Dong Xie |
| author_facet | Gong-Ao Xiao Qiang-Ming Xia Jia-Qin Ren Yao-Yuan Duan Xiao-Meng Wu Wen-Wu Guo Kai-Dong Xie |
| author_sort | Gong-Ao Xiao |
| collection | DOAJ |
| description | Abstract The centromere plays a pivotal role in the karyotype of citrus chromosomes. However, the development of markers capable of distinguishing individual chromosomes remains a challenge. Oligo-FISH provides an efficient method for generating citrus centromere-specific markers. Accurate identification of centromere positions is a prerequisite for marker development. In this study, centromere locations on each chromosome were recalibrated using previously published ChIP-seq data of CsCENH3, aligned with the high-quality sweet orange genome (SWO v3). A total of 16,827 45-nucleotide oligos spanning nine centromeric regions were screened, with each region containing between 868 and 5,965 oligos, yielding an approximate density of one oligo per kilobase. Oligos from the centromere regions of chromosomes 1 (Chr1) and 4 (Chr4) were randomly selected to synthesize centromere-specific probes. Dual-color FISH assays on mitotic and meiotic chromosomes revealed distinct signals from each probe on homologous chromosomes. These signals coincided with those from the previously identified centromeric marker CL34contig88, demonstrating the ability of the probes to differentiate centromeres of individual chromosomes. Furthermore, chromosome painting was conducted across several citrus species, including Citrus sinensis, C. reticulata, C. limon, C. grandis, Fortunella japonica, and Poncirus trifoliata, with centromeric signals for Chr1 and Chr4 observable in all species. Chr1 and Chr4 exhibited characteristics of submetacentric and metacentric chromosomes, respectively, based on arm ratios, reflecting the conserved karyotypic structure of these chromosomes across citrus species and their consistent centromeric oligo sequences. These findings underscore the potential of centromere-specific probes in advancing citrus cytology and provide a robust foundation for exploring centromeric sequence evolution in citrus. |
| format | Article |
| id | doaj-art-b6193ccb232d4ae5b9e67fbc85492b83 |
| institution | DOAJ |
| issn | 2948-1104 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Springer |
| record_format | Article |
| series | Horticulture Advances |
| spelling | doaj-art-b6193ccb232d4ae5b9e67fbc85492b832025-08-20T03:05:04ZengSpringerHorticulture Advances2948-11042025-07-013111110.1007/s44281-025-00076-5Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus speciesGong-Ao Xiao0Qiang-Ming Xia1Jia-Qin Ren2Yao-Yuan Duan3Xiao-Meng Wu4Wen-Wu Guo5Kai-Dong Xie6National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityNational Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture & Forestry Sciences, Huazhong Agricultural UniversityAbstract The centromere plays a pivotal role in the karyotype of citrus chromosomes. However, the development of markers capable of distinguishing individual chromosomes remains a challenge. Oligo-FISH provides an efficient method for generating citrus centromere-specific markers. Accurate identification of centromere positions is a prerequisite for marker development. In this study, centromere locations on each chromosome were recalibrated using previously published ChIP-seq data of CsCENH3, aligned with the high-quality sweet orange genome (SWO v3). A total of 16,827 45-nucleotide oligos spanning nine centromeric regions were screened, with each region containing between 868 and 5,965 oligos, yielding an approximate density of one oligo per kilobase. Oligos from the centromere regions of chromosomes 1 (Chr1) and 4 (Chr4) were randomly selected to synthesize centromere-specific probes. Dual-color FISH assays on mitotic and meiotic chromosomes revealed distinct signals from each probe on homologous chromosomes. These signals coincided with those from the previously identified centromeric marker CL34contig88, demonstrating the ability of the probes to differentiate centromeres of individual chromosomes. Furthermore, chromosome painting was conducted across several citrus species, including Citrus sinensis, C. reticulata, C. limon, C. grandis, Fortunella japonica, and Poncirus trifoliata, with centromeric signals for Chr1 and Chr4 observable in all species. Chr1 and Chr4 exhibited characteristics of submetacentric and metacentric chromosomes, respectively, based on arm ratios, reflecting the conserved karyotypic structure of these chromosomes across citrus species and their consistent centromeric oligo sequences. These findings underscore the potential of centromere-specific probes in advancing citrus cytology and provide a robust foundation for exploring centromeric sequence evolution in citrus.https://doi.org/10.1007/s44281-025-00076-5CitrusCentromere markerOligo-FISHKaryotypeHomologous chromosome |
| spellingShingle | Gong-Ao Xiao Qiang-Ming Xia Jia-Qin Ren Yao-Yuan Duan Xiao-Meng Wu Wen-Wu Guo Kai-Dong Xie Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species Horticulture Advances Citrus Centromere marker Oligo-FISH Karyotype Homologous chromosome |
| title | Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species |
| title_full | Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species |
| title_fullStr | Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species |
| title_full_unstemmed | Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species |
| title_short | Chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse Citrus species |
| title_sort | chromosome painting reveals conserved centromere oligonucleotide sequences and comparable karyotypes across diverse citrus species |
| topic | Citrus Centromere marker Oligo-FISH Karyotype Homologous chromosome |
| url | https://doi.org/10.1007/s44281-025-00076-5 |
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