PMID- 38267860 OWN - NLM STAT- MEDLINE DCOM- 20240126 LR - 20240206 IS - 1471-2229 (Electronic) IS - 1471-2229 (Linking) VI - 24 IP - 1 DP - 2024 Jan 25 TI - Genomic and cytogenetic analyses reveal satellite repeat signature in allotetraploid okra (Abelmoschus esculentus). PG - 71 LID - 10.1186/s12870-024-04739-9 [doi] LID - 71 AB - BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes. RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA. CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes. CI - (c) 2024. The Author(s). FAU - Liu, Jiarui AU - Liu J AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Lin, Xinyi AU - Lin X AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Wang, Xiaojie AU - Wang X AD - College of Life Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Feng, Liqing AU - Feng L AD - College of Life Science, Fujian Normal University, Fuzhou, 350117, China. FAU - Zhu, Shixin AU - Zhu S AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Tian, Runmeng AU - Tian R AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Fang, Jingping AU - Fang J AD - College of Life Science, Fujian Normal University, Fuzhou, 350117, China. FAU - Tao, Aifen AU - Tao A AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Fang, Pingping AU - Fang P AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Qi, Jianmin AU - Qi J AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Zhang, Liwu AU - Zhang L AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. FAU - Huang, Yongji AU - Huang Y AD - Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, College of Geography and Oceanography, Minjiang University, Fuzhou, 350108, China. scolandry@foxmail.com. FAU - Xu, Jiantang AU - Xu J AD - Scientific Observing and Experimental Station of Southeastern kenaf & jute, Ministry of Agriculture and Rural Affairs of the People's Republic of China, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Provincial Key Laboratory of Crop Breeding by Design, National Engineering Research Center for Sugarcane, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. xujiantang@fafu.edu.cn. LA - eng GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ GR - CARS-16/the China Agriculture Research System of MOF and MARA/ PT - Journal Article DEP - 20240125 PL - England TA - BMC Plant Biol JT - BMC plant biology JID - 100967807 RN - 0 (DNA, Intergenic) RN - 0 (DNA, Ribosomal) SB - IM MH - *Abelmoschus/genetics MH - In Situ Hybridization, Fluorescence MH - Genomics MH - Cytogenetic Analysis MH - DNA, Intergenic MH - DNA, Ribosomal PMC - PMC10809672 OTO - NOTNLM OT - Abelmoschus esculentus OT - Allotetraploid OT - Fluorescence in situ hybridization OT - Intergenic spacer region OT - Satellite repeat OT - rDNA COIS- We declare that there is no competing interest among the authors. EDAT- 2024/01/25 00:42 MHDA- 2024/01/26 06:43 PMCR- 2024/01/25 CRDT- 2024/01/24 23:44 PHST- 2023/09/20 00:00 [received] PHST- 2024/01/10 00:00 [accepted] PHST- 2024/01/26 06:43 [medline] PHST- 2024/01/25 00:42 [pubmed] PHST- 2024/01/24 23:44 [entrez] PHST- 2024/01/25 00:00 [pmc-release] AID - 10.1186/s12870-024-04739-9 [pii] AID - 4739 [pii] AID - 10.1186/s12870-024-04739-9 [doi] PST - epublish SO - BMC Plant Biol. 2024 Jan 25;24(1):71. doi: 10.1186/s12870-024-04739-9.