Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly
Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of <i>Populus...
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MDPI AG
2023-06-01
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| Series: | International Journal of Molecular Sciences |
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| author | Yilian Zhao Guangxin Liu Ziyue Wang Yihang Ning Runxin Ni Mengli Xi |
| author_facet | Yilian Zhao Guangxin Liu Ziyue Wang Yihang Ning Runxin Ni Mengli Xi |
| author_sort | Yilian Zhao |
| collection | DOAJ |
| description | Poplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of <i>Populus simonii</i> which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for <i>P. simonii</i> to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current <i>P. simonii</i> genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the <i>P. simonii</i> chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly. |
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| spelling | doaj.art-bc51b2c7fd094e3887f6e6f2982765b62023-11-18T10:46:27ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-06-012412995010.3390/ijms24129950Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome AssemblyYilian Zhao0Guangxin Liu1Ziyue Wang2Yihang Ning3Runxin Ni4Mengli Xi5State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaState Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing 210037, ChinaPoplar was one of the first woody species whose individual chromosomes could be identified using chromosome specific painting probes. Nevertheless, high-resolution karyotype construction remains a challenge. Here, we developed a karyotype based on the meiotic pachytene chromosome of <i>Populus simonii</i> which is a Chinese native species with many excellent traits. This karyotype was anchored by oligonucleotide (oligo)-based chromosome specific painting probes, a centromere-specific repeat (Ps34), ribosomal DNA, and telomeric DNA. We updated the known karyotype formula for <i>P. simonii</i> to 2n = 2x = 38 = 26m + 8st + 4t and the karyotype was 2C. The fluorescence in situ hybridization (FISH) results revealed some errors in the current <i>P. simonii</i> genome assembly. The 45S rDNA loci were located at the end of the short arm of chromosomes 8 and 14 by FISH. However, they were assembled on pseudochromosomes 8 and 15. In addition, the Ps34 loci were distributed in every centromere of the <i>P. simonii</i> chromosome in the FISH results, but they were only found to be present in pseudochromosomes 1, 3, 6, 10, 16, 17, 18, and 19. Our results reveal that pachytene chromosomes oligo-FISH is a powerful tool for constructing high-resolution karyotypes and improving the quality of genome assembly.https://www.mdpi.com/1422-0067/24/12/9950pachytene chromosomeoligo-FISHkaryotyperepeats assembly<i>Populus simonii</i>forest model species |
| spellingShingle | Yilian Zhao Guangxin Liu Ziyue Wang Yihang Ning Runxin Ni Mengli Xi Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly International Journal of Molecular Sciences pachytene chromosome oligo-FISH karyotype repeats assembly <i>Populus simonii</i> forest model species |
| title | Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly |
| title_full | Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly |
| title_fullStr | Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly |
| title_full_unstemmed | Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly |
| title_short | Oligo-FISH of <i>Populus simonii</i> Pachytene Chromosomes Improves Karyotyping and Genome Assembly |
| title_sort | oligo fish of i populus simonii i pachytene chromosomes improves karyotyping and genome assembly |
| topic | pachytene chromosome oligo-FISH karyotype repeats assembly <i>Populus simonii</i> forest model species |
| url | https://www.mdpi.com/1422-0067/24/12/9950 |
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