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Oligo-FISH of Populus simonii 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 Populus simonii...

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Autores principales: Zhao, Yilian, Liu, Guangxin, Wang, Ziyue, Ning, Yihang, Ni, Runxin, Xi, Mengli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297927/
https://www.ncbi.nlm.nih.gov/pubmed/37373099
http://dx.doi.org/10.3390/ijms24129950
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author Zhao, Yilian
Liu, Guangxin
Wang, Ziyue
Ning, Yihang
Ni, Runxin
Xi, Mengli
author_facet Zhao, Yilian
Liu, Guangxin
Wang, Ziyue
Ning, Yihang
Ni, Runxin
Xi, Mengli
author_sort Zhao, Yilian
collection PubMed
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 Populus simonii 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 P. simonii 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 P. simonii 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 P. simonii 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 pubmed-102979272023-06-28 Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly Zhao, Yilian Liu, Guangxin Wang, Ziyue Ning, Yihang Ni, Runxin Xi, Mengli Int J Mol Sci Article 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 Populus simonii 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 P. simonii 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 P. simonii 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 P. simonii 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. MDPI 2023-06-09 /pmc/articles/PMC10297927/ /pubmed/37373099 http://dx.doi.org/10.3390/ijms24129950 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhao, Yilian
Liu, Guangxin
Wang, Ziyue
Ning, Yihang
Ni, Runxin
Xi, Mengli
Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title_full Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title_fullStr Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title_full_unstemmed Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title_short Oligo-FISH of Populus simonii Pachytene Chromosomes Improves Karyotyping and Genome Assembly
title_sort oligo-fish of populus simonii pachytene chromosomes improves karyotyping and genome assembly
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10297927/
https://www.ncbi.nlm.nih.gov/pubmed/37373099
http://dx.doi.org/10.3390/ijms24129950
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