Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH
Abstract
:1. Introduction
2. Results
2.1. Phylogenetic Relationships Established Based on 45S rDNA
2.2. Development of Oligo-FISH Probes Using Single-Copy Sequences from Chinese Cherry
2.3. Chromosome Identification in Chinese Cherry and Related Species
2.4. Distribution of 5S rDNA and 45S rDNA in Different Species
2.5. Comparative Karyotype Analyses
3. Discussion
4. Materials and Methods
4.1. Sequencing Reads and Phylogenetic Analyses
4.2. Plant Materials and Chromosome Preparation
4.3. Chromosome-Specific Oligonucleotide Probe Development
4.4. Repetitive and Single-Copy Oligo Probe Synthesis
4.5. FISH and Karyotyping
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Contigs | Contigs Length (bp) | Oligo Number | Corresponding Chromosome | Region Length (bp) | Density Oligos/kb | Primers Flanking Oligos * |
---|---|---|---|---|---|---|
Contig_27 | 2,252,344 | 6790 | Chr_1 | 1,699,807 | 3.99 | W1.F + P1.F—P1.R + W1.R |
Contig_29 | 2,199,550 | 7513 | Chr_1 | 2,141,321 | 3.42 | W1.F + P1.F—P1.R + W1.R |
Contig_25 | 2,290,169 | 7413 | Chr_2 | 1,399,377 | 5.30 | W2.F + P2.F—P2.R + W2.R |
Contig_02 | 5,439,059 | 6568 | Chr_3 | 1,594,437 | 4.11 | W2.F + P3.F—P3.R + W2.R |
Contig_09 | 4,505,147 | 6618 | Chr_3 | 1,462,969 | 4.41 | W2.F + P3.F—P3.R + W2.R |
Contig_04 | 5,080,108 | 6964 | Chr_4 | 1,480,858 | 4.64 | W1.F + P4.F—P4.R + W1.R |
Contig_01 | 7,149,121 | 7960 | Chr_5 | 1,998,387 | 3.98 | W1.F + P5.F—P5.R + W1.R |
Contig_37 | 1,734,690 | 7162 | Chr_5 | 1,676,082 | 4.21 | W2.F + P5.F—P5.R + W2.R |
Contig_45 | 1,603,937 | 7120 | Chr_6 | 1,541,098 | 4.45 | W2.F + P6.F—P6.R + W2.R |
Contig_07 | 4,762,281 | 7080 | Chr_6 | 1,765,125 | 3.93 | W1.F + P6.F—P6.R + W1.R |
Contig_34 | 2,027,033 | 6780 | Chr_7 | 1,516,158 | 4.52 | W1.F + P7.F—P7.R + W1.R |
Contig_08 | 4,598,159 | 5407 | Chr_7 | 1,598,107 | 3.38 | W2.F + P7.F—P7.R + W2.R |
Contig_20 | 2,726,937 | 5146 | Chr_8 | 1,879,060 | 2.71 | W1.F + P8.F—P8.R + W1.R |
Contig_52 | 1,520,798 | 6773 | Chr_8 | 1,418,134 | 4.84 | W1.F + P8.F—P8.R + W1.R |
Species | Accession Name or Code | Ploidy | Origin (Location) |
---|---|---|---|
True cherry | |||
Prunus pseudocerasus | HC; BZ; HF; PJHH; FM2 * | 2n = 4x = 32 | Chongzhou City, Sichuan Province, China |
Prunus yedoensis | DJYH | 2n = 2x = 16 | Chengdu City, Sichuan Province, China |
Prunus campanulata | ZHYT | 2n = 2x = 16 | |
Prunus avium | Mazzard; Van | 2n = 2x = 16 | Zhengzhou Fruit Institute, Chinese Academy of Agriculture Sciences |
Prunus cerasus | SYT | 2n = 4x = 32 | |
Dwarf cherry | |||
Prunus humilis | Ouli | 2n = 2x = 16 | Zhengzhou Fruit Institute, Chinese Academy of Agriculture Sciences |
Prunus tomentosa | red_fruit; white_fruit | 2n = 2x = 16 | |
Closely related species | |||
Prunus armeniaca | DGX | 2n = 2x = 16 | Akesu, Xinjiang Uygur Autonomous Region, China |
Prunus dulcis | BT | 2n = 2x = 16 | Luntai, Xinjiang Uygur Autonomous Region, China |
Prunus salicina | SYL | 2n = 2x = 16 | Chengdu City, Sichuan Province, China |
Prunus persica | MT | 2n = 2x = 16 |
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Wang, L.; Feng, Y.; Wang, Y.; Zhang, J.; Chen, Q.; Liu, Z.; Liu, C.; He, W.; Wang, H.; Yang, S.; et al. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. Int. J. Mol. Sci. 2022, 23, 13213. https://doi.org/10.3390/ijms232113213
Wang L, Feng Y, Wang Y, Zhang J, Chen Q, Liu Z, Liu C, He W, Wang H, Yang S, et al. Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH. International Journal of Molecular Sciences. 2022; 23(21):13213. https://doi.org/10.3390/ijms232113213
Chicago/Turabian StyleWang, Lei, Yan Feng, Yan Wang, Jing Zhang, Qing Chen, Zhenshan Liu, Congli Liu, Wen He, Hao Wang, Shaofeng Yang, and et al. 2022. "Accurate Chromosome Identification in the Prunus Subgenus Cerasus (Prunus pseudocerasus) and its Relatives by Oligo-FISH" International Journal of Molecular Sciences 23, no. 21: 13213. https://doi.org/10.3390/ijms232113213