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基于超高拷贝167碱基对串联重复序列和核糖体DNA的精细核型。

A refined karyotype based on an ultra-high copy 167-bp tandem repeat and ribosomal DNAs.

作者信息

Waminal Nomar Espinosa, Choi Hong-Il, Kim Nam-Hoon, Jang Woojong, Lee Junki, Park Jee Young, Kim Hyun Hee, Yang Tae-Jin

机构信息

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.

Department of Life Science, Plant Biotechnology Institute, Sahmyook University, Seoul, Republic of Korea.

出版信息

J Ginseng Res. 2017 Oct;41(4):469-476. doi: 10.1016/j.jgr.2016.08.002. Epub 2016 Aug 11.

DOI:10.1016/j.jgr.2016.08.002
PMID:29021693
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5628329/
Abstract

BACKGROUND

Meyer (Asian ginseng) has a large nuclear genome size of > 3.5 Gbp in haploid genome equivalent of 24 chromosomes. Tandem repeats (TRs) occupy significant portions of the genome in many plants and are often found in specific genomic loci, making them a valuable molecular cytogenetic tool in discriminating chromosomes. In an effort to understand the genome structure, we characterized an ultrahigh copy 167-bp TR (Pg167TR) and explored its chromosomal distribution as well as its utility for chromosome identification.

METHODS

Polymerase chain reaction amplicons of Pg167TR were labeled, along with 5S and 45S rDNA amplicons, using a direct nick-translation method. Direct fluorescence hybridization (FISH) was used to analyze the chromosomal distribution of Pg167TR.

RESULTS

Recently, we reported a method of karyotyping the 24 chromosome pairs of using rDNA and DAPI (4',6-diamidino-2-phenylindole) bands. Here, a unique distribution of Pg167TR in all 24 chromosomes was observed, allowing easy identification of individual homologous chromosomes. Additionally, direct labeling of 5S and 45S rDNA probes allowed the identification of two additional 5S rDNA loci not previously reported, enabling the refinement of the karyotype.

CONCLUSION

Identification of individual chromosomes was achieved using Pg167TR-FISH. Chromosome identification is important in understanding the genome structure, and our method will be useful for future integration of genetic linkage maps and genome scaffold anchoring. Additionally, it is a good tool for comparative studies with related species in efforts to understand the evolution of .

摘要

背景

迈耶人参（亚洲人参）单倍体基因组相当于24条染色体，其核基因组大小超过3.5 Gbp。串联重复序列（TRs）在许多植物基因组中占据显著部分，且常位于特定基因组位点，使其成为鉴别染色体的宝贵分子细胞遗传学工具。为了解基因组结构，我们对一个超高拷贝的167 bp TR（Pg167TR）进行了特征分析，并探索了其染色体分布及其在染色体鉴定中的效用。

方法

采用直接切口平移法对Pg167TR的聚合酶链反应扩增子以及5S和45S rDNA扩增子进行标记。使用直接荧光原位杂交（FISH）分析Pg167TR的染色体分布。

结果

最近，我们报道了一种利用rDNA和DAPI（4',6-二脒基-2-苯基吲哚）带对24对染色体进行核型分析的方法。在此，观察到Pg167TR在所有24条染色体中的独特分布，便于轻松识别各个同源染色体。此外，5S和45S rDNA探针的直接标记使得能够鉴定出两个先前未报道的5S rDNA位点，从而完善了核型。

结论

利用Pg167TR-FISH实现了对各个染色体的鉴定。染色体鉴定对于理解基因组结构很重要，我们的方法将有助于未来遗传连锁图谱的整合和基因组支架的锚定。此外，它是与相关物种进行比较研究以了解进化的良好工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/457de74e11ab/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/5b3a22358b29/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/38ebbe42ca07/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/1f11d38a18b0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/bacd5e96ede7/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/817ea0e56729/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/457de74e11ab/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/5b3a22358b29/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/38ebbe42ca07/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/1f11d38a18b0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/bacd5e96ede7/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/817ea0e56729/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8b77/5628329/457de74e11ab/gr6.jpg

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