comparative-karyotype-analysis-lycoris-aurea-herb-populations-using

Comparative Karyotype Analysis of <em>Lycoris aurea</em> Herb Populations Using Fluorochrome Banding and 45S and 5S rDNA-FISH

To understand karyotype variation in eight populations, detailed karyotypes were meticulously established using chromosomal measurements, fluorescence ...

Hunan University

In this study, we performed sequentially combined PI and DAPI (CPD) staining and FISH with two different 45S rDNA clones on meiotic pachytene and mitotic metaphase chromosomes in tomato. Ten red CPD bands were shown on eight pachytene bivalents, and 12 bands were shown on six pairs of mitotic metaphase chromosomes. The CPD bands exhibited on mitotic metaphase chromosomes corresponded to the prominent bands exhibited on the pachytene chromosomes. The distinctive CPD bands, which could be constantly and clearly detected using the CPD staining procedure we improved, provided new landmarks for chromosome identification in tomato. FISH with the tomato 45S rDNA clone revealed very strong signal(s) in the satellite(s) on the short arm of chromosome 2 as well as weak signals in five CPD banded regions at pachytene or four pairs of CPD banded regions at metaphase chromosomes. However, FISH with pTa71 plasmid only revealed signals in the satellite. Considering the difference in sequence between the two rDNA clones, we inferred that only the satellite contains the coding regions of 45S rDNA unit in tomato. The property of CPD bands as well as the DNA sequences probably involved in the five CPD banded regions was discussed.

CPD banding patterns and identification of 45S rDNA sites in tomato.

Centromeres are the chromosomal domains necessary for faithful chromosome segregation and transmission during mitosis and meiosis in eukaryotes. In the last decade, centromeres in some plant species including Arabidopsis, rice and maize have been deeply studied at molecular level. Centromeric DNAs evolve rapidly and are little conserved among various plants, but the types of centromeric DNA sequences and their organization patterns within centromeres are basically similar in plants. Plant centromeres are usually composed of clusters of tandemly arrayed satellite repeats that are interspersed with centromere-specific retrotransposons. In contrast to centromeric DNA, structural and transient centromeric/kinetochoric proteins are conserved among eukaryotes including plants. As the cases in other eukaryotes, the presence of CENH3 (centromeric histone H3)-containing nucleosomes is the fundamental feature of plant functional centromeres, and CENH3 plays critical roles in the identity and maintenance of plant centromeric chromatin.

[Advances in research of the structure and function of plant centromeres].

The distribution of repetitive DNAs along chromosomes is one of the crucial elements for understanding the organization and the evolution of plant genomes. Using a modified genomic in situ hybridization (GISH) procedure, fluorescence in situ hybridization (FISH) with genomic DNA to their own chromosomes (called self-genomic in situ hybridization, self-GISH) was carried out in six selected plant species with different genome size and amount of repetitive DNA. Nonuniform distribution of the fluorescent labeled probe DNA was observed on the chromosomes of all the species that were tested. The signal patterns varied among species and were related to the genome size. The chromosomes of the small Arabidopsis genome were labeled almost only in the pericentromeric regions and the nucleolus organizer regions (NORs). The signals in the relatively small genomes, rice, sorghum, and Brassica oleracea var. capitata L., were dispersed along the chromosome lengths, with a predominant distribution in the pericentromeric or proximal regions and some heterochromatic arms. All chromosomes of the large genomes, maize and barley, were densely labeled with strongly labeled regions and weakly labeled or unlabeled regions being arranged alternatively throughout the lengths. In addition, enhanced signal bands were shown in all pericentromeres and the NORs in B. oleracea var. capitata and in all pericentromeric regions and certain intercalary sites in barley. The enhanced signal band pattern in barley was found consistent with the N-banding pattern of this species. The GISH with self-genomic DNA was compared with FISH with C(o)t-1 DNA in rice, and their signal patterns are found to be basically consistent. Our results showed that the self-GISH signals actually reflected the hybridization of genomic repetitive DNAs to the chromosomes, thus the self-GISH technique would be useful for revealing the distribution of the regions where repetitive DNAs concentrate along chromosomes and some chromatin differentiation associated with repetitive DNAs in plants.

The distribution of repetitive DNAs along chromosomes in plants revealed by self-genomic in situ hybridization.

In order to analyze the conservation of maize centromeric satellite DNA (CentC) and centromeric retrotransposon (CRM) in the subspecies and relatives of Zea mays, dual fluorescence in situ hybridization (FISH) was used to detect the existence and distribution of the above two repetitive sequences in Zea mays ssp. mexicana, Z. diploperennis, Z. perennis, Tripsacum dactyloides, Coix lacryma-jobi, and Sorghum bicolor. In Z. mays ssp. mexicana, Z. diploperennis, and Z. perennis, both CentC and CRM probes produced strong or relatively strong signals in the centromeric regions of all chromosomes. There was an obvious variation in the intensity of hybridization signals on different chromosomes, indicating that different centromeres have different amounts of CentC and CRM sequences. In some centromeres, the intensity of CentC signals differed from that of CRM signals and was free from overlapping. In T. dactyloides, only weak CentC and CRM signals were detected in the centromeric regions of most chromosomes, while in C. lacryma-jobi and S. bicolor only relatively strong or strong CRM signals primarily located in the centromeric regions were detected. This result indicates that CentC is highly conserved among the subspecies of Z. mays and the species of Zea, and has high conservation in Tripsacum, a genus that is most closely related to Zea, and CRM is conserved among the species of grass family either closely or distantly related to Zea.

[Detection of maize centromeric repeats in the relatives of maize using fluorescence in situ hybridization].

To have an insight into the karyotype variation of eight Cucurbitaceae crops including  Linnaeus, 1753,  Linnaeus, 1753,  (Thunberg, 1794) Matsumura et Nakai, 1916,  (Thunberg, 1784) Cogniaux, 1881,  Linnaeus, 1753,  (Linnaeus, 1753) Roemer, 1846, Lagenariasicerariavar.hispida (Thunberg, 1783) Hara, 1948 and  Duchesne ex Poiret, 1819, well morphologically differentiated mitotic metaphase chromosomes were prepared using the enzymatic maceration and flame-drying method, and the chromosomal distribution of heterochromatin and 18S-5.8S-26S rRNA genes (45S rDNA) was investigated using sequential combined PI and DAPI (CPD) staining and fluorescence  hybridization (FISH) with 45S rDNA probe. Detailed karyotypes were established using the dataset of chromosome measurements, fluorochrome bands and rDNA FISH signals. Four karyotype asymmetry indices, CV, CV, M and Stebbins' category, were measured to elucidate the karyological relationships among species. All the species studied had symmetrical karyotypes composed of metacentric and submetacentric or only metacentric chromosomes, but their karyotype structure can be discriminated by the scatter plot of M vs. CV. The karyological relationships among these species revealed by PCoA based on , 2, TCL, M, CV and CV was basically in agreement with the phylogenetic relationships revealed by DNA sequences. CPD staining revealed all 45S rDNA sites in all species, (peri)centromeric GC-rich heterochromatin in , , ,  and , terminal GC-rich heterochromatin in . DAPI counterstaining after FISH revealed pericentromeric DAPI heterochromatin in . rDNA FISH detected two 45S loci in five species and five 45S loci in three species. Among these 45S loci, most were located at the terminals of chromosome arms, and a few in the proximal regions. In , individual chromosomes can be precisely distinguished by the CPD band and 45S rDNA signal patterns, providing an easy method for chromosome identification of cucumber. The genome differentiation among these species was discussed in terms of genome size, heterochromatin, 45S rDNA site, and karyotype asymmetry based on the data of this study and previous reports.

﻿Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH.

To characterize the chromosomes of the four species of  Miller, 1754, used in traditional Chinese medicine,  Hua, 1892,  Collett et Hemsley, 1890,  (Miller, 1768) Druce, 1906, and  Redouté, 1811, and have an insight into the karyotype variation of the genus , fluorescence  hybridization (FISH) with 5S and 45S rDNA oligonucleotide probes was applied to analyze the karyotypes of 9 populations of the four species. Detailed molecular cytogenetic karyotypes of the 9 populations were established for the first time using the dataset of chromosome measurements and FISH signals of 5S and 45S rDNA. Four karyotype asymmetry indices, CV, CV, M and Stebbins' category, were measured to elucidate the asymmetry of the karyotypes and karyological relationships among species. Comparison of their karyotypes revealed distinct variations in the karyotypic parameters and rDNA patterns among and within species. The basic chromosome numbers detected were  = 9, 11 and 13 for ,  = 15 for ,  = 10 and 11 for , and  = 12 for . The original basic chromosome numbers of the four species were inferred on the basis of the data of this study and previous reports. All the 9 karyotypes were of moderate asymmetry and composed of metacentric, submetacentric and subtelocentric chromosomes or consisted of two of these types of chromosomes. Seven populations have one locus of 5S rDNA and two loci of 45S rDNA, and two populations added one 5S or 45S locus. The karyological relationships among the four species revealed by comparison of rDNA patterns and PCoA based on , 2, TCL, CV, M and CV were basically accordant with the phylogenetic relationships revealed by molecular phylogenetic studies. The mechanisms of both intra- and inter-specific dysploidy in  were discussed based on the data of this study and literature.

Article	Year
CPD banding patterns and identification of 45S rDNA sites in tomato. Yi chuan xue bao = Acta genetica Sinica\| PubMed ID: 16252707	2005
[Advances in research of the structure and function of plant centromeres]. Yi chuan = Hereditas\| PubMed ID: 17138549	2006
The distribution of repetitive DNAs along chromosomes in plants revealed by self-genomic in situ hybridization. Journal of genetics and genomics = Yi chuan xue bao\| PubMed ID: 17560530	2007
[Detection of maize centromeric repeats in the relatives of maize using fluorescence in situ hybridization]. Yi chuan = Hereditas\| PubMed ID: 20233704	2010
Comparative karyotype analysis of eight Cucurbitaceae crops using fluorochrome banding and 45S rDNA-FISH. Comparative cytogenetics\| PubMed ID: 37305810	2023
Molecular cytogenetic characterization of 9 populations of four species in the genus (Asparagaceae). Comparative cytogenetics\| PubMed ID: 38798789	2024

Chaowen She

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