Genomic DNA is constantly exposed to various types of exogenous and endogenous stimulants that induce DNA lesions, including single-strand breaks (SSBs) and double-strand breaks (DSBs). Unrepaired DNA damages eventually cause adverse effects on a wide range of cellular and physiological processes; therefore, it is of great interest to map the damaged and repaired DNA to elucidate the damage distribution on a genome-wide scale. In the past decade, several sequence-based approaches for detection and quantification of such modified DNA have been established via technological innovation in sequencing analysis, which have expanded our understanding of DNA damage and repair. This review provides an overview of next-generation sequence-based methods for damaged DNA analysis with a focus on DNA strand breaks, SSBs, and DSBs.
In this study, chromosome numbers of five Cardamine taxa [C. bulbifera Crantz, C. impatiens var. pectinata (Pall. ex DC.) Trautv., C. lazica Boiss. & Bal., C. tenera Gmel ex Mey. and C. graeca L.] from Turkey have been informed for the first time. The chromosome numbers were determined as 2n=4x=24 in C. bulbifera, 2n=2x=16 in C. impatiens var. pectinata and C. tenera, 2n=2x=14 in C. lazica, and 2n=2x=12 in C. graeca. Also, C. bulbifera was different from the others with having satellite. Chromosomes of the studied taxa were assessed according to the terms of a systematic overview of some previous cytogenetic reports.
Bride rose poppy (Papaver fugax Poir.) is a source of several pharmaceutical benzylisoquinoline alkaloids such as morphine and codeine. In order to determine the best method for the production of the autotetraploid population in this species, seeds and seedlings were treated with different colchicine concentrations (0, 0.05, 0.1, 0.2, and 0.5%) for 12, 24, and 48 h. Flow cytometry and chromosome observation from leaves confirmed the chromosome doubling in some of the treated plants. Chromosome doubled plants were studied in terms of morphological and physiological traits. The highest induction frequency of the tetraploid plants (18.35%) obtained by treatment of seeds or seedlings with 0.1% colchicine for 48 h. In induced tetraploid plants, the density of stomata, average internode length, and plant height decreased, while, stomata size, leaf thickness, length and width, number of leaves, fresh and dry weight of plants, capsule size, chlorophyll, protein, and carbohydrate contents and activity of catalase and peroxidase antioxidant enzymes increased.
Artificial tetraploid and octaploid strains were induced from the wild species of Drosera rotundifolia (2n=2x=20) and D. anglica (2n=4x=40), respectively. The optimal condition of colchicine-treatments for polyploid inductions was determined first. A flow cytometry (FCM) analysis showed that the highest mixoploid score of D. rotundifolia was 20% in the treatment of 0.3% for 2 days (d), or 0.5% for 3 d, while the highest mixoploid score of D. anglica was 20% in the treatment of 0.5% for 2 d. Next, to remove chimeric cells, adventitious bud inductions were carried out using the FCM-selected individuals in both species. One strain from a total of 360 colchicine-treated leaf explants in each species had pure chromosome-double numbers of 2n=40 (tetraploid) in D. rotundifolia and 2n=80 (octaploid) in D. anglica. In both species, the guard cell sizes of the chromosome-doubled strains were larger than those of the wild types. The leaves of the chromosome-doubled strains of D. rotundifolia were larger than those of the wild diploid D. rotundifolia, while the leaves of the chromosome-doubled strains of D. anglica were smaller than those of the wild tetraploid D. anglica.
Nyssaceae, consisting of 36 species in five genera (Camptotheca, Davidia, Diplopanax, Mastixia and Nyssa), are poorly known concerning their karyomorphology. Here we present karyomorphological features of seven species in all five genera and discuss chromosome evolution in the family. With a few dubious chromosome counts, information available shows that the chromosome number is consistent within a genus, i.e., 2n=42 in Campthotheca, Davidia and Diplopanax, 2n=44 in Nyssa, and 2n=26 in Mastixia. Their distribution on a phylogenetic tree suggests that 2n=42 is plesiomorphic with 2n=44 and 2n=26 apomorphic. Karyotype analyses show that 2n=42 of Camptotheca and Davidia comprise six sets of seven chromosomes, suggesting that Nyssaceae are of hexaploid origin with the basic number x=7.
India is a repository of many native crop species of the family Cucurbitaceae contributing to the agro-economic growth of the country. Luffa acutangula (L.) Roxb. is one of the major vegetables of Cucurbitaceae with extensive distribution across the eco-climatic zones. Relationships with wild relatives are one of the fundamental requirements to expand the genetic base of cultivated crops like Luffa. We have adopted the enzymatic maceration and air-drying (EMA) method to accomplish comparative karyotype analysis and fluorescence banding patterns on chromosomes of the ridged gourd and its wild relative L. echinata Roxb. The species have 2n=26 chromosomes. The karyotypes of both species have six satellited chromosomes and a predominance of nearly metacentric pairs. Prominent 4′,6-diamidino-2-phenylindole (DAPI) bands have been encountered in all chromosomes of the two species while six distinct chromomycin A3 (CMA) bands were found associated with satellites. The conservation of banding patterns between the species raises the possibility to revise genomic kinships and evolutionary distance. Our study provides a chromosomal dataset of the Indian Luffa germplasm that may be utilized for genome research and programmed breeding strategies.
Costus spicatus (Jacq.) Sw. is a species of Costaceae (Zingiberaceae) family, which is most familiar as a medicinal plant because of its therapeutic values. A detailed karyological analysis has been accomplished through aceto-orcein staining, chromosome number was reported 2n=18 along with the presence of one B-chromosome, which exhibited with a karyotype formula as 16m+2sm. It would be a new report for C. spicatus. The esteems of various karyomorphological indices regarding the aspect of asymmetry, demonstrated its symmetry in the karyotype. Therefore, the basic chromosomal information of the current investigation will contribute to deposit chromosomal knowledge and conservation of plant genetic resources of C. spicatus as an invaluable medicinal plant.
Panstrongylus megistus (Burmeister) and Triatoma infestans (Klug), blood-sucking hemipterans in the Reduviidae family, are vectors of Chagas disease. Both species exhibit holocentric chromosomes and conspicuous heterochromatin bodies (chromocenters), but they differ in chromosome number and chromocenter structure and composition patterns. In the Malpighian tubule cells of T. infestans, the chromocenters are positioned close to the nuclear periphery throughout the life of the insect, with no apparent association with overall gene silencing. Because chromocenter topology may vary in different species of the same genus and the spatial distribution pattern of the chromocenter of P. megistus has not yet been described, we used confocal microscopy to evaluate the spatial organization of this heterochromatic body in the Malpighian tubule cells of this species during nymphal development and in the adult phase compared to data reported for T. infestans. Despite the differences in chromocenter composition, structural pattern, and size between P. megistus and T. infestans, the chromocenter of P. megistus nymphs and adults, similar to those of T. infestans, was found to occupy a nonincidental position close to the nuclear periphery. The topological pattern observed at the chromocenter of P. megistus, which is consistent with the previous report of highly concentrated dimethylated histone H3 lysine 9 residues at the nuclear periphery was not found to be directly related to gene silencing or modulation.
The contents of auxin (indole-3-acetic acid, IAA), cytokinins, and abscisic acid (ABA) were determined in explants (megagametophyte and embryo), proliferating embryonal-suspensor mass (ESM), and non-embryogenic callus of Pinus sibirica and Larix sibirica. Furthermore, the localization of hormones in the cells was studied with immunohistochemical analysis. It was shown that the formation of embryogenic cultures in both species is associated with the content of phytohormones and their localization in cells. In L. sibirica the content of IAA in ESM was about 100 times higher than in non-embryogenic calli. At the same time, a low ABA content was characteristic of embryogenic cultures. Non-embryogenic callus contains an increased content of cytokinins and ABA. The transition of somatic cells to the path of embryogenic development is characterized by elongation of cells, their asymmetric division, and localization of IAA at one of the ends of elongated cells. Non-embryogenic callus consisted of isodiametric, actively dividing cells.
Chromosome numbers of wild species in the genus Epidendrum have previously been reported in the range of 2n=24–240. However, the ploidy levels of cultivars in the given genus originating from interspecific hybridization among several wild species have never been reported. To elucidate their ploidy levels, we analyzed the chromosome number of cultivars and related wild species. Four wild species showed a new record of chromosome number in the present study, namely, E. radicans 2n=38, 80, E. secundum 2n=60, and E. cinnabarinum 2n=64. Six cultivars examined were revealed to have more chromosomes than the wild species, with a range of 2n=84–164, suggesting that the cultivars have high polyploid levels. A significant correlation between the nuclear DNA amount and the chromosome number in wild species as well as cultivars was observed. Those cultivars originated from hybridization. Thus, the results from the present study suggest that the polyploid cultivars in this genus could have resulted from pollination involving unreduced gametes during breeding.
Radiation-induced chromosomal aberrations in cultured human peripheral blood lymphocytes have been investigated as a validated measure for biodosimetry. The analysis of the kinetics of cells carrying chromosomal aberrations in the early stage of cell proliferation is expected to provide a better understanding of the mechanisms underlying the transmission and persistence of chromosomal aberrations. However, studies on the fate of unstable aberrations in consecutive divisions are limited. In this work, morphology-based analyses of the chromosomal aberrations in the second metaphase (M2) cells by comparing with those in the first metaphase (M1) cells were conducted by using peripheral blood lymphocytes cultured in the presence of 5-bromo-2′-deoxyuridine (BrdU) for 48 and 72 h after in vitro 2.0 Gy gamma irradiation. Unstable chromosomal aberrations were analyzed by 4′,6-diaminido-2-phenylindole (DAPI) staining, in combination with fluorescence in situ hybridization (FISH) using painting probes of three different colors (three-color FISH). As a result, a high frequency of duplicated fragments was detected in unstable M2 cells, implying the persistence of cells with excess fragments generated in the first mitotic division by unequal segregation. A close microscopic observation of M2 cells showed irregularly shaped chromatin structure generated probably through the asynchronous replication of fragments generated in the first mitotic division. When compared with the results of M1 cells, the frequency of M2 cells carrying unstable chromosomal aberrations decreased by 43% and that of dicentric chromosomes per cell decreased by 46%. By revisiting morphology-oriented microscopic examinations, the cytogenetic features of cells carrying unstable chromosomal aberrations were precisely described.
A cytogenetic analysis of chromosomes in mitotic metaphase of Dermatophyllum secundiflorum, a recently synonymized species, collected in the municipality of Cardonal (Hidalgo State, Mexico) was performed. The objective was not only to obtain the karyotype, but also cytogenetic markers such as secondary constrictions and satellites. A conventional method of air drying and Giemsa staining was used in cells from root meristems which confirmed a 2n=18. The formula for the haploid karyotype was 6m+2sm+1stsat. The secondary constrictions and microsatellites were clearly located on the short arm of the st chromosomes, which differs from a previous study that placed them on metacentric chromosomes. Occasionally, metaphase plates exhibited satellite associations involving the secondary constrictions and satellites of the st chromosomes, the role of which is discussed in light of the limited information available.
The tropical Asian genus Holigarna Buch.-Ham. ex Roxb. (Anacardiaceae) is represented by seven species in India. The present paper describes the somatic chromosome number and karyotype analysis of the H. arnottiana Hook. f. It is an endemic species to the southern Western Ghats. Chromosome number is reported to be 2n=58 for the first time in the genus Holigarna. The study suggests that the genus is related the genus Semecarpus L.f. that exhibits the same chromosome number. H. arnottiana exhibited the karyotype formula: 21m+8sm. Karyotype was moderately symmetrical and fell into the 4b category of Stebbins.
It is thought that mitochondria were generated by the symbiosis of autonomous α-proteobacteria and a eukaryote-like organism derived from an archaeon of the species Sulfolobus. Soon after the symbiosis, most of the genome of the α-proteobacterium, which was required for autonomy, was lost. Many genes were transferred into the host genome. However, a small amount of DNA—the mitochondrial genome (mt-genome, mtDNA)—remained in the symbiotic organelle. The primitive eukaryotic cells increased the mtDNA copy number and formed a mitochondrial nucleus (mt-nucleus). The primitive unicellular eukaryote evolved into organisms with one mitochondrion containing multiple mtDNA copies per cell, and organisms with multiple mitochondria with a small number of mtDNA copies in each cell. There have been many studies on the mitochondria and mt-genomes of amoeba, plants, and animals which contain many mitochondria per cell, but only a few studies have reported morphological characteristics of the mitochondria and their genomes in primitive unicellular organisms that have only a single mitochondrion per cell. Here, we show that centrally located mt-nuclei in the primitive red alga Cyanidioschyzon merolae form smooth rings following the application of a drying method that produces slight cell swelling. We discuss regulatory mechanisms for genome function in endosymbiotic organelles on the basis of the differences between the copy number of mtDNA in smooth-ring shaped mt-nuclei and plastid DNA in bead-shaped plastid nuclei.
Eriocaulon dalzellii, E. sharmae and E. ramnadense are endemic to the Western Ghats of India. Chromosome numbers for these species have been reported for the first time. E. dalzellii and E. sharmae are tetraploid with 2n=4x=32 chromosomes whereas E. ramnadense is a triploid with 2n=3x=24 chromosomes.