A-T rich sequences in vertebrate DNA. A possible explanation of q-banding in metaphase chromosomes

Characterization and Comparison of the Two Mitochondrial Genomes in the Genus Rana

The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this study, we aimed to determine the complete mitogenomes of two morphologically similar Rana species (Rana hanluica and Rana longicrus) using next-generation sequencing. The entire circular mitogenome was successfully identified, with a length of 19,395 bp for R. hanluica and 17,833 bp for R. longicrus. The mitogenomes of both species contained 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region; mitogenome size varied predominantly with the length of the control region. The two synonymous codon usages in 13 PCGs showed that T and A were used more frequently than G and C. The ratios of non-synonymous to synonymous substitutions of all 13 PCGs were <1 in the Rana species, indicating that the PCGs were under purifying selection. Finally, phylogenetic relationship analyses suggested that R. hanluica and R. longicrus were classified in the R. japonica group. Our study provides valuable reference material for the taxonomy of the genus Rana.

Historical effective population size of North American hoary bat (Lasiurus cinereus) and challenges to estimating trends in contemporary effective breeding population size from archived samples

Background

Hoary bats (Lasiurus cinereus) are among the bat species most commonly killed by wind turbine strikes in the midwestern United States. The impact of this mortality on species census size is not understood, due in part to the difficulty of estimating population size for this highly migratory and elusive species. Genetic effective population size (Ne) could provide an index of changing census population size if other factors affecting Ne are stable.

Methods

We used the NeEstimator package to derive effective breeding population size (Nb) estimates for two temporally spaced cohorts: 93 hoary bats collected in 2009-2010 and an additional 93 collected in 2017-2018. We sequenced restriction-site associated polymorphisms and generated a de novo genome assembly to guide the removal of sex-linked and multi-copy loci, as well as identify physically linked markers.

Results

Analysis of the reference genome with psmc suggested at least a doubling of Ne in the last 100,000 years, likely exceeding Ne = 10,000 in the Holocene. Allele and genotype frequency analyses confirmed that the two cohorts were comparable, although some samples had unusually high or low observed heterozygosities. Additionally, the older cohort had lower mean coverage and greater variability in coverage, and batch effects of sampling locality were observed that were consistent with sample degradation. We therefore excluded samples with low coverage or outlier heterozygosity, as well as loci with sequence coverage far from the mode value, from the final data set. Prior to excluding these outliers, contemporary Nb estimates were significantly higher in the more recent cohort, but this finding was driven by high values for the 2018 sample year and low values for all other years. In the reduced data set, Nb did not differ significantly between cohorts. We found base substitutions to be strongly biased toward cytosine to thymine or the complement, and further partitioning loci by substitution type had a strong effect on Nb estimates. Minor allele frequency and base quality bias thresholds also had strong effects on Nb estimates. Instability of Nb with respect to common data filtering parameters and empirically identified factors prevented robust comparison of the two cohorts. Given that confidence intervals frequently included infinity as the stringency of data filtering increased, contemporary trends in Nb of North American hoary bats may not be tractable with the linkage disequilibrium method, at least using the protocol employed here.

The complete mitochondrial genome of Exostoma gaoligongense (Siluriformes: Sisoridae) and its phylogenetic analysis within glyptosternine catfishes

Exostoma gaoligongense is an endemic glyptosternine catfish distributed in the Nujiang River drainage, Yunnan Province, China, with few published genetic information. In this study, we sequenced and characterized the complete mitochondrial genome of E. gaoligongense, which was circular, 16529 bp in length, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, one replication origin and one control region. Phylogenetic analysis revealed that E. gaoligongense had the closest relationship with its congener E. labiatum. They clustered with the clade containing most genera of glyptosternine catfishes and then cluster with the more primitive genera Glaridoglanis and Glyptosternon.

Complete mitochondrial genome of Triplophysa nasobarbatula

The complete mitochondrial DNA genome of Triplophysa nasobarbatula was sequenced and characterized. Triplophysa nasobarbatula revealed that the complete length of its mitochondrial genome was 16,316 bp, composed of A (29.71%), C (24.79%), G (17.22%), T (28.29%), A + T (57.99%), and C + G (42.01%). Its genetic constitution and arrangement were consistent with the taxon of the Teleost, including 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 2 main non-coding regions, D-loop region and O_L region. All genes were encoded by the H-strand, except for 1 protein-coding gene (ND6) and 8 tRNA genes (tRNA-Gln, tRNA-Ala, tRNA-Cys, tRNA-Asn, tRNA-Tyr, tRNA-Ser, tRNA-Glu and tRNA-Pro) are encoded by the L-strand. Our mitochondrial genome data may provide information for taxonomic resolution, taxonomic resolution, and other studies about this genus of Triplophysa.

The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light-strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA-Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination-associated sequence, six conserved sequence blocks (CSB-1, CSB-2, CSB-3, CSB-D, CSB-E, CSB-F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.

The complete mitochondrial genome sequence of the Sichuan Digging Frog, Kaloula rugifera (Anura: Microhylidae) and its phylogenetic implications

The Sichuan Digging Frog (Kaloula rugifera) belongs to the family Dicroglossidae, which is endemic to northeastern Sichuan and southernmost Gansu provinces, in southwestern China. In this study, the complete mitochondrial genome of K. rugifera was sequenced. The mitogenome was 17,074bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the K. rugifera is 30.32% A, 25.76% C, 29.72% T, and 14.20% G, which is consistent with the lowest frequency for G content in typical amphibian animals' mitochondrial genomes. The alignment of the Kaloula species control regions exhibited high genetic variability and rich A+T content. Besides, 3 types of tandem repeat units were also identified in the control region. Phylogenetic tree demonstrated that K. rugifera was clustered together with K. borealis and K. verrucosa and they had a close relationship with each other. The complete mitogenome of K. rugifera can provide an important data for the studies on phylogenetic relationship to further explore the taxonomic status of Kaloula species.

Complete Mitochondrial Genome Sequences of Chinese Indigenous Sheep with Different Tail Types and an Analysis of Phylogenetic Evolution in Domestic Sheep

China has a long history of sheep (Ovis aries [O. aries]) breeding and an abundance of sheep genetic resources. Knowledge of the complete O. aries mitogenome should facilitate the study of the evolutionary history of the species. Therefore, the complete mitogenome of O. aries was sequenced and annotated. In order to characterize the mitogenomes of 3 Chinese sheep breeds (Altay sheep [AL], Shandong large-tailed sheep [SD], and small-tailed Hulun Buir sheep [sHL]), 19 sets of primers were employed to amplify contiguous, overlapping segments of the complete mitochondrial DNA (mtDNA) sequence of each breed. The sizes of the complete mitochondrial genomes of the sHL, AL, and SD breeds were 16,617 bp, 16,613 bp, and 16,613 bp, respectively. The mitochondrial genomes were deposited in the GenBank database with accession numbers KP702285 (AL sheep), KP981378 (SD sheep), and KP981380 (sHL sheep) respectively. The organization of the 3 analyzed sheep mitochondrial genomes was similar, with each consisting of 22 tRNA genes, 2 rRNA genes (12S rRNA and 16S rRNA), 13 protein-coding genes, and 1 control region (D-loop). The NADH dehydrogenase subunit 6 (ND6) and 8 tRNA genes were encoded on the light strand, whereas the rest of the mitochondrial genes were encoded on the heavy strand. The nucleotide skewness of the coding strands of the 3 analyzed mitogenomes was biased toward A and T. We constructed a phylogenetic tree using the complete mitogenomes of each type of sheep to allow us to understand the genetic relationships between Chinese breeds of O. aries and those developed and utilized in other countries. Our findings provide important information regarding the O. aries mitogenome and the evolutionary history of O. aries inside and outside China. In addition, our results provide a foundation for further exploration of the taxonomic status of O. aries.

The complete mitochondrial genome of Rhodeus lighti (Cypriniformes: Cyprinidae): sequencing and analysis

Phylogenetic placement of Rhodeus lighti (R. lighti) remains unresolved. We determined the first complete mitochondrial genome of R. lighti (Cypriniformes: Cyprinidae). The genome is 16,597 bp in length. It consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions. The gene composition and order were similar to most of the other vertebrates. The complete mitochondrial genome sequence of R. lighti should contribute towards clarifying the systematics of Rhodeus fishes. The phylogenetic relationships using partitioned Neighbor-Joining tree indicated that (((((Pseudorasbora, Rhodeus) Ctenopharyngodon) (Acheilognathus, Tanakia) Carassius)) Danio rerio). This study will contribute to confirm the phylogenetic status of Rhodeus within family Cyprinidae.

Complete mitochondrial genome of the Tyto longimembris (Strigiformes: Tytonidae)

The complete mitochondrial genome of Tyto longimembris has been determined in this study. It is 18,466 bp in length and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a non-coding control region (D-loop). The overall base composition of the heavy strand of the T. longimembris mitochondrial genome is A: 30.1%, T: 23.5%, C: 31.8% and G: 14.6%. The structure of control region should be characterized by a region containing tandem repeats as two definitely separated clusters of tandem repeats were found. This study provided an important data set for phylogenetic and taxonomic analyses of Tyto species.

Complete mitochondrial genome of the Tamiops swinhoei (Rodentia: Sciuridae)

The complete mitochondrial genome of Tamiops swinhoei has been determined in this study. It is 16,513 bp in size and consists of 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes and one non-coding region (D-loop). The overall base composition of the heavy strand of the T. swinhoei mitochondrial genome is A: 32.63%, T: 28.67%, C: 26.33% and G: 12.37%. The alignment of the Tamiops species control regions exhibited high genetic variability and rich A + T content (63.42%).

Complete mitochondrial genome of the natural triploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae)

Abstract The complete mitochondrial genome of the natural triploid loach Misgurnus anguillicaudatus is a circular molecule of 16,646 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 main noncoding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and 8 tRNAs. The control region is 918 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the triploid M. anguillicaudatus.

Complete mitochondrial genome of Triplophysa robusta (Teleostei: Cypriniformes: Balitoridae)

The complete mitochondrial genome of the Triplophysa robusta has been determined in this study. It is 16,572 bp in size and consists of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one non-coding control region (D-loop). The overall base composition of the heavy strand of the T. robusta mitochondrial genome was A: 28.20%, T: 28.27%, C: 25.37%, and G: 18.16%. The total length of the 13 protein-coding genes was 11,428 bp. Analysis of the genes indicated the high genetic variability among Triplophysa species.

Complete mitochondrial genome of the natural pentaploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae)

The complete mitochondrial genome of the natural pentaploid loach Misgurnus anguillicaudatus is a circular molecule of 16,643 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two main noncoding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. The control region is 918 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the pentaploid M. anguillicaudatus.

Complete mitochondrial genome of Schizopygopsis malacanthus (Teleostei: Cypriniformes: Cyprinidae)

The complete mitochondrial genome of Schizopygopsis malacanthus is a circular molecule of 16,677 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 main non-coding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. The control region is 938 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the S. malacanthus.

Complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Ancherythroculter nigrocauda (♂)

The complete mitochondrial genome of the hybrid of Megalobrama amblycephala (♀) × Ancherythroculter nigrocauda (♂) is 16,623 bp in size, consisting of 13 protein coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 main non-coding regions. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for ND6 and 8 tRNAs. The overall nucleotide composition was 31.23% A, 24.68% T, 27.90% C, and 16.19% G, with an A + T content of 55.91%. The mitochondrial genome sequence data may provide useful information for the elucidation of evolutionary mechanisms in the hybrid fish of Cyprinidae.

Comparative analysis of mitochondrial genomes in distinct nuclear ploidy loach Misgurnus anguillicaudatus and its implications for polyploidy evolution

Misgurnus anguillicaudatus has several natural ploidy types. To investigate whether nuclear polyploidy have an impact on mitochondrial DNA (mtDNA), the complete mitochondrial genomes (mitogenomes) of five distinct ploidy M. anguillicaudatus (natural diploid, triploid, tetraploid, pentaploid and hexaploid), which were collected in central China, were sequenced and analyzed. The five mitogenomes share the same gene arrangement and have similar gene size, base composition and codon usage pattern. The most variable regions of the mitogenome were the protein-coding genes, especially the ND4L (5.39% mutation rate). Most variations occurred in tetraploids. The phylogenetic tree showed that the tetraploid M. anguillicaudatus separated early from other ploidy loaches. Meanwhile, the mitogenomes from pentaploids, and hexaploids have the closest phylogenetic relations, but far from that of tetraploids, implying that pentaploids and hexaploids could not be formed from tetraploids, possibly from the diploids and triploids. The genus Misgurnus species were divided into two divergent inter-genus clades, and the five ploidy M. anguillicaudatus were monophyletic, which support the hypotheses about the mitochondrial introgression in loach species.

Mitochondrial genome of silver gudgeon, Squalidus argentatus (Teleostei, Cypriniformes)

In this paper, we first determined the complete mitochondrial genome sequence of Squalidus argentatus, which was 16,607 bp in size and the whole base composition was estimated to be 30.48% A, 25.45% T, 27.36% C, 16.72% G with AT bias of 55.93%. The complete mitogenome comprised 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 1 control region, with the gene order and content identical to other vertebrate mitogenomes. The complete mitogenome of S. argentatus provides the valuable information for population genetics and phylogeography studies on this species.

Complete mitochondrial genome of the Amur weatherfish, Misgurnus mohoity (Teleostei: Cypriniformes: Cobitididae)

The complete mitochondrial genome of the Amur weatherfish, Misgurnus mohoity is a circular molecule of 16,566 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and 2 main non-coding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. The control region is 915 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the M. mohoity.

Mitochondrial genome of the natural tetraploid loach Misgurnus anguillicaudatus

The mitochondrial genome of the natural tetraploid loach Misgurnus anguillicaudatus is a circular molecule of 16,645 bp in length, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two main noncoding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. All the protein-coding genes are initiated with ATG except for COX1, which began with GTG instead. However, the termination codons of 13 protein-coding genes are varied with TAA, TA-, T-- or TAG. The control region is 917 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the tetraploid M. anguillicaudatus.

The complete mitochondrial genome sequence analysis of Tibetan argali (Ovis ammon hodgsoni): implications of Tibetan argali and Gansu argali as the same subspecies

The genus Ovis (Bovidae, Artiodactyla) includes six species, i.e. Ovis ammon, Ovis aries, Ovis canadensis, Ovis dalli, Ovis nivicola and Ovis vignei. Based on morphology, geographical location, habitat, etc., the species O. ammon is divided into nine subspecies. The near threatened Tibetan argali is distributed across the Tibetan Plateau and its peripheral mountains, and believed to be one of the O. ammon subspecies (O. a. hodgsoni). However, considering its morphological features and distributions, a question has been proposed by some researchers about the subspecies status of Tibetan argali. In this study, we employed complete mitochondrial DNA (mtDNA) to explore the phylogenetic relationship and population genetic structure of Tibetan argali. The results revealed that the nucleotide composition, gene arrangement and codon usage pattern of the mitochondrial genome of Tibetan argali are similar to those of other caprines. Phylogenetic analyses showed that Tibetan argali was clustered with O. ammon. Interestingly, five Tibetan argali individuals and one of the three Gansu argali (O. a. dalailamae) individuals were clustered in the same branch, which is a sister group to other two Gansu argali individuals. Together with morphological characteristics, our results suggested that Tibetan argali and Gansu argali may belong to the same subspecies (O. a. hodgsoni) of O. ammon, rather than two different subspecies.

Complete mitochondrial genome of the natural hexaploid loach, Misgurnus anguillicaudatus (Teleostei: Cypriniformes: Cobitididae)

The complete mitochondrial genome of the natural hexaploid loach Misgurnus anguillicaudatus is a circular molecule of 16,643 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 main noncoding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. The control region is 918 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the hexaploid M. anguillicaudatus.

Complete mitochondrial genome of the stone loach, Triplophysa stoliczkae (Teleostei: Cypriniformes: Balitoridae)

The complete mitochondrial genome of the stone loach Triplophysa stoliczkae is 16,571 bp in size, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a noncoding control region. As in other vertebrates, most mitochondrial genes are encoded on the heavy strand, except for nd6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the heavy strand of the T. stoliczkae mitochondrial genome is A: 28.1%, T: 29.0%, C: 25.0%, and G: 17.9%. The alignment of the Triplophysa species control regions exhibited high genetic variability and rich A+T content.

Influence of percentage of guanine molecules, OH radicals, UV irradiation and temperature on electrooxidation of short synthetic oligonucleotides

The electrooxidation of short synthetic 20-nucleotides DNA sequences with various amount of guanine molecules has been studied in a wide temperature range by square wave voltammetry and the results were compared with UV-vis and CD spectra. A twofold increase of dsDNA voltammetric peak, related to an increase in the number of electrons transferred in the guanine electrooxidation process was found to begin at a temperature lower by circa 20 °C compared to the well known increase of the dsDNA absorbance upon denaturation. Since the dsDNA voltammetric peaks are related directly to the electrooxidation of guanine and adenine, early conformational changes in dsDNA are responsible for this effect. An increase in percentage of guanine in the DNA chains caused a delay in the conformational, predenaturation changes. An exception to this behavior was found for polyguanine (100% guanine). Interestingly, two distinct ranges of change in ellipticity in the CD spectra correlate well with the changes obtained by voltammetry. We have also checked the influence of OH radicals and UV irradiation on the dsDNA oxidation.

The involvement of nucleosomes in Giemsa staining of chromosomes. A new hypothesis on the banding mechanism

A new hypothesis is proposed on the involvement of nucleosomes in Giemsa banding of chromosomes. Giemsa staining as well as the concomitant swelling can be explained as an insertion of the triple charged hydrophobic dye complex between the negatively-charged super-coiled helical DNA and the denatured histone cores of the nucleosomes still present in the fixed chromosomes. New cytochemical data and recent results from biochemical literature on nucleosomes are presented in support of this hypothesis. Chromosomes are stained by the Giemsa procedure in a purple (magenta) colour. Giemsa staining of DNA and histone (isolated or in a simple mixture) in model experiments results in different colours, indicating that a higher order configuration of these chromosomal components lies at the basis of the Giemsa method. Cytophotometry of Giemsa dye absorbance of chromosomes shows that the banding in the case of saline pretreatment is due to a relative absence of the complex in the faintly coloured bands (interbands). Pretreatment with trypsin results in an increase in Giemsa dye uptake in the stained bands. Cytophotometric measurements of free phosphate groups before and after pretreatment with saline, reveal a blocking of about half of the free phosphate groups indicating that a substantial number of free amino groups is still present in the fixed chromosomes. Glutaraldehyde treatment inhibited Giemsa-banding irreversibly while the formaldehyde-induced disappearance of the bands could be restored by a washing procedure. These results correlate with those of biochemical nucleosome studies using the same aldehydes. Based on these findings and on the known properties of nucleosomes, a mechanism is proposed that explains the collapse of the chromosome structure when fixed chromosomes are transferred to aqueous buffer solutions. During homogeneous Giemsa staining reswelling of the unpretreated chromosome is explained by insertion of the hydrophobic Giemsa complex between the hydrophobic nucleosome cores and the superhelix DNA. Selective Giemsa staining of the AT-enriched bands after saline pretreatment is thought to be due to the, biochemically well-documented, higher affinity of arginine-rich proteins present in the core histones for GC-enriched DNA, which prevents the insertion of the Giemsa complex in the interbands. Production of Giemsa bands by trypsin pretreatment can be related to the action of this enzyme on the H1 histones and subsequent charge rearrangements.(ABSTRACT TRUNCATED AT 400 WORDS)

Characterization of extrachromosomal DNA in the flesh fly Sarcophaga bullata

The polytene pupal foot pad cells of the flesh fly Sarcophaga bullata contain numerous extrachromosomal DNA containing granules. We have determined both the origin and the nature of the DNA sequences present in these granules. Studies done with quinacrine staining of seven day old pupal foot-pad polytene nuclei showed that the granules fluoresced very brightly while the chromosomal bands to which the granules were attached did not. The only other highly fluorescent regions of the polytene karyotype were the centromeric heterochromatin of chromosomes C and E and several bands associated with the nucleolus of Chromsome A. When polytene nuclei were hybridized in situ with cRNA made from highly repetitive DNA, many of the granules positively labeled. Most of the label on these slides was concentrated on the centromeric heterochromatin of chromosomes C and E. Quinacrine staining of the foot-pad cells at very early stages of pupal development showed that when granules were present, they were always closely associated with the same two centromeric regions, those of chromosomes C and E. Since the highly repetitive DNA located in these centromeric regions is underreplicated, we conclude that the granules result from an extrusion process which takes place early during the polytenization of these cells. The chromosomal integrity of the centromeric heterochromatin of chromosomes C and E is apparently disrupted and repetitive sequences are dissociated from the chromosomes as DNA granules which then secondarily become associated with chromosomal bands throughout the nucleus.