The chromosomes of Rhynchosciara baschanti (Diptera: Sciaridae): Molecular cytogenetic comparisons with taxa in the americana-like group

Genome ◽  
2000 ◽  
Vol 43 (5) ◽  
pp. 786-795 ◽  
Author(s):  
Ann Jacob Stocker ◽  
Eduardo Gorab
Keyword(s):  
Dna Sequences ◽  
Thymidine Incorporation ◽  
Polytene Chromosomes ◽  
Chromosome Analysis ◽  
Chromosomal Evolution ◽  
Single Copy ◽  
Molecular Cytogenetic ◽  
Dna Puffs ◽  
Morphological Differences ◽  
Active Genes

Polytene chromosome analysis is presented for Rhynchosciara baschanti, a species belonging to the americana-like group of Rhynchosciara. R. baschanti chromosomes show morphological differences in centromeric and telomeric regions compared to two other members within the group, R. americana and R. hollaenderi. In addition, fixed band and autosomal inversion differences were noted. Physical mapping data showed synteny among the taxa under study for DNA puffs and single-copy or histone gene probes, whereas rDNA and poly-(r)A probes showed different diagnostic patterns. The activity of developmentally active genes and the pattern of thymidine incorporation into DNA puff sites of R. baschanti are consistent with those found in the two previously studied species, except for lower levels of expression at some of these sites. These results suggest that differential duplication of specific DNA sequences, in particular repetitive and homopolymeric DNA, has played a role in the chromosomal evolution of these Rhynchosciara species. Inversions and band dimorphisms have also occurred, but the processes leading to their maintenance and fixation appear to have been slow, since these three species are in general chromosomally monomorphic.Key words: Rhynchosciara, polytene chromosomes, chromosomal evolution.

A molecular cytogenetic comparison between Rhynchosciara americana and Rhynchosciara hollaenderi (Diptera: Sciaridae)

Genome ◽  
1993 ◽  
Vol 36 (5) ◽  
pp. 831-843 ◽  
Author(s):  
Ann Jacob Stocker ◽  
Eduardo Gorab ◽  
J. M. Amabis ◽  
F. J. S. Lara
Keyword(s):  
In Situ Hybridization ◽  
Species Complex ◽  
Polytene Chromosomes ◽  
Chromosomal Evolution ◽  
Molecular Cytogenetic ◽  
The Third ◽  
Dna And Rna ◽  
Rhynchosciara Americana ◽  
Telomeric Heterochromatin

The polytene chromosomes of Rhynchosciara americana and R. hollaenderi, a pair of sibling species in the americana-like group of Rhynchosciara, were compared using a number of techniques, including in situ hybridization. With classical cytological techniques, the only differences observed were in the morphology of centromeric and telomeric heterochromatin, in the size of a DNA and RNA puff, and in the presence of an inversion polymorphism in R. hollaenderi. However, after in situ hybridization with rDNA and poly-r(A) probes, differences between the two species appeared at a number of sites. Differences in poly-r(A) sites were especially informative in establishing phylogenetic relationships between these two species and a third species currently being examined from this group. Chromosomal evolution between these species appears to have occurred mainly through differential amplification and transposition of repetitive sequence DNA, of which dA:dT tracts are an important component. The R. hollaenderi karyotype is tentatively considered more ancestral than that of R. americana because it has features present in the third Rhynchosciara species. Explanations for the monomorphisms observed in Rhynchosciara species and mechanisms of speciation in the group are considered within the context of the species' complex behavior.Key words: Rhynchosciara, chromosome homology, in situ hybridization, phylogeny, evolution.

scholarly journals EVIDENCE FOR A COMPLEX CLASS OF NONADENYLATED mRNA IN DROSOPHILA

Genetics ◽  
1980 ◽  
Vol 95 (3) ◽  
pp. 673-691
Author(s):  
J Lynn Zimmerman ◽  
David L Fouts ◽  
Jerry E Manning
Keyword(s):  
Dna Sequences ◽  
Polytene Chromosomes ◽  
Single Copy ◽  
Drosophila Genome ◽  
Coding Sequences ◽  
Sequence Complexity ◽  
Relative Contribution ◽  
Copy Dna ◽  
Average Size ◽  
Single Copy Dna

ABSTRACT The amount, by mass, of poly(A+) mRNA present in the polyribosomes of third-instar larvae of Drosophila melanogaster, and the relative contribution of the poly(A+) mRNA to the sequence complexity of total polysomal RNA, has been determined, Selective removal of poly(A+) mRNA from total polysoma1 RNA by use of either oligo-dT-cellulose, or poly (U)-sepharose affinity chromatography, revealed that only 0.15% of the mass of the polysomal RNA was present as poly(A+) mRNA. The present study shows that this RNA hybridized at saturation with 3.3% of the single-copy DNA in the Drosophila genome. After correction for asymmetric transcription and reactability of the DNA, 7.4% of the single-copy DNA in the Drosophila genome is represented in larval poly(A+) mRNA. This corresponds to 6.73 × 1O6 nucleotides of mRNA coding sequences, or approximately 5,384 diverse RNA sequences of average size 1,250 nucleotides. However, total polysomal RNA hybridizes at saturation to 10.9% of the single-copy DNA sequences. After correcting this value for asymmetric transcripti0n and tracer DNA reactability, 24% of the single-copy DNA in Drosophila is represented in total polysomal RNA. This corresponds to 2.18 × 107 nucleotides of RNA coding sequences or 17,440 diverse RNA molecules of size 1,250 nucleotides. This value is 3.2 times greater than that observed for poly(A+) mRNA, and indicates that ≃69% of the polysomal RNA sequence complexity is contributed by n0nadenylated RNA. Furthermore, if the number of different structural genes represented in total polysomal RNA is ≃1.7 × 104, then the number of genes expressed in thirdinstar larvae exceeds the number of chromomeres in Drosophila by about a factor of three. This numerology indicates that the number of chromomeres observed in polytene chromosomes does not reflect the number of structural gene sequences in the Drosophila genome.

Identifying a single-copy DNA sequence associated with the expression of a heterochromatic gene, the light locus of Drosophila melanogaster

Genome ◽  
1990 ◽  
Vol 33 (3) ◽  
pp. 405-415 ◽  
Author(s):  
Robert H. Devlin ◽  
David G. Holm ◽  
Karen R. Morin ◽  
Barry M. Honda
Keyword(s):  
Drosophila Melanogaster ◽  
In Situ Hybridization ◽  
Dna Sequences ◽  
Polytene Chromosomes ◽  
Single Copy ◽  
Molecular Organization ◽  
Copy Dna ◽  
Single Copy Dna ◽  
P Transposon

Although little is known about the molecular organization of most genes within heterochromatin, the unusual properties of these chromosomal regions suggest that genes therein may be organized and expressed very differently from those in euchromatin. We report here the cloning, by P transposon tagging, of sequences associated with the expression of the light locus, an essential gene found in the heterochromatin of chromosome 2 of Drosophila melanogaster. We conclude that this DNA is either a segment of the light locus, or a closely linked, heterochromatic sequence affecting its expression. While other functional DNA sequences previously described in heterochromatin have been repetitive, light gene function may be associated, at least in part, with single-copy DNA. This conclusion is based upon analysis of DNA from mutations and reversions induced by P transposable elements. The cloned region is unusual in that this single-copy DNA is embedded within middle-repetitive sequences. The in situ hybridization experiments also show that, unlike most other sequences in heterochromatin, this light-associated DNA evidently replicates in polytene chromosomes, but its diffuse hybridization signal may suggest an unusual chromosomal organization.Key words: polytene chromosomes, P transposon, in situ hybridization, middle-repetitive DNA.

High resolution molecular cytogenetic techniques in plants: Pachytene- and fibre-FISH

2012 ◽  
Vol 60 (2) ◽  
pp. 157-165
Author(s):  
G. Linc ◽  
M. Molnár-Láng
Keyword(s):  
Dna Sequences ◽  
Physical Map ◽  
Single Copy ◽  
Molecular Cytogenetic ◽  
Plant Chromosomes ◽  
Powerful Research Tool ◽  
Increased Sensitivity ◽  
Molecular Cytogenetic Techniques ◽  
Copy Dna ◽  
Fibre Fish

Fluorescence in situ hybridization (FISH) is the most versatile and accurate molecular cytogenetic technique for determining euchromatic-heterochromatic boundaries and the locations of repetitive and single-copy DNA sequences and of chromosome-specific BAC clones on chromosomes. The combination of cytogenetic and genetic methods yields a highresolution physical map. FISH allows direct mapping of specific DNA sequences inside the cell (interphase nuclei), along meiotic pachytene chromosomes and isolated chromatin (DNA fibres). The increased sensitivity of the technique and its ability to detect gene locations provide a powerful research tool for genetic and pre-breeding studies. FISH-based physical mapping plays an important role and is increasingly used for studies at the cytological level on the chromatin organization that controls gene expression and regulation. The present minireview describes some of the benefits of alternative FISH-based techniques and their application for studying plant chromosomes and genomes.

Chironomus alchichica sp. n. (Diptera: Chironomidae) from Lake Alchichica, Mexico

Zootaxa ◽  
2017 ◽  
Vol 4365 (1) ◽  
pp. 53 ◽  
Author(s):  
RAÚL ACOSTA ◽  
NARCÍS PRAT ◽  
CARLES RIBERA ◽  
PARASKEVA MICHAILOVA ◽  
MARÍA DEL CARMEN HERNÁNDEZ-FONSECA ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Abdominal Segment ◽  
Developmental Stages ◽  
Polytene Chromosomes ◽  
Nucleolar Organizer ◽  
Bootstrap Support ◽  
Cytological Analysis ◽  
Balbiani Rings ◽  
Morphological Differences

Morphological analysis of all developmental stages (except female), mitochondrial DNA sequences from cytochrome c oxidase subunit I (cox1) and cytological analysis of the polytene chromosomes were used to describe a new species of Chironomus found in the littoral and profundal zones of an endorheic, warm-monomictic lake in Mexico. Male imago is distinguished by the shape of superior volsella and by an antennal and bristle ratio lower than two. The pupa is characterized by the spur morphology of abdominal segment VIII. There is also a continuous row of hooklets on abdominal segment II. The larva is distinguished by a combination of antenna, mentum, mandible, and pecten epipharyngis characteristics, and abdominal ventral tubules. Molecular and cytological analysis supported the morphological differences found. The maximum likelihood tree obtained shows that Chironomus alchichica sp. n. clusters together with Chironomus decorus-group sp. 2 Butler et al. (1995) (bootstrap support = 92%), but genetic p-distances within C. alchichica sp. n. (0.004) were lower than the p-distances between other species of the decorus-group (C. decorus-group sp. 2, Chironomus bifurcatus Wülker et al., 2009 and Chironomus maturus Johannsen, 1908) confirming that it is a different species. The new species belongs to thummi cytocomplex, (decorus-group), with chromosome set- 2n = 8 and chromosome arm combinations: AB CD EF G. Karyologically, the species is closest to Chironomus riihimaekiensis Wülker (1973). This species has very compact salivary gland chromosomes with well heterochromatinized centromere regions in chromosomes AB CD G. Several fixed homozygous inversions distinguish arm A of the species from that of C. riihimaekiensis. Arm E differs from that of C. riihimaekiensis by simple fixed homozygous inversion. Some similarities in band sequences of this arm were found with species from the decorus-group as Chironomus blaylocki Wülker et al., 2009 and C. bifurcatus (decorus-group). The position of the key constrictions in chromosome G: Nucleolar organizer (NOR) and Balbiani rings (BRs) is similar to the species of decorus-group. C. alchichica sp. n. has been found in soft sediments rich in organic matter in well mineralized waters (where conductivity >10 mS cm-1) and with a high pH (≥9). The profundal zone is inhabited only during the mixing period, when dissolved oxygen is present. 

Mapping by Sequencing the Pneumocystis Genome Using the Ordering DNA Sequences V3 Tool

Genetics ◽  
2003 ◽  
Vol 163 (4) ◽  
pp. 1299-1313
Author(s):  
Zheng Xu ◽  
Britton Lance ◽  
Claudia Vargas ◽  
Budak Arpinar ◽  
Suchendra Bhandarkar ◽  
...  
Keyword(s):  
Physical Mapping ◽  
Dna Sequences ◽  
Pneumocystis Carinii ◽  
Single Copy ◽  
Fungal Genome ◽  
Mapping Data ◽  
Genome Database ◽  
Rdna Genes ◽  
Genome Map ◽  
Mapping By Sequencing

Abstract A bioinformatics tool called ODS3 has been created for mapping by sequencing. The tool allows the creation of integrated genomic maps from genetic, physical mapping, and sequencing data and permits an integrated genome map to be stored, retrieved, viewed, and queried in a stand-alone capacity, in a client/server relationship with the Fungal Genome Database (FGDB), and as a web-browsing tool for the FGDB. In that ODS3 is programmed in Java, the tool promotes platform independence and supports export of integrated genome-mapping data in the extensible markup language (XML) for data interchange with other genome information systems. The tool ODS3 is used to create an initial integrated genome map of the AIDS-related fungal pathogen, Pneumocystis carinii. Contig dynamics would indicate that this physical map is ∼50% complete with ∼200 contigs. A total of 10 putative multigene families were found. Two of these putative families were previously characterized in P. carinii, namely the major surface glycoproteins (MSGs) and HSP70 proteins; three of these putative families (not previously characterized in P. carinii) were found to be similar to families encoding the HSP60 in Schizosaccharomyces pombe, the heat-shock Ψ protein in S. pombe, and the RNA synthetase family (i.e., MES1) in Saccharomyces cerevisiae. Physical mapping data are consistent with the 16S, 5.8S, and 26S rDNA genes being single copy in P. carinii. No other fungus outside this genus is known to have the rDNA genes in single copy.

scholarly journals A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

Insects ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 167
Author(s):  
John H. Boyle ◽  
Pasi M. A. Rastas ◽  
Xin Huang ◽  
Austin G. Garner ◽  
Indra Vythilingam ◽  
...  
Keyword(s):  
Linkage Map ◽  
Aedes Albopictus ◽  
Dna Sequences ◽  
Genome Assembly ◽  
Single Copy ◽  
Health Concern ◽  
Candidate Snps ◽  
Single Location ◽  
Asian Tiger ◽  
Photoperiodic Diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19–1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.

Fluorescence in situ hybridization on plant extended chromatin DNA fibers for single-copy and repetitive DNA sequences

2011 ◽  
Vol 30 (9) ◽  
pp. 1779-1786 ◽  
Author(s):  
Kun Yang ◽  
Hecui Zhang ◽  
Richard Converse ◽  
Yong Wang ◽  
Xiaoying Rong ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Single Copy ◽  
Repetitive Dna Sequences

Polytene and mitotic chromosome analysis in Ceratitis capitata (Diptera; Tephritidae)

1986 ◽  
Vol 28 (2) ◽  
pp. 180-188 ◽  
Author(s):  
D. G. Bedo
Keyword(s):  
X Chromosome ◽  
Silver Staining ◽  
Mitotic Chromosome ◽  
Ceratitis Capitata ◽  
Fat Body ◽  
Polytene Chromosomes ◽  
Chromosome Analysis ◽  
Mitotic Chromosomes ◽  
Chromosome Separation ◽  
Ectopic Pairing

Polytene chromosomes were found in several larval and pupal tissues of the Medfly, Ceratitis capitata, during a search for chromosomes suitable for detailed cytological analysis. Well-banded highly polytene chromosomes, which could be adequately separated and spread, were found in trichogen cells of the spatulate superior orbital bristles of male pupae. These chromosomes proved suitable for full polytene analysis. Thoracic trichogen cells of both male and female pupae also contain useful polytene chromosomes, although they are considerably thinner and thus more difficult to analyze. Contrasting with those in pupal trichogen cells, the chromosomes in the salivary glands, Malphighian tubules, midgut, hindgut, and fat body of larvae and pupae were difficult to prepare because of high levels of ectopic pairing and chromosome fragmentation. In hindgut preparations partial separation of up to three chromosomes was achieved, but in all other tissues no useful chromosome separation was possible. In trichogen polytene cells, five banded chromosomes and a prominent heterochromatic network associated with a nucleolus are found. The mitotic chromosomes respond to C- and Q-banding and silver staining with considerable variation. This is especially so in the X chromosome, which displays an extensive array of bands following both Q-banding and silver staining. Comparison of Q-banded metaphase and polytene chromosomes demonstrates that the five autosomes are represented by conventional polytene chromosomes, while the sex chromosomes are contained in the heterochromatic net, most of which fluoresces strongly. This suggests that the Q-bands of the mitotic X chromosome are replicated to a greater extent than the nonfluorescent material in polytene cells. This investigation shows C. capitata to have excellent cytological material for both polytene and mitotic analysis.Key words: Ceratitis capitata, Medfly, chromosomes (polytene), banding (chromosome).

scholarly journals Multiple Origins of Cytologically Identical Chromosome Inversions in the Anopheles gambiae Complex

Genetics ◽  
1998 ◽  
Vol 150 (2) ◽  
pp. 807-814
Author(s):  
Adalgisa Caccone ◽  
Gi-Sik Min ◽  
Jeffrey R Powell
Keyword(s):  
Anopheles Gambiae ◽  
Dna Sequences ◽  
Parallel Evolution ◽  
Polytene Chromosomes ◽  
Gambiae Complex ◽  
Chromosomal Inversions ◽  
Multiple Origins ◽  
Naturally Occurring ◽  
Anopheles Gambiae Complex ◽  
History Of

Abstract For more than 60 years, evolutionary cytogeneticists have been using naturally occurring chromosomal inversions to infer phylogenetic histories, especially in insects with polytene chromosomes. The validity of this method is predicated on the assumption that inversions arise only once in the history of a lineage, so that sharing a particular inversion implies shared common ancestry. This assumption of monophyly has been generally validated by independent data. We present the first clear evidence that naturally occurring inversions, identical at the level of light microscopic examination of polytene chromosomes, may not always be monophyletic. The evidence comes from DNA sequence analyses of regions within or very near the breakpoints of an inversion called the 2La that is found in the Anopheles gambiae complex. Two species, A. merus and A. arabiensis, which are fixed for the “same” inversion, do not cluster with each other in a phylogenetic analysis of the DNA sequences within the 2La. Rather, A. merus 2La is most closely related to strains of A. gambiae homozygous for the 2L+. A. gambiae and A. merus are sister taxa, the immediate ancestor was evidently homozygous 2L+, and A. merus became fixed for an inversion cytologically identical to that in A. arabiensis. A. gambiae is polymorphic for 2La/2L+, and the 2La in this species is nearly identical at the DNA level to that in A. arabiensis, consistent with the growing evidence that introgression has or is occurring between these two most important vectors of malaria in the world. The parallel evolution of the “same” inversion may be promoted by the presence of selectively important genes within the breakpoints.

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