This is likely due to the hybrid assembly of the neo-X and neo-Y element F fused to the X, and element F fused to the Y, respectively , as the neo-Y is not yet fully degenerated and some neo-Y-derived reads are included in the assembly. Because this hybrid assembly differs from the true sequence of the neo-X, female reads will not fully map to it, leading to decreased female coverage.
This bias disappeared when only female reads were used for the assembly Fig.
The pig X and Y Chromosomes: structure, sequence, and evolution.
This female-only assembly was therefore used for all further analyses. The resulting D. Hits with a match score below 50 were excluded. A perl script was used to count the number of Drosophila genes per Muller element that mapped to each scaffold. The scaffold was assigned to the Muller element with the largest number of matching genes. When the same number of genes from different Muller elements mapped to a scaffold, a score was calculated for each Muller element by summing the match scores of all the hits for that element, and the scaffold was assigned to the element with the largest score.
The rate of concordance of genes on scaffolds the number of genes that map to the element their scaffold was assigned to vs. Male and female forward reads were mapped separately to the genomic scaffolds using BWA 32 set to the default parameters for paired-end reads. The resulting SAM alignments were used to estimate the male and female coverage depth for each scaffold using SoapCov soap. Figures S2 to S7 show the male and female coverage distributions for each Muller element for all the species investigated. The results of the tests are presented in Table S2.
From the blat results D. The genomic regions corresponding to this conserved set of genes were extracted from the genomic scaffolds using a perl script. Genewise was used to infer the protein sequence of the genes in the different outgroups from the corresponding genomic region. To avoid potential biases that could arise by using the D. For each gene, the inferred protein sequences and the D. We concatenated the Muscle output files, and ran the resulting concatenated alignment through Gblocks to remove gaps and regions of low alignment quality.
The final alignment, consisting of amino acids, was used as input for PhyML to obtain the phylogenetic tree and associated bootstrap values Fig. Differences between elements A and F versus autosomes elements B—E were tested by re-sampling n genes times from the autosomal sample where n is the number of genes for element A or F present in the sample. Male and female adults were placed in separate vials immediately after emergence, and aged on standard Drosophila food for 4 days. Paired-end RNA-seq reads were obtained from testis, ovary and female and male carcass and whole body. For each species, the resulting paired-end bps reads were trimmed, pooled and assembled using SOAPdenovo soap.
Scaffolds were mapped to D. When more than one scaffold overlapped on the same D. When several scaffolds mapped to different parts of the same gene, or had an overlap shorter than 20bps, their sequences were concatenated. The resulting B. For each adult tissue, reads were mapped to the B. In order to assess early embryonic expression, adult individuals of B. The dechorionated embryos were staged by observation under a light microscope after immersion in halocarbon oil. Stage 5 embryos were selected, as in D.
Libraries were made at the Bachtrog lab following the protocol of ref.
Coates Genomics Sequencing Laboratory, Berkeley. The first 20 bps of the resulting reads were trimmed before further analysis. Reads were mapped to the B. The male DNA-seq reads available for P. One lane of forward female and male DNA-seq reads were mapped back to these male scaffolds separately using BWA with default parameters and male and female coverage was estimated using SoapCoverage.
We used single-end mapping of the forward read rather than paired-ended mapping because the insert size of the paired-end fragments bps is longer than the minimum size of the fragments. One lane of forward female and male DNA-seq reads were mapped back separately to the resulting male transcripts using BWA with default parameters and male and female coverage was estimated using SoapCoverage. Genomic scaffolds and transcripts containing homologues to these proteins were identified using tblastn with an E-value cut-off of 0.
Sequences identified in our blast search that had no coverage in females, but had coverage higher than 0 in males, were classified as candidate homologues to the Drosophila Y-linked genes Tables S3 and S4. No such sequences were found in the male transcriptome or genome of S. Primers designed to amplify fragments of the candidate Y-linked P. In Diptera, there is a general tendency for the rDNA to reside on the sex chromosomes, but its location often differs between closely related species For example, both the X and the Y of D.
Thus, the absence or presence of rDNA on sex chromosomes contains limited information on whether the Y chromosomes of Diptera are homologous across families, and we therefore focused our analysis on protein-coding genes. Cytological studies have found that some but not all true fruit flies have rDNA loci on their Y including B. The trimmed whole-body male and female RNA-seq reads of S.
PCRs with primers designed for 10 candidate transcripts of S. S9 , confirming that the sample contains Y-derived sequences. In order to check for Y-linkage of these candidate sequences in D. The male and female coverage of each genomic scaffold was estimated by mapping the male and female DNA-seq reads against the assembled genome with bowtie2 keeping only fully mapped reads, and filtering out reads with mismatches and processing the SAM alignment with SoapCoverage.
The candidate Y-linked transcripts of S. As a control, 12 known Y-linked genes of D. All 12 D. Finally, the single B. National Center for Biotechnology Information , U. Author manuscript; available in PMC Aug 4. Beatriz Vicoso and Doris Bachtrog. Author information Copyright and License information Disclaimer. Correspondence and request for materials should be addressed to D. Copyright notice.
The publisher's final edited version of this article is available at Nature. See other articles in PMC that cite the published article. Associated Data Supplementary Materials 1. Open in a separate window. Figure 1. Figure 2. Properties of the dot chromosome in Drosophila melanogaster that resemble that of an X a.
Figure 3. Gene expression in early embryos and adult gonads in outgroup Diptera species a. Figure 4. Turnover of sex chromosomes in Drosophila Hypothetical transition from an ancestral karyotype with element F segregating as a sex chromosome, to the karyotype observed in Drosophila where element A is the sex chromosome. Methods S1.
Supplementary Material 1 Click here to view.
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References 1. Bull JJ.
Evolution of sex determining mechanisms. Transitions between sex-determining systems in reptiles and amphibians. Annu Rev Genomics Hum Genet. Pokorna M, Kratochvil L. Phylogeny of sex-determining mechanisms in squamate reptiles: are sex chromosomes an evolutionary trap?
Zoological Journal of the Linnean Society. Ohno S. Sex Chromosomes and sex-linked genes. Springer Verlag; Bridges CB. Sex in relation to chromosomes and genes. Am Nat. Painting of fourth, a chromosome-specific protein in Drosophila. Reconstructing the evolution of vertebrate sex chromosomes. Muller HJ. Bearing of the Drosophila work on systematics. The new systematics.
The genome sequence of the malaria mosquito Anopheles gambiae. Cline TW. The Drosophila sex determination signal: how do flies count to two? Trends Genet. Zacharopoulou A. Cytogenetic analysis of mitotic and salivary gland chromosomes in the Medfly Ceratitis capitata. White MJ.
Cytological evidence on the phylogeny and classification of the Diptera. Vicoso B, Bachtrog D. Lack of global dosage compensation in Schistosoma mansoni , a female-heterogametic parasite. Genome Biol Evol. Paucity of genes on the Drosophila X chromosome showing male-biased expression. Lifschytz E, Lindsley DL. The role of X-chromosome inactivation during spermatogenesis. Drosophila dosage compensation: a complex voyage to the X chromosome. Painting of fourth in genus Drosophila suggests autosome-specific gene regulation.
A lot about a little dot - lessons learned from Drosophila melanogaster chromosome 4. Cell Biol. Coordinated Regulation of Heterochromatic Genes in Drosophila melanogaster males. Sex-determining mechanisms in insects. The technique of determining the karyotype is usually called karyotyping. Cells can be locked part-way through division in metaphase in vitro in a reaction vial with colchicine. Like many sexually reproducing species, humans have special gonosomes sex chromosomes, in contrast to autosomes. These are XX in females and XY in males.
Investigation into the human karyotype took many years to settle the most basic question: How many chromosomes does a normal diploid human cell contain? It took until before the human diploid number was confirmed as Chromosomal aberrations are disruptions in the normal chromosomal content of a cell and are a major cause of genetic conditions in humans, such as Down syndrome , although most aberrations have little to no effect. Some chromosome abnormalities do not cause disease in carriers, such as translocations , or chromosomal inversions , although they may lead to a higher chance of bearing a child with a chromosome disorder.
Abnormal numbers of chromosomes or chromosome sets, called aneuploidy , may be lethal or may give rise to genetic disorders. The gain or loss of DNA from chromosomes can lead to a variety of genetic disorders. Human examples include:. From Wikipedia, the free encyclopedia.
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This is the latest accepted revision , reviewed on 23 September DNA molecule containing genetic material of a cell. This article may be too technical for most readers to understand. Please help improve it to make it understandable to non-experts , without removing the technical details. April Learn how and when to remove this template message. Walter Sutton left and Theodor Boveri right independently developed the chromosome theory of inheritance in See also: Eukaryotic chromosome fine structure.
See also: mitosis and meiosis. Estimated number of genes and base pairs in mega base pairs on each human chromosome. Main article: List of organisms by chromosome count. Main article: Karyotype. Nature Reviews. Molecular Cell Biology. New York: Garland Science. Essential Cell Biology Fourth ed. Microscopical researches into the accordance in the structure and growth of animals and plants. Current Opinion in Cell Biology. Merriam-Webster Dictionary. Commission on Standardization of Biological Stains. From the Caryologia foundation to present". Plant Biosystems - an International Journal Dealing.
Caryologia - International Journal of Cytology, Cytosystematics. Retrieved The Cell in Development and Heredity , Ed. Macmillan, New York. The growth of biological thought. Archived from the original PDF on 15 December Retrieved 13 July Journal of Structural Biology. Current Biology. Scientific Reports. Bibcode : NatSR Molecular Microbiology. Trends in Microbiology. Journal of Cellular Biochemistry.
Bibcode : Sci Cellular and Molecular Life Sciences. Archives of Microbiology. Bibcode : PNAS Current Opinion in Structural Biology. Telomeres , centromeres , and other heterochromatic regions have been left undetermined, as have a small number of unclonable gaps. Journal of Experimental Botany. Bibcode : PNAS.. Annals of Botany. Sridhar, K. The Journal of Heredity. Chromosome Research. Mammalian Genome. Cytogenetic and Genome Research. W4", Rabbits, Hares and Pikas.
Status Survey and Conservation Action Plan , pp. Cytogenetics and Cell Genetics. International Immunopharmacology. The Japanese Journal of Genetics. Animal Genetics. Shokubutsugaku Zasshi. Organization of the prokaryote genome. Insect Biochemistry and Molecular Biology. The chromosomes 6th ed. Archives de Biologie. April The spermatogenesis of man". Journal of Experimental Zoology. Bibcode : Natur. Human and mammalian cytogenetics: a historical perspective.
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Vertebrate Sex Chromosomes (Reprint Of: Cytogenetic and Genome Research 2002, 1-4)
Bread wheat hexaploid . Cultivated tobacco tetraploid . Adder's tongue fern polyploid . Chromosome numbers 2n in some animals Species Indian muntjac. Pill millipede Arthrosphaera fumosa . Earthworm Octodrilus complanatus . Domestic cat .