scholarly journals Dynamic evolution of euchromatic satellites on the X chromosome in Drosophila melanogaster and the simulans clade

2019 ◽  
Author(s):  
J.S. Sproul ◽  
D.E. Khost ◽  
D.G. Eickbush ◽  
S. Negm ◽  
X. Wei ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Molecular Mechanisms ◽  
Evolutionary Dynamics ◽  
Dynamic Evolution ◽  
Satellite Dnas ◽  
Genomic Location ◽  
Evolutionary Consequences ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACTSatellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here we use high-quality genome assemblies to study evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 gm/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spreads by inserting into existing clusters of the older, more abundant 1.688 satellite, in events that were likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher-order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

scholarly journals Dynamic Evolution of Euchromatic Satellites on the X Chromosome in Drosophila melanogaster and the simulans Clade

2020 ◽  
Vol 37 (8) ◽  
pp. 2241-2256 ◽  
Author(s):  
John S Sproul ◽  
Danielle E Khost ◽  
Danna G Eickbush ◽  
Sherif Negm ◽  
Xiaolu Wei ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Molecular Mechanisms ◽  
Evolutionary Dynamics ◽  
Dynamic Evolution ◽  
Satellite Dnas ◽  
Genomic Location ◽  
Evolutionary Consequences ◽  
Genome Assemblies ◽  
High Quality Genome

Abstract Satellite DNAs (satDNAs) are among the most dynamically evolving components of eukaryotic genomes and play important roles in genome regulation, genome evolution, and speciation. Despite their abundance and functional impact, we know little about the evolutionary dynamics and molecular mechanisms that shape satDNA distributions in genomes. Here, we use high-quality genome assemblies to study the evolutionary dynamics of two complex satDNAs, Rsp-like and 1.688 g/cm3, in Drosophila melanogaster and its three nearest relatives in the simulans clade. We show that large blocks of these repeats are highly dynamic in the heterochromatin, where their genomic location varies across species. We discovered that small blocks of satDNA that are abundant in X chromosome euchromatin are similarly dynamic, with repeats changing in abundance, location, and composition among species. We detail the proliferation of a rare satellite (Rsp-like) across the X chromosome in D. simulans and D. mauritiana. Rsp-like spread by inserting into existing clusters of the older, more abundant 1.688 satellite, in events likely facilitated by microhomology-mediated repair pathways. We show that Rsp-like is abundant on extrachromosomal circular DNA in D. simulans, which may have contributed to its dynamic evolution. Intralocus satDNA expansions via unequal exchange and the movement of higher order repeats also contribute to the fluidity of the repeat landscape. We find evidence that euchromatic satDNA repeats experience cycles of proliferation and diversification somewhat analogous to bursts of transposable element proliferation. Our study lays a foundation for mechanistic studies of satDNA proliferation and the functional and evolutionary consequences of satDNA movement.

scholarly journals Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

2017 ◽  
Author(s):  
David Thybert ◽  
Maša Roller ◽  
Fábio C.P. Navarro ◽  
Ian Fiddes ◽  
Ian Streeter ◽  
...  
Keyword(s):  
Mus Musculus ◽  
Evolutionary Dynamics ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
High Quality ◽  
Phylogenetic Structure ◽  
Mus Caroli ◽  
Nucleotide Mutation ◽  
Genome Assemblies ◽  
High Quality Genome

ABSTRACTUnderstanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 to 6 MYA, but that are absent in the Hominidae. In fact, Hominidae show between four-and seven-fold lower rates of nucleotide change and feature turnover in both neutral and functional sequences suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. For example, recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli. This process resulted in thousands of novel, species-specific CTCF binding sites. Our results demonstrate that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

scholarly journals Nanopore sequencing and Hi-C scaffolding provide insight into the evolutionary dynamics of transposable elements and piRNA production in wild strains of Drosophila melanogaster

2019 ◽  
Vol 48 (1) ◽  
pp. 290-303 ◽  
Author(s):  
Christopher E Ellison ◽  
Weihuan Cao
Keyword(s):  
Drosophila Melanogaster ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Population Level ◽  
Chromosome Length ◽  
Nanopore Sequencing ◽  
Long Reads ◽  
Wild Strains ◽  
Genome Assemblies ◽  
Insight Into

Abstract Illumina sequencing has allowed for population-level surveys of transposable element (TE) polymorphism via split alignment approaches, which has provided important insight into the population dynamics of TEs. However, such approaches are not able to identify insertions of uncharacterized TEs, nor can they assemble the full sequence of inserted elements. Here, we use nanopore sequencing and Hi-C scaffolding to produce de novo genome assemblies for two wild strains of Drosophila melanogaster from the Drosophila Genetic Reference Panel (DGRP). Ovarian piRNA populations and Illumina split-read TE insertion profiles have been previously produced for both strains. We find that nanopore sequencing with Hi-C scaffolding produces highly contiguous, chromosome-length scaffolds, and we identify hundreds of TE insertions that were missed by Illumina-based methods, including a novel micropia-like element that has recently invaded the DGRP population. We also find hundreds of piRNA-producing loci that are specific to each strain. Some of these loci are created by strain-specific TE insertions, while others appear to be epigenetically controlled. Our results suggest that Illumina approaches reveal only a portion of the repetitive sequence landscape of eukaryotic genomes and that population-level resequencing using long reads is likely to provide novel insight into the evolutionary dynamics of repetitive elements.

scholarly journals Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: steppingstones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

2022 ◽  
Author(s):  
Hugo Darras ◽  
Natalia de Souza Araujo ◽  
Lyam Baudry ◽  
Nadege Guiglielmoni ◽  
Pedro Lorite ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Gene Annotation ◽  
Thermal Adaptation ◽  
Thermal Limit ◽  
Chromosome Conformation ◽  
Long Read ◽  
Genomic Studies ◽  
Genetic Mechanisms ◽  
Genome Assemblies ◽  
High Quality Genome

Cataglyphis are thermophilic ants that forage during the day when temperatures are highest and sometimes close to their critical thermal limit. Several Cataglyphis species have evolved unusual reproductive systems such as facultative queen parthenogenesis or social hybridogenesis, which have not yet been investigated in detail at the molecular level. We generated high-quality genome assemblies for two hybridogenetic lineages of the Iberian ant Cataglyphis hispanica using long-read Nanopore sequencing and exploited chromosome conformation capture (3C) sequencing to assemble contigs into 26 and 27 chromosomes, respectively. Males of one lineage were karyotyped to confirm the number of chromosomes inferred from 3C data. We obtained transcriptomic data to assist gene annotation and built custom repeat libraries for each of the two assemblies. Comparative analyses with 19 other published ant genomes were also conducted. These new genomic resources pave the way for exploring the genetic mechanisms underlying the remarkable thermal adaptation and the molecular mechanisms associated with transitions between different genetic systems characteristics of the ant genus Cataglyphis.

scholarly journals Patterns of DNA Variability at X-Linked Loci in Mus domesticus

Genetics ◽  
1997 ◽  
Vol 147 (3) ◽  
pp. 1303-1316
Author(s):  
Michael W Nachman
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
House Mouse ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Mus Domesticus ◽  
Substantial Variation ◽  
Intraspecific Polymorphism ◽  
Recombination Rates ◽  
Interspecific Divergence

Introns of four X-linked genes (Hprt, Plp, Glra2, and Amg) were sequenced to provide an estimate of nucleotide diversity at nuclear genes within the house mouse and to test the neutral prediction that the ratio of intraspecific polymorphism to interspecific divergence is the same for different loci. Hprt and Plp lie in a region of the X chromosome that experiences relatively low recombination rates, while Glra2 and Amg lie near the telomere of the X chromosome, a region that experiences higher recombination rates. A total of 6022 bases were sequenced in each of 10 Mus domesticus and one M. caroli. Average nucleotide diversity (π) for introns within M. domesticus was quite low (π = 0.078%). However, there was substantial variation in the level of heterozygosity among loci. The two telomeric loci, Glra2 and Amg, had higher ratios of polymorphism to divergence than the two loci experiencing lower recombination rates. These results are consistent with the hypothesis that heterozygosity is reduced in regions with lower rates of recombination, although sampling of additional genes is needed to establish whether there is a general correlation between heterozygosity and recombination rate as in Drosophila melanogaster.

scholarly journals Elimination of Introns at the Drosophila suppressor-of-forked Locus by P-Element-Mediated Gene Conversion Shows That an RNA Lacking a Stop Codon is Dispensable

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 345-351
Author(s):  
Carol J Williams ◽  
Kevin O'Hare
Keyword(s):  
X Chromosome ◽  
Stop Codon ◽  
Alternative Polyadenylation ◽  
Gene Replacement ◽  
P Element ◽  
Wild Type ◽  
Genomic Location ◽  
Chromosomal Breaks ◽  
White Locus ◽  
Cleavage Stimulation Factor

Abstract The suppressor of forked [su(f)] locus affects the phenotype of mutations caused by transposable element insertions at unlinked loci. It encodes a putative 84-kD protein with homology to two proteins involved in mRNA 3′ end processing; the product of the yeast RNA14 gene and the 77-kD subunit of human cleavage stimulation factor. Three su(f) mRNAs are produced by alternative polyadenylation. The 2. 6 and 2.9-kb mRNAs encode the same 84-kD protein while a 1.3-kb RNA, which terminates within the fourth intron, is unusual in having no stop codon. Using P-element-mediated gene replacement we have copied sequences from a transformation construct into the su(f) gene creating a su(f) allele at the normal genomic location that lacks the first five introns. This allele is viable and appears wild type for su(f) function, demonstrating that the 1.3-kb RNA and the sequences contained within the deleted introns are dispensable for su(f) function. Compared with studies on gene replacement at the white locus, chromosomal breaks at su(f) appear to be less efficiently repaired from ectopic sites, perhaps because of the location of su(f) at the euchromatin/heterochromatin boundary on the X chromosome.

scholarly journals SITE-SPECIFIC INSTABILITY IN DROSOPHILA MELANOGASTER: EVIDENCE FOR TRANSPOSITION OF DESTABILIZING ELEMENT

Genetics ◽  
1982 ◽  
Vol 101 (3-4) ◽  
pp. 461-476
Author(s):  
Todd R Laverty ◽  
J K Lim
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Lethal Mutation ◽  
Chromosome Rearrangements ◽  
Chromosome Break ◽  
Secondary Mutation ◽  
X Chromosomes ◽  
Site Specific ◽  
Normal Sequence ◽  
Lethal Mutations

ABSTRACT In this study, we show that at least one lethal mutation at the 3F-4A region of the X chromosome can generate an array of chromosome rearrangements, all with one chromosome break in the 3F-4A region. The mutation at 3F-4A (secondary mutation) was detected in an X chromosome carrying a reverse mutation of an unstable lethal mutation, which was mapped in the 6F1-2 doublet (primary mutation). The primary lethal mutation at 6F1-2 had occurred in an unstable chromosome (Uc) described previously (Lim 1979). Prior to reversion, the 6F1-2 mutation had generated an array of chromosome rearrangements, all having one break in the 6F1-2 doublet (Lim 1979, 1980). In the X chromosomes carrying the 3F-4A secondary lethal mutation the 6F1-2 doublet was normal and stable, as was the 3F-4A region in the X chromosome carrying the primary lethal mutation. The disappearance of the instability having a set of genetic properties at one region (6F1-2) accompanied by its appearance elsewhere in the chromosome (3F-4A) implies that a transposition of the destabilizing element took place. The mutant at 3F-4A and other secondary mutants exhibited all but one (reinversion of an inversion to the normal sequence) of the eight properties of the primary lethal mutations. These observations support the view that a transposable destabilizing element is responsible for the hypermutability observed in the unstable chromosome and its derivaties.

scholarly journals Hybrid dysgenesis-induced quantitative variation on the X chromosome of Drosophila melanogaster.

Genetics ◽  
1990 ◽  
Vol 124 (3) ◽  
pp. 627-636
Author(s):  
C Q Lai ◽  
T F Mackay
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Quantitative Traits ◽  
Natural Populations ◽  
Quantitative Variation ◽  
Hybrid Dysgenesis ◽  
X Chromosomes ◽  
Bristle Number ◽  
Seven Generations ◽  
Polygenic Variation

Abstract To determine the ability of the P-M hybrid dysgenesis system of Drosophila melanogaster to generate mutations affecting quantitative traits, X chromosome lines were constructed in which replicates of isogenic M and P strain X chromosomes were exposed to a dysgenic cross, a nondysgenic cross, or a control cross, and recovered in common autosomal backgrounds. Mutational heritabilities of abdominal and sternopleural bristle score were in general exceptionally high-of the same magnitude as heritabilities of these traits in natural populations. P strain chromosomes were eight times more mutable than M strain chromosomes, and dysgenic crosses three times more effective than nondysgenic crosses in inducing polygenic variation. However, mutational heritabilities of the bristle traits were appreciable for P strain chromosomes passed through one nondysgenic cross, and for M strain chromosomes backcrossed for seven generations to inbred P strain females, a result consistent with previous observations on mutations affecting quantitative traits arising from nondysgenic crosses. The new variation resulting from one generation of mutagenesis was caused by a few lines with large effects on bristle score, and all mutations reduced bristle number.

scholarly journals Genome sequencing of four culinary herbs reveals terpenoid genes underlying chemodiversity in the Nepetoideae

DNA Research ◽  
2020 ◽  
Vol 27 (3) ◽  
Author(s):  
Nolan Bornowski ◽  
John P Hamilton ◽  
Pan Liao ◽  
Joshua C Wood ◽  
Natalia Dudareva ◽  
...  
Keyword(s):  
Leaf Tissue ◽  
Terpene Synthases ◽  
Genomic Analyses ◽  
Genes Encoding ◽  
Medicinal Properties ◽  
Culinary Herbs ◽  
Rosmarinus Officinalis L ◽  
Origanum Majorana ◽  
Genome Assemblies ◽  
High Quality Genome

Abstract Species within the mint family, Lamiaceae, are widely used for their culinary, cultural, and medicinal properties due to production of a wide variety of specialized metabolites, especially terpenoids. To further our understanding of genome diversity in the Lamiaceae and to provide a resource for mining biochemical pathways, we generated high-quality genome assemblies of four economically important culinary herbs, namely, sweet basil (Ocimum basilicum L.), sweet marjoram (Origanum majorana L.), oregano (Origanum vulgare L.), and rosemary (Rosmarinus officinalis L.), and characterized their terpenoid diversity through metabolite profiling and genomic analyses. A total 25 monoterpenes and 11 sesquiterpenes were identified in leaf tissue from the 4 species. Genes encoding enzymes responsible for the biosynthesis of precursors for mono- and sesqui-terpene synthases were identified in all four species. Across all 4 species, a total of 235 terpene synthases were identified, ranging from 27 in O. majorana to 137 in the tetraploid O. basilicum. This study provides valuable resources for further investigation of the genetic basis of chemodiversity in these important culinary herbs.

Specificity of Chromosome Damage Caused by the Rex Element of Drosophila melanogaster

Genetics ◽  
1996 ◽  
Vol 144 (1) ◽  
pp. 109-115 ◽  
Author(s):  
Leonard G Robbins
Keyword(s):  
Drosophila Melanogaster ◽  
Early Development ◽  
X Chromosome ◽  
Ribosomal Rna ◽  
Chromosome Damage ◽  
Genetic Element ◽  
Single Chromosome ◽  
Experimental Cross ◽  
Rdna Array ◽  
Early Embryos

Abstract Rex is a multicopy genetic element that maps within an X-linked ribosomal RNA gene (rDNA) array of D. melanogaster. Acting maternally, Rex causes recombination between rDNA arrays in a few percent of early embryos. With target chromosomes that contain two rDNA arrays, the exchanges either delete all of the material between the two arrays or invert the entire intervening chromosomal segment. About a third of the embryos produced by Rex homozygotes have cytologically visible chromosome damage, nearly always involving a single chromosome. Most of these embryos die during early development, displaying a characteristic apoptosis-like phenotype. An experiment that tests whether the cytologically visible damage is rDNA-specific is reported here. In this experiment, females heterozygous for Rex and an rDNA-deficient X chromosome were crossed to males of two genotypes. Some of the progeny from the experimental cross entirely lacked rDNA, while all of the progeny from the control cross had at least one rDNA array. A significantly lower frequency of early-lethal embryos in the experimental cross, proportionate to the fraction of rDNA-deficient embryos, demonstrates that Rex preferentially damages rDNA.

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