Chromatin diminution in the copepod <i>Mesocyclops edax</i>: elimination of both highly repetitive and nonhighly repetitive DNA

McKinnon, Christian; Drouin, Guy

doi:10.1139/gen-2012-0097

Cited by 17 publications

(18 citation statements)

References 59 publications

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“…This may be important, as eukaryotic genomes are not homogenous and selection can vary greatly across the genome [76]. Microsatellites located in or near functional genes are likely to be more exposed to selection and selective sweeps than those occurring in gene deserts, and it is known that vertebrate microsatellites are often found in expressed genes [77].…”

Section: Discussionmentioning

confidence: 99%

The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)

et al. 2014

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Biologists routinely use molecular markers to identify conservation units, to quantify genetic connectivity, to estimate population sizes, and to identify targets of selection. Many imperiled eagle populations require such efforts and would benefit from enhanced genomic resources. We sequenced, assembled, and annotated the first eagle genome using DNA from a male golden eagle (Aquila chrysaetos) captured in western North America. We constructed genomic libraries that were sequenced using Illumina technology and assembled the high-quality data to a depth of ∼40x coverage. The genome assembly includes 2,552 scaffolds >10 Kb and 415 scaffolds >1.2 Mb. We annotated 16,571 genes that are involved in myriad biological processes, including such disparate traits as beak formation and color vision. We also identified repetitive regions spanning 92 Mb (∼6% of the assembly), including LINES, SINES, LTR-RTs and DNA transposons. The mitochondrial genome encompasses 17,332 bp and is ∼91% identical to the Mountain Hawk-Eagle (Nisaetus nipalensis). Finally, the data reveal that several anonymous microsatellites commonly used for population studies are embedded within protein-coding genes and thus may not have evolved in a neutral fashion. Because the genome sequence includes ∼800,000 novel polymorphisms, markers can now be chosen based on their proximity to functional genes involved in migration, carnivory, and other biological processes.

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Section: Discussionmentioning

confidence: 99%

The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)

et al. 2014

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“…In the nematode Parascaris univalens and copepod Mesocyclops edax , the eliminated sequences account for ~90% of the germline genome as part of genome differentiation (26, 27). Similarly in Lamprey, an order of jawless fish, 20% of the germline sequences are eliminated during somatic differentiation.…”

Section: Introductionmentioning

confidence: 99%

Programmed Genome Rearrangements in the Ciliate Oxytricha

Yerlici

Landweber

2014

Microbiol Spectr

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The ciliate Oxytricha is a microbial eukaryote with two genomes, one of which experiences extensive genome remodeling during development. Each round of conjugation initiates a cascade of events that construct a transcriptionally active somatic genome from a scrambled germline genome, with considerable help from both long and small noncoding RNAs. This process of genome remodeling entails massive DNA deletion and reshuffling of remaining DNA segments to form functional genes from their interrupted and scrambled germline precursors. The use of Oxytricha as a model system provides an opportunity to study an exaggerated form of programmed genome rearrangement. Furthermore, studying the mechanisms that maintain nuclear dimorphism and mediate genome rearrangement has demonstrated a surprising plasticity and diversity of non-coding RNA pathways, with new roles that go beyond conventional gene silencing. Another aspect of ciliate genetics is their unorthodox patterns of RNA-mediated, epigenetic inheritance, that rival Mendelian inheritance. This review takes the reader through the key experiments in a model eukaryote that led to fundamental discoveries in RNA biology and pushes the biological limits of DNA processing.

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“…However, MITEs that are even larger than m Pok have now been discovered in phylogenetically diverse eukaryotes (reviewed in [30]) suggesting that large MITEs are more common than once thought. One mechanism to explain the origin of large MITEs is progressive internal deletion of autonomous DNA TEs and subsequent selection for increasing transposition rate among the resultant elements over time [31].…”

Section: Discussionmentioning

confidence: 99%

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

et al. 2013

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BackgroundOnly a few transposable elements are known to exhibit site-specific insertion patterns, including the well-studied R-element retrotransposons that insert into specific sites within the multigene rDNA. The only known rDNA-specific DNA transposon, Pokey (superfamily: piggyBac) is found in the freshwater microcrustacean, Daphnia pulex. Here, we present a genome-wide analysis of Pokey based on the recently completed whole genome sequencing project for D. pulex.ResultsPhylogenetic analysis of Pokey elements recovered from the genome sequence revealed the presence of four lineages corresponding to two divergent autonomous families and two related lineages of non-autonomous miniature inverted repeat transposable elements (MITEs). The MITEs are also found at the same 28S rRNA gene insertion site as the Pokey elements, and appear to have arisen as deletion derivatives of autonomous elements. Several copies of the full-length Pokey elements may be capable of producing an active transposase. Surprisingly, both families of Pokey possess a series of 200 bp repeats upstream of the transposase that is derived from the rDNA intergenic spacer (IGS). The IGS sequences within the Pokey elements appear to be evolving in concert with the rDNA units. Finally, analysis of the insertion sites of Pokey elements outside of rDNA showed a target preference for sites similar to the specific sequence that is targeted within rDNA.ConclusionsBased on the target site preference of Pokey elements and the concerted evolution of a segment of the element with the rDNA unit, we propose an evolutionary path by which the ancestors of Pokey elements have invaded the rDNA niche. We discuss how specificity for the rDNA unit may have evolved and how this specificity has played a role in the long-term survival of these elements in the subgenus Daphnia.

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Chromatin diminution in the copepod Mesocyclops edax: elimination of both highly repetitive and nonhighly repetitive DNA

Cited by 17 publications

References 59 publications

The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)

The Genome Sequence of a Widespread Apex Predator, the Golden Eagle (Aquila chrysaetos)

Programmed Genome Rearrangements in the Ciliate Oxytricha

In and out of the rRNA genes: characterization of Pokey elements in the sequenced Daphnia genome

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