Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod developmentReportar como inadecuado




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BMC Genomics

, 15:186

Multicellular invertebrate genomics

Abstract

BackgroundChromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 – 75 Gb, 12–74 Gb of which are lost from pre-somatic cell lineages at germline – soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown.

ResultsHere, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1 verifiable transposable elements TEs, or 2 non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger i.e. less divergent elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome.

ConclusionsOur results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.

KeywordsChromatin diminution Genome size Transposable elements Germline-soma differentiation Copepod Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-15-186 contains supplementary material, which is available to authorized users.

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Autor: Cheng Sun - Grace Wyngaard - D Brian Walton - Holly A Wichman - Rachel Lockridge Mueller

Fuente: https://link.springer.com/







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