Comparative genome analysis of programmed DNA elimination in nematodes
| Autor: | Laura K. White, Pui-Yan Kwok, Yuanyuan Kang, Alice V. Easton, Richard E. Davis, Shenghan Gao, Jianbin Wang, Martin K. Nielsen, Yongqiao Sun, Thomas B. Nutman, Yulia Mostovoy, Songnian Hu, Maxim V. Zagoskin, Bing Zhang |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
Male Nematoda Biology Genome Evolution Molecular 03 medical and health sciences chemistry.chemical_compound Chromosome Breakpoints 0302 clinical medicine Ascaridoidea Genetics Animals Gene Ascaris suum Genetics (clinical) Germ-Line Mutation Repetitive Sequences Nucleic Acid Sex Chromosomes Research Chromosome Toxocara canis Chromosome Breakage Molecular Sequence Annotation Sequence Analysis DNA DNA Helminth Telomere biology.organism_classification Alternative Splicing 030104 developmental biology chemistry Female Programmed DNA elimination Chromosome breakage RNA Helminth Transcriptome 030217 neurology & neurosurgery DNA Reference genome |
| Zdroj: | Genome research. 27(12) |
| ISSN: | 1549-5469 |
| Popis: | Programmed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA elimination typically occurs in somatic cells during early development, leaving the germline genome intact. Reference genomes for metazoa that undergo DNA elimination are not available. Here, we generated germline and somatic reference genome sequences of the DNA eliminating pig parasitic nematode Ascaris suum and the horse parasite Parascaris univalens. In addition, we carried out in-depth analyses of DNA elimination in the parasitic nematode of humans, Ascaris lumbricoides, and the parasitic nematode of dogs, Toxocara canis. Our analysis of nematode DNA elimination reveals that in all species, repetitive sequences (that differ among the genera) and germline-expressed genes (approximately 1000–2000 or 5%–10% of the genes) are eliminated. Thirty-five percent of these eliminated genes are conserved among these nematodes, defining a core set of eliminated genes that are preferentially expressed during spermatogenesis. Our analysis supports the view that DNA elimination in nematodes silences germline-expressed genes. Over half of the chromosome break sites are conserved between Ascaris and Parascaris, whereas only 10% are conserved in the more divergent T. canis. Analysis of the chromosomal breakage regions suggests a sequence-independent mechanism for DNA breakage followed by telomere healing, with the formation of more accessible chromatin in the break regions prior to DNA elimination. Our genome assemblies and annotations also provide comprehensive resources for analysis of DNA elimination, parasitology research, and comparative nematode genome and epigenome studies. |
| Databáze: | OpenAIRE |
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