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Stable recombination hotspots in birds

ABSTRACT: We show the fine-scale recombination landscape is stable across tens of millions of years in birds, in sharp contrast to what is seen in primates and mice.

PROVIDER: PRJEB10586 | ENA |

REPOSITORIES: ENA

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Dataset's files

Source:

			Action	DRS
	DB.allchrs.vqsr.filtered.snps.indels.vcf	Other
	gatk.ug.ltf.all_chrs.masked.filtered.phased.vqsr2.vcf	Other
	gatk.ug.zf.all_chrs.masked.filtered.vqsr2.vcf	Other
	ERR1013140.fastq.gz	Fastqsanger.gz
	ERR1013140_1.fastq.gz	Fastqsanger.gz

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Stable recombination hotspots in birds.

Project description:The DNA-binding protein PRDM9 has a critical role in specifying meiotic recombination hotspots in mice and apes, but it appears to be absent from other vertebrate species, including birds. To study the evolution and determinants of recombination in species lacking the gene that encodes PRDM9, we inferred fine-scale genetic maps from population resequencing data for two bird species: the zebra finch, Taeniopygia guttata, and the long-tailed finch, Poephila acuticauda. We found that both species have recombination hotspots, which are enriched near functional genomic elements. Unlike in mice and apes, most hotspots are shared between the two species, and their conservation seems to extend over tens of millions of years. These observations suggest that in the absence of PRDM9, recombination targets functional features that both enable access to the genome and constrain its evolution.

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Project description:In Schizosaccharomyces pombe, DNA replication origins (ORIs) and meiotic recombination hotspots lack consensus sequences and show a bias towards mapping at large intergenic regions (IGRs). To explore whether this preference depended on underlying chromatin features, we have generated genome-wide nucleosome profiles during mitosis and meiosis. We have found that meiotic double-strand break sites (DSB) colocalize strictly with nucleosome-depleted regions (NDRs) and that large IGRs include clusters of NDRs that overlap with almost half of all DSBs. By contrast, ORIs do not colocalize with NDRs and they are regulated independently of DSBs. Physical relocation of NDRs at ectopic loci or modification of their genomic distribution during meiosis was paralleled by the generation of new DSB sites. Over 80% of all meiotic DSBs colocalize with NDRs that are also present during mitosis, indicating that the recombination pattern is largely dependent on constitutive properties of the genome and, to a lesser extent, on the transcriptional profile during meiosis. The organization of ORIs and of DSBs regions in S. pombe reveals similarities and differences relative to Saccharomyces cerevisiae.

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Project description:Meiotic recombination does not occur randomly along a chromosome, but instead tends to be concentrated in small regions, known as "recombination hotspots." Recombination hotspots are thought to be short-lived in evolutionary time due to their self-destructive nature, as gene conversion favors recombination-suppressing alleles over recombination-promoting alleles during double-strand repair. Consistent with this expectation, hotspots in humans are highly dynamic, with little correspondence in location between humans and chimpanzees. Here, we identify recombination hotspots in two lineages of the yeast Saccharomyces paradoxus, and compare their locations to those found previously in Saccharomyces cerevisiae. Surprisingly, we find considerable overlap between the two species, despite the fact that they are at least 10 times more divergent than humans and chimpanzees. We attribute this unexpected result to the low frequency of sex and outcrossing in these yeasts, acting to reduce the population genetic effect of biased gene conversion. Traces from two other signatures of recombination, namely high mutagenicity and GC-biased gene conversion, are consistent with this interpretation. Thus, recombination hotspots are not inevitably short-lived, but rather their persistence through evolutionary time will be determined by the frequency of outcrossing events in the life cycle.

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