Dataset Information

Effect of recombination on genetic diversity of Caenorhabditis elegans

ABSTRACT: Analysis of natural variants of C. elegans

INSTRUMENT(S): Illumina, Oxford Nanopore PromethION

ORGANISM(S): Caenorhabditis Elegans

SUBMITTER: Johns Hopkins University

PROVIDER: PRJEB80000 | EVA | 2024-09-15

REPOSITORIES: EVA

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Dataset's files

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			Action	DRS
	AB1.clair3.ilmn.bwa.flt.accessioned.vcf.gz	Vcf
	AB1.clair3.ilmn.bwa.flt.accessioned.vcf.gz.csi	Vcf
	AB1.clair3.ilmn.bwa.flt.vcf.csi	Other
	AB1.clair3.ilmn.bwa.flt.vcf.gz	Vcf
	CB4853.clair3.ilmn.bwa.flt.accessioned.vcf.contigs	Other

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Project description:Aspergillus flavus is the major producer of carcinogenic aflatoxins in crops worldwide. Natural populations of A. flavus show tremendous variation in aflatoxin production some of which can be attributed to extreme environmental conditions (e.g., drought), differential regulation of the aflatoxin biosynthetic pathway, missing cluster genes or loss-of-function mutations. Understanding the evolutionary processes that generate genetic diversity in A. flavus may also explain quantitative and qualitative differences in aflatoxigenicity. Several population studies provide indirect evidence of recombination in the aflatoxin gene cluster and genome-wide, using multilocus genealogical approaches. More recently A. flavus has been shown to be functionally heterothallic and capable of sexual reproduction in laboratory crosses. In the present study, we characterize the progeny from nine A. flavus crosses and show that crossovers in the aflatoxin cluster coincide with inferred recombination blocks and hotspots in natural populations, which suggests that recombination in the cluster is primarily driven by sex. Moreover, we show that a single crossover event in the cluster can restore aflatoxigenicity, which is significant as mycotoxin production in A. flavus is highly heritable. aCGH was used to corroborate inferences from cluster-based MLSTs and to possibly identify additional crosovers within the cluster. aCGH comparison between 3 strains of A. flavus: 2 parental (P) and 1 progeny (F1) analyzed at the probe level. A total of 9 trio comparisons were made from a total of 18 isolates analyzed by aCGH. Trio comparisons are as follows: IC278 (P), IC1179 (P) and IC1650 (F1); IC201 (P), IC310 (P) and IC1719 (F1); IC307 (P), IC308 (P) and IC1751 (F1); IC277 (P), IC311 (P) and IC1766 (F1); IC277 (P), IC311 (P) and IC1775 (F1); IC244 (P), IC277 (P) and IC2205 (F1); IC244 (P), IC277 (P) and IC2207 (F1); IC301 (P), IC1179 (P) and IC2171 (F1); and finally IC244 (P), IC277 (P) and IC2209 (F1).

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Effect of recombination on genetic diversity of Caenorhabditis elegans

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