PT  - JOURNAL ARTICLE
AU  - Benjamin Jaegle
AU  - Luz Mayela Soto-Jiménez
AU  - Robin Burns
AU  - Fernando A. Rabanal
AU  - Magnus Nordborg
TI  - Extensive gene duplication in Arabidopsis revealed by pseudo-heterozygosity
AID  - 10.1101/2021.11.15.468652
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.11.15.468652
4099  - http://biorxiv.org/content/early/2021/11/22/2021.11.15.468652.short
4100  - http://biorxiv.org/content/early/2021/11/22/2021.11.15.468652.full
AB  - Background It is becoming apparent that genomes harbor massive amounts of structural variation, and that this variation has largely gone undetected for technical reasons. In addition to being inherently interesting, structural variation can cause artifacts when short-read sequencing data are mapped to a reference genome. In particular, spurious SNPs (that do not show Mendelian segregation) may result from mapping of reads to duplicated regions. Recalling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million heterozygous SNPs (44% of total). Given that Arabidopsis thaliana (A. thaliana) is highly selfing, we hypothesized that these SNPs reflected cryptic copy number variation, and investigated them further.Results While genuine heterozygosity should occur in tracts within individuals, heterozygosity at a particular locus is instead shared across individuals in a manner that strongly suggests it reflects segregating duplications rather than actual heterozygosity. Focusing on pseudo-heterozygosity in annotated genes, we used GWAS to map the position of the duplicates, identifying 2500 putatively duplicated genes. The results were validated using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that, in fact, transpose together.Conclusions Our study confirms that most heterozygous SNPs calls in A. thaliana are artifacts, and suggest that great caution is needed when analysing SNP data from short-read sequencing. The finding that 10% of annotated genes are copy-number variables, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggest that future analyses based on independently assembled genomes will be very informative.Competing Interest StatementThe authors have declared no competing interest.