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Sequencher contig color4/1/2023 In Brassica rapa, gene CNV has been shown to be involved in morphological variation and an analysis of the poplar “pan-genome” revealed at least 3000 genes affected by CNV. While early investigation of CNV focused on mammals, several subsequent studies have looked at plant genomes. One example is the duplication of MWS/MLS, associated with better trichromatic color vision. In mammals, many examples of CNVs with a major phenotypic effect have been found. With the development of NGS, our ability to detect CNVs increased dramatically, using tools based on split reads, paired-end mapping, sequencing depth, or even de novo assembly. These methods had severe weaknesses, leading to low resolution and problems detecting novel and rare mutations. Of particular interest from a functional point of view is gene duplication, leading to copy number variation (CNV).īefore Next-Generation Sequencing (NGS) was available, genome-wide detection of CNVs was achieved using DNA microarrays. There are many kinds of SVs, e.g., indels, inversions, and translocations. With the sequencing of genomes becoming routine, it is evident that structural variants (SVs) play a major role in genome variation. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggests that future analyses based on independently assembled genomes will be very informative. thaliana are artifacts and suggest that great caution is needed when analyzing SNP data from short-read sequencing. Our study confirms that most heterozygous SNP calls in A. We also demonstrate that cryptic structural variation produces highly inaccurate estimates of DNA methylation polymorphism. Specific examples included an annotated gene and nearby transposon that transpose together. We identify 2500 putatively duplicated genes and validate them using de novo genome assemblies from six lines. Focusing on such pseudo-heterozygosity in annotated genes, we use genome-wide association to map the position of the duplicates. The heterozygosity we observe consists of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. thaliana) is highly selfing, and that extensively heterozygous individuals have been removed, we hypothesize that these SNPs reflected cryptic copy number variation. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million (44%) heterozygous SNPs. Spurious SNPs may result from mapping of reads to unrecognized duplicated regions. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome. It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons.
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