Zea mays RNA-seq estimated transcript abundances are strongly affected by read mapping bias
| Autor: | Cortland K. Griswold, Lewis Lukens, Shuhua Zhan |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
RNA-Seq Biology QH426-470 Mapping bias Zea mays 01 natural sciences Genome Genetic diversity 03 medical and health sciences Genetic variation Genetics Allele Gene 030304 developmental biology 0303 health sciences Sequence Analysis RNA Gene Expression Profiling Sequence divergence Transcriptome variation food and beverages Maize eQTL analysis Gene coexpression analysis DNA microarray Transcriptome TP248.13-248.65 Research Article 010606 plant biology & botany Reference genome Biotechnology |
| Zdroj: | BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021) BMC Genomics |
| ISSN: | 1471-2164 |
| Popis: | Background Genetic variation for gene expression is a source of phenotypic variation for natural and agricultural species. The common approach to map and to quantify gene expression from genetically distinct individuals is to assign their RNA-seq reads to a single reference genome. However, RNA-seq reads from alleles dissimilar to this reference genome may fail to map correctly, causing transcript levels to be underestimated. Presently, the extent of this mapping problem is not clear, particularly in highly diverse species. We investigated if mapping bias occurred and if chromosomal features associated with mapping bias. Zea mays presents a model species to assess these questions, given it has genotypically distinct and well-studied genetic lines. Results In Zea mays, the inbred B73 genome is the standard reference genome and template for RNA-seq read assignments. In the absence of mapping bias, B73 and a second inbred line, Mo17, would each have an approximately equal number of regulatory alleles that increase gene expression. Remarkably, Mo17 had 2–4 times fewer such positively acting alleles than did B73 when RNA-seq reads were aligned to the B73 reference genome. Reciprocally, over one-half of the B73 alleles that increased gene expression were not detected when reads were aligned to the Mo17 genome template. Genes at dissimilar chromosomal ends were strongly affected by mapping bias, and genes at more similar pericentromeric regions were less affected. Biased transcript estimates were higher in untranslated regions and lower in splice junctions. Bias occurred across software and alignment parameters. Conclusions Mapping bias very strongly affects gene transcript abundance estimates in maize, and bias varies across chromosomal features. Individual genome or transcriptome templates are likely necessary for accurate transcript estimation across genetically variable individuals in maize and other species. |
| Databáze: | OpenAIRE |
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