Biology subjects

Brohammer, A. B.

Publications and source records attributed to Brohammer, A. B..

4 recordsLinked to original sources

bioRxiv2019

Using multiple reference genomes to identify and resolve annotation inconsistencies

BackgroundAdvances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses.\n\nResultsWe developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrate the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we find several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3-5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilize RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts.\n\nConclusionsSplit-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.

bioinformatics↗

bioRxiv2019

Transposable elements contribute to dynamic genome content in maize

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content. Significance StatementThe majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.

genomics↗

bioRxiv2017

Tandem Duplicate Genes in Maize are Abundant and Date to Two Distinct Periods of Time

Tandem duplicate genes are proximally duplicated and as such occur in the same genomic neighborhood. Using the maize B73 and PH207 de novo genome assemblies, we identified thousands of tandem gene duplicates that account for ~10% of the genes. These tandem duplicates have a bimodal distribution of estimated ages corresponding to known periods of genomic instability. Tandem duplicates had a number of associated features that suggest origins in nonhomologous recombination based on smaller size distribution and higher rate of containing LTRs than non-tandem duplicates. Within relatively recent tandem duplicate genes, ~26% appear to be undergoing degeneration or divergence in function from the ancestral copy. Our results show that tandem duplicates are abundant in maize, arose in bursts throughout maize evolutionary history under multiple potential mechanisms, and may provide a substrate for novel phenotypic variation.

genomics↗

bioRxiv2017

Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Maize is a diverse paleotetraploid species with widespread presence/absence variation and copy number variation. One mechanism through which presence/absence variation can arise is differential fractionation. Fractionation refers to the loss of duplicate gene pairs from one of the maize subgenomes during diploidization and differential fractionation refers to non-shared gene loss events between individuals. We investigated the prevalence of presence/absence variation resulting from differential fractionation in the syntenic portion of the genome using two whole genome de novo assemblies of the inbred lines B73 and PH207. Between these two genomes, syntenic genes were highly conserved with less than 1% of syntenic genes being subject to differential fractionation. The few variable syntenic genes that were identified are unlikely to contribute to functional phenotypic variation, as there is a significant depletion of these genes in annotated gene sets. In further comparisons of 60 diverse inbred lines, non-syntenic genes were six times more likely to be variable compared to syntenic genes, suggesting that comparisons among additional genome assemblies are not likely to result in the discovery of large-scale presence/absence variation among syntenic genes.\n\nSIGNIFICANCE STATEMENTThere is a large amount of presence/absence variation for gene content in maize. One mechanism that has been hypothesized to contribute to this variation is differential fractionation between individuals following the maize whole genome duplication event. Using comparative genomics, with sorghum and rice representing the ancestral state, we observed little evidence of differential fractionation among elite inbred lines and the few differentially fractionated genes identified did not appear to confer functional significance.

plant biology↗