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

Abstract

SUMMARYMaize is a diverse paleotetraploid species with considerable 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. Differential fractionation refers to non-shared gene loss events between individuals following a whole-genome duplication event. 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 variably fractionated 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 than 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.

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

“…Only 17% of the duplicate gene clusters that were identified had an interval of greater than two intervening genes between members of the cluster. To determine if specific tandem duplicates were shared between the assemblies, we used homology information that linked the B73 and PH207 gene models (Brohammer et al 2018). Only 50.3% of the B73 tandem duplicate gene clusters and 60% of the PH207 tandem duplicate clusters were shared between the two genomes (Figure 1B).…”

“…Putative tandem duplicate clusters were identified by comparing the B73 version 4 (Jiao et al 2017) and PH207 version 1 (Hirsch et al 2016) maize genome assemblies each to the Sorghum bicolor v3.1 genome assembly (DOE-JGI, http://phytozome.jgi.doe.gov/) with SynMap v2 (Lyons et al 2008) as described in (Brohammer et al 2018). Up to 15 intervening genes were allowed between potential tandem duplicates.…”

“…Gene and transposable element annotations were obtained from Gramene (ftp://ftp.gramene.org/pub/gramene/release-57/gff3/zea_mays/repeat_annotation/B73v4.TE.filtered.gff3.gz). Subgenome assignments were from previously reported syntenic block assignments (Brohammer et al 2018). Windows were classified into “maize1,” “maize2,” or “nonsyntenic” based on majority assignment.…”

“…Amino acid alignments of the subgenome homeologues, tandem duplicates, and putative Sorghum ancestral genes that were previously determined (Brohammer et al 2018) were generated with Clustal-omega version 1.2.1 (Sievers et al 2011). The alignments were back-translated to nucleotides.…”

“…High-quality SNP calls from 62 diverse inbred lines (Brohammer et al , 2018) were used for diversity data. The number of nucleotide differences between the B73 v4 genome assembly and the Sorghum bicolor v. 3.1 genome assembly was used for divergence data.…”