Variation in cytonuclear expression accommodation among allopolyploid plants

Abstract

Cytonuclear coevolution is a common feature among plants, which coordinates gene expression and protein products between the nucleus and organelles. Consequently, lineage-specific differences may result in incompatibilities between the nucleus and cytoplasm in hybrid taxa. Allopolyploidy is also a common phenomenon in plant evolution. The hybrid nature of allopolyploids may result in cytonuclear incompatibilities, but the massive nuclear redundancy created during polyploidy affords additional avenues for resolving cytonuclear conflict (i.e., cytonuclear accommodation). Here we evaluate expression changes in organelle-targeted nuclear genes for six allopolyploid lineages that represent four genera (i.e., Arabidopsis, Arachis, Chenopodium, and Gossypium) and encompass a range in polyploid ages. Because incompatibilities between the nucleus and cytoplasm could potentially result in biases toward the maternal homoeolog and/or maternal expression level, we evaluate patterns of homoeolog usage, expression bias, and expression level dominance in cytonuclear genes relative to the background of non-cytonuclear expression changes and to the diploid parents. Although we find subsets of cytonuclear genes in most lineages that match our expectations of maternal preference, these observations are not consistent among either allopolyploids or categories of organelle-targeted genes. Our results indicate that cytonuclear expression accommodation may be a subtle and/or variable phenomenon that does not capture the full range of mechanisms by which allopolyploid plants resolve nuclear-cytoplasmic incompatibilities.

Organellar transcripts dominate the cellular mRNA pool across plants of varying ploidy levels

“…Briefly, RNA was extracted from the allopolyploid and its model diploid progenitors, ribo-depleted, and then sequenced as PE150 on a NovaSeq 6000 S4 flow cell. Reads from all three species within each genus were mapped to the annotated protein-coding sequences from the polyploid nuclear genome and from the organellar genomes of a representative member of the genus using Kallisto (67), as described elsewhere (57). We analyzed five biological replicates for each species with the exceptions of Arachis hypogaea and C. suecicum .…”

“…In the case of recent insertions, true mitochondrial and plastid reads can map equally well to numt/nupt pseudogenes or to the actual organellar genomes, resulting in an underestimate of organellar expression. These cases were accounted for prior to read mapping by excluding numts and nupts that were annotated as protein-coding genes from each nuclear reference (57). Second, because we employed a ribo-depletion strategy rather than polyA selection, sequencing produced large quantities of reads from non-coding RNAs (ncRNAs) that lack polyA tails and would be excluded from typical mRNA-seq libraries (69), such as signal recognition particle RNAs and U1 and U2 spliceosomal RNAs.…”

“…For direct comparisons of nuclear gene expression between polyploids and related diploids, we used the set of previously identified gene “quartets” that were present as two homoeologous copies in an allopolyploid and a single copy in each of the corresponding diploid relatives (57). Because read mapping for all species was performed against the polyploid reference genome, we summed TPM values for the two homoeologs in each quartet for subsequent comparisons of expression.…”

“…The sampling of diploids and polyploids from Arabidopsis , Arachis , Chenopodium , and Gossypium is described elsewhere, including a summary of the history of allopolyploidization in each lineage, plant growth conditions, RNA extraction, sequencing, and read mapping (57). Briefly, RNA was extracted from the allopolyploid and its model diploid progenitors, ribo-depleted, and then sequenced as PE150 on a NovaSeq 6000 S4 flow cell.…”

“…Previous work in these allopolyploids has found that homoeologs in both nuclear subgenomes are expressed at similar levels for most cytonuclear interaction functional categories (57). As such, doubling of the nuclear genome has the potential to alter the balance of cytonuclear gene expression, at least in principle (22).…”