Genome Expression Balance in a Triploid Trihybrid Vertebrate McElroy et al. 2017

Ambystoma Hybrids = unisexually female polyploid salamanders Range from 3-5 genomes Single monophyletic mitochondrial lineage from ~5 Mya Parental species A. laterale A. tigrinum A. texanum

Fun fact: unisexual Ambystoma are the oldest unisexual vertebrates known (Bi and Bogart 2010)

Overlapping distribution of unisexual populations (range in grey) and A. laterale

Rationale Few gene expression studies for polyploid animals Mechanism(s) of successful polyploid species not well understood Does kleptogenesis have consequences for epigenetic stability, nuclear and mitonuclear discordance? Find link between differential gene/genome expression and ecological success Be honest, this is super cool anyway, so why not.

Question: Prediction: Are homeologs from the three subgenomes being expressed equally, or is there genome dominance, or are there specific expression patterns for different genes? Prediction: Subgenomes of a unisexual individual will display relatively similar patterns of expression, probably associated with maintenance of a diverse array of “captured” genome combinations

Methods 4 Illumina TruSeq Stranded mRNA libraries (100-400 bp) Illumina HiSeq 2000 single end 100 bp reads

Methods 4 Illumina TruSeq Stranded mRNA libraries (100-400 bp) Illumina HiSeq 2000 single end 100 bp reads Trinity CD-IT-EST clustered the sequences per transcriptome, reducing redundancy BLAST+ Blast2GO for GO annotations

Methods 4 Illumina TruSeq Stranded mRNA libraries (100-400 bp) Illumina HiSeq 2000 single end 100 bp reads Trinity CD-IT-EST clustered the sequences per transcriptome, reducing redundancy BLAST+ Blast2GO for GO annotations Unique and identical GO ortholog set “Competitive mapping” of RNA reads to reference orthologs

Methods 4 Illumina TruSeq Stranded mRNA libraries (100-400 bp) Illumina HiSeq 2000 single end 100 bp reads Trinity CD-IT-EST clustered the sequences per transcriptome, reducing redundancy BLAST+ Blast2GO for GO annotations Unique and identical GO ortholog set “Competitive mapping” of RNA reads to reference orthologs Corrected expression of the unisexual sequences Normalized expression (FPKM) Evaluation of expression

Results Some differentially expressed genes

Results Some differentially expressed genes No apparent genome dominance No clear trend of differential expression by gene type (GO)

Results Some differentially expressed genes No apparent genome dominance No clear trend of differential expression by gene type (GO) However, statistically, interacting genes and/or pathways are more likely to be expressed by the same subgenome No relationship for the expression levels of genes/pathways that do not interact and the subgenome that encodes them

Conclusions There is balanced gene expression across subgenomes Differentially expressed genes are consistent within functional pathways Suggests epistatic interactions affect gene expression regulation Possible helps negate genomic incompatibility consequences Unisexual Ambystoma expresses its genes similarly to its three sexual progenitor species Possible strong selection to maintain the expression profile of an introgressed genome (avoids issue of loss of a dominant genome)

Limitations These methods measure relative expression differences among subgenomes in a polyploid Since absolute expression differences are not measure, cannot assess if gene expression levels are on the same scale as the genes in the diploid relative This study uses a single unisexual individual of one particular biotype (LTTi) but there are many other subgenome combinations

Questions How could absolute gene expression differences be measured? Does this method of comparing expression profiles of individual genes (vs whole transcriptome) appear adequate? Why is the A. laterale genome present in all unisexual Ambystoma if there is no genome dominance, or biased gene expression (except a few genes from A. tigrinum)? Do differences in number of subgenomes and/or subgenome combinations affect gene expression patterns?