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

2. 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

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

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

5. 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.

6. 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

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

8. 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

9. 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

10. 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

11. Results
Some differentially expressed genes

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

13. 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

14. 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)

15. 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

16. 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?