Fragaria chiloensis Genome v1.0 Assembly & Annotation

Analysis NameFragaria chiloensis Genome v1.0 Assembly & Annotation
MethodHifiasm (0.13)
SourcePacBio HiFi reads
Date performed2022-06-08


Caroline M S Cauret, Sebastian M E Mortimer, Marcelina C Roberti, Tia-Lynn Ashman, Aaron Liston. Chromosome-scale assembly with a phased sex-determining region resolves features of early Z and W chromosome differentiation in a wild octoploid strawberry. G3 Genes|Genomes|Genetics, (2022)


When sex chromosomes stop recombining, they start to accumulate differences. The sex-limited chromosome (Y or W) especially is expected to degenerate via the loss of nucleotide sequence and the accumulation of repetitive sequences. However, how early signs of degeneration can be detected in a new sex chromosome is still unclear. The sex determining region (SDR) of the octoploid strawberries is young, small, and dynamic. Using PacBio HiFi reads, we obtained a chromosome scale assembly of a female (ZW) Fragaria chiloensis plant carrying the youngest and largest of the known SDR on the W in strawberries. We fully characterized the previously incomplete SDR, confirming its gene content, genomic location and evolutionary history. Resolution of gaps in the previous characterization of the SDR added 10 kbp of sequence including a non-canonical LTR-retrotransposon; whereas the Z sequence revealed a Harbinger transposable element adjoining the SDR insertion site. Limited genetic differentiation of the sex chromosomes coupled with structural variation may indicate an early stage of W degeneration. The sex chromosomes have a similar percentage of repeats but differ in their repeat distribution. Differences in the pattern of repeats (transposable element polymorphism) apparently precede sex chromosome differentiation, thus potentially contributing to recombination cessation as opposed to being a consequence of it.


The Fragaria chiloensis Genome v1.0 assembly file is available in FASTA format.


Chromosomes (FASTA file) Fragaria_chiloensis_v1.0.fasta.gz


Gene Predictions

The Fragaria chiloensis v1.0 genome gene prediction file is available in GFF3 format.


Genes (GFF3 file) Fragaria_chiloensis_v1.0.genes.gff3.gz