Data for: Genome assembly, annotation, and SNP discovery of the blackstripe livebearer Poeciliopsis prolifica shed light on fish placenta evolution

Abstract

Poeciliidae is a family of live-bearing fish in which some species fully provision eggs before fertilization (lecithotrophy) and some continue to provision embryos after fertilization (matrotrophy). The viviparous matrotrophic species have evolved a structure with functional similarity to the mammalian placenta. In placental mammals, the evolutionary innovation of placenta led to parental conflict, resulting in a phenomenon known as genomic imprinting. To investigate potential genome imprinting in placental fish, crosses from inbred lines are needed to track the parental allele transmission directions to estimate allele-specific expression. In this study, we developed two inbred lines of blackstripe livebearer Poeciliopsis prolifica, a placental Poeciliid whose embryos increase in dry mass by a factor of 7 during development. We reported a 674,152,735 Mbp genome assembly of Poeciliopsis prolifica in 504 contigs with excellent continuity (contig N50 7.7 Mb) and completeness (BUSCO score 97.2%). A total of 27,227 protein-coding genes were annotated from the merged data sets based on bioinformatic prediction and RNA sequencing and homology evidencesupport. Among them, 19,337 have informative SNPs between the two inbred lines, providing sufficient SNP density to infer allele-specific expression genome-wide. Phylogenomic analyses revealed that Poeciliopsis prolifica diverged from the guppy approximately 19 million years ago. Gene family analysis identified the rapid expansion of families with T-cell activation and other immune-related functions in Poeciliopsis prolifica, which may be functionally related to the evolution of the placenta. Our research provides the necessary resources and the genomic toolkit for investigating parental allele-specific gene expression, which will shed light on the evolution of the placenta and genomic imprinting.