Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis)

Abstract

North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here we present two chromosome-scale reference genome assemblies Spikedace (Meda fulgida) and Loach Minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for Spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb and L75 = 18. The complete assembly for Loach Minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for Spikedace and ∼98% for Loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58% and 29.04% of Spikedace and Loach Minnow total genome lengths to be comprised of protein coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions and evidence of positive selection in both genomes.

A high-quality reference genome for the common creek chub, Semotilus atromaculatus

“…Efforts in the last year have increased and diversified available genomes (e.g. high quality assemblies for Meda fulgida and Tiaroga cobiti , Alexandre et al 2023 ), but Leuciscidae is a hyper-diverse and geographically ubiquitous clade, and there is still a need for genomic resources. Previous genomic studies of creek chub have relied on artificial reference genomes or reference genomes from distantly related taxa (e.g.…”