Methods

Tissues from single, wild-collected individuals were used for this study. DNA extraction was performed using the Qiagen DNEasy genomic extraction kit using the standard process. Paired-end sequencing libraries were constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequences and low-quality regions with Trimmomatic v0.33 (Bolger, Lohse, and Usadel 2014). The trimmed sequence was assembled by SPAdes v3.15.4 (Bankevich et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).

Results and Data Availability

All genomes are available on Genbank:

Amblyopsis hoosieri JAODUE000000000
Amblyopsis rosae JAODTR000000000
Amblyopsis spelaea JAODUF000000000
Aphredoderus sayanus JAODUG000000000
Chologaster cornuta JAODVN000000000
Forbesichthys agassizii JAODLL000000000
Forbesichthys papilliferus JAODOY000000000
Percopsis omiscomaycus JAODLI000000000
Percopsis transmontana JAOEHI000000000
Speoplatyrhinus poulsoni JAOEGT000000000
Typhlichthys eigenmanni JAODUK000000000
Typhlichthys subterraneus JAODUH000000000

Funding

Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.