Abstract
We present genome sequences of 63 species of catfish from the Ariidae family. Illumina sequencing was performed on tissue from wild-collected museum specimens. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data are publicly available via Genbank.
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 raw read data and assembled genomes are available on Genbank:
| Amissidens hainesi | JANZXU000000000 |
| Ariopsis seemanni | JAOANJ000000000 |
| Arius gagora | JAODTS000000000 |
| Arius madagascariensis | JANZXT000000000 |
| Bagre pinnimaculatus | JAPEKL000000000 |
| Batrachocephalus mino | JAOBAL000000000 |
| Brustiarius nox | JAODHU000000000 |
| Brustiarius proximus | JAOXJH000000000 |
| Brustiarius solidus | JAODKP000000000 |
| Cathorops aguadulce | JAPEIY000000000 |
| Cathorops dasycephalus | JAPEKN000000000 |
| Cathorops festae | JAODXR000000000 |
| Cathorops hypophthalmus | JAPEKO000000000 |
| Cathorops melanopus | JAODLJ000000000 |
| Cathorops multiradiatus | JAPEKM000000000 |
| Cephalocassis borneensis | JAOPUC000000000 |
| Amissidens hainesi | JANZXU000000000 |
| Cephalocassis melanochir | JAODOG000000000 |
| Chinchaysuyoa labiata | JAODLF000000000 |
| Cinetodus carinatus | JAODOI000000000 |
| Cinetodus crassilabris | JAODKQ000000000 |
| Cinetodus froggatti | JAODOL000000000 |
| Cochlefelis danielsi | JAODKR000000000 |
| Cochlefelis spatula | JAODKX000000000 |
| Galeichthys feliceps | JAODTV000000000 |
| Genidens genidens | JAODOH000000000 |
| Genidens machadoi | JAOTJA000000000 |
| Genidens planifrons | JAOANL000000000 |
| Hemiarius dioctes | JAODID000000000 |
| Hemiarius stormii | JAODOD000000000 |
| Nedystoma dayi | JAODIC000000000 |
| Nedystoma novaeguineae | JAODLB000000000 |
| Nemapteryx armiger | JAODOB000000000 |
| Nemapteryx augusta | JAODHT000000000 |
| Nemapteryx nenga | JAODOC000000000 |
| Neoarius berneyi | JAODIF000000000 |
| Neoarius graeffei | JALHSM000000000 |
| Neoarius leptaspis | JAODTU000000000 |
| Neoarius midgleyi | JAPEKJ000000000 |
| Neoarius paucus | JAPUBO000000000 |
| Neoarius pectoralis | JAPTHB000000000 |
| Neoarius utarus | JAODOJ000000000 |
| Netuma bilineata | JAODOK000000000 |
| Notarius cookei | JAOEHH000000000 |
| Notarius kessleri | JAOBAM000000000 |
| Notarius lentiginosus | JAODVO000000000 |
| Notarius quadriscutis | JANZLB000000000 |
| Occidentarius platypogon | JAOBRE000000000 |
| Osteogeneiosus militaris | JANZLE000000000 |
| Plicofollis layardi | JAODHV000000000 |
| Plicofollis nella | JAODOM000000000 |
| Plicofollis tonggol | JAODOE000000000 |
| Potamarius nelsoni | JAODKY000000000 |
| Potamarius usumacintae | JAOEHJ000000000 |
| Potamosilurus coatesi | JAODKU000000000 |
| Potamosilurus latirostris | JAODKZ000000000 |
| Potamosilurus macrorhynchus | JAOBYD000000000 |
| Potamosilurus velutinus | JAODLA000000000 |
| Sciades assimilis | JAODJS000000000 |
| Sciades dowii | JAODKS000000000 |
| Sciades herzbergii | JAPFFA000000000 |
| Sciades mastersi | JAODKO000000000 |
| Sciades proops | JAODOF000000000 |
| Sciades troschelii | JAODIB000000000 |
Funding
Funding was provided by Iridian Genomes grant# IRGEN_RG_2021–1345: Genomic Studies of Eukaryotic Taxa.
REFERENCES
- Bankevich Anton, Nurk Sergey, Antipov Dmitry, Gurevich Alexey A., Dvorkin Mikhail, Kulikov Alexander S., Lesin Valery M., et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77. 10.1089/cmb.2012.0021. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bolger Anthony M., Lohse Marc, and Usadel Bjoern. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. 10.1093/bioinformatics/btu170. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kieras M, O’Neill K, and Pirro S. 2021. “Zanfona, a Genome Assembly Finishing Tool for Paired-End Illumina Reads.” 2021. https://github.com/zanfona734/zanfona.