The Complete Genome Sequence of Haemulon aurolineatum (Haemulidae, Lutjaniformes), the Tomtate Grunt

Carmen D. Pedraza Marron; Stacy Pirro; Ricardo Betancur

doi:10.56179/001c.125785

Pedraza Marron, Carmen D., Stacy Pirro, and Ricardo Betancur. 2024. “The Complete Genome Sequence of Haemulon Aurolineatum (Haemulidae, Lutjaniformes), the Tomtate Grunt.” Biodiversity Genomes, November. https://doi.org/10.56179/001c.125785.

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Abstract

We present the whole genome sequence of Haemulon aurolineatum. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR28478403) and assembled genome (JBCAUF000000000).

Methods

A single wild-collected specimen was used for sequencing. DNA extraction was performed using the Qiagen DNAeasy genomic extraction kit using the standard process. A paired-end sequencing library was constructed using the Illumina TruSeq kit according to the manufacturer’s instructions. The library was sequenced on an Illumina Hi-Seq platform in paired-end, 2 × 150 bp 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 v2.5 (Bankevich, Nurk, Antipov, et al. 2012) followed by a finishing step using Zanfona v1.0 (Kieras 2021) to make additional contig joins based on conserved regions in related species.

Data availability

Raw and assembled data are publicly available via GenBank.

Raw genome data: SRR28478403

Assembled genome: JBCAUF000000000

Funding

Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345.

Submitted: November 01, 2024 EDT

Accepted: November 10, 2024 EDT

References

Bankevich, A., S. Nurk, D. Antipov, et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” J Comput Biol 19 (5): 455–77. https://doi.org/10.1089/cmb.2012.0021.

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Bolger, A. M., M. Lohse, and B. Usadel. 2014. “Trimmomatic: A Flexible Trimmer for Illumina Sequence Data.” Bioinformatics 30 (15): 2114–20. https://doi.org/10.1093/bioinformatics/btu170.

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Kieras, M. 2021. “Zanfona, a Genome Finishing Process for Use with Paired-End Short Reads.” https://github.com/zanfona734/zanfona.

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