The Complete Genome Sequence of Ajuga reptans (Lamiaceae, Lamiales), Bugleweed

Toby Pirro; Stacy Pirro

doi:10.56179/001c.117758

Pirro, Toby, and Stacy Pirro. 2024. “The Complete Genome Sequence of Ajuga Reptans (Lamiaceae, Lamiales), Bugleweed.” Biodiversity Genomes, May. https://doi.org/10.56179/001c.117758.

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Abstract

We present the whole genome sequence of Ajuga reptans. 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 (SRR24502601) and assembled genome (JAUEKW000000000).

Methods

A single leaf from a cultivated plant was used for this study.

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 × 150bp format. The resulting fastq files were trimmed of adapter/primer sequence 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 reads (SRR24502601) and the assembled genome (JAUEKW000000000) are available in Genbank.

Funding

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

Submitted: May 19, 2024 EDT

Accepted: May 23, 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.” 2021. https://github.com/zanfona734/zanfona.