The Complete Genome Sequence of <i>Adansonia digitata</i> (Malvaceae, Malvales), the African Baobab

Stephen Woods; Kathleen O'Neill; Stacy Pirro

doi:10.56179/001c.72789

Woods, Stephen, Kathleen O’Neill, and Stacy Pirro. 2023. “The Complete Genome Sequence of Adansonia Digitata (Malvaceae, Malvales), the African Baobab.” Biodiversity Genomes, March. https://doi.org/10.56179/001c.72789.

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Abstract

Adansonia digitata, the African Baobab, is a long-lived tree species found in sub-Saharan Africa. We present the whole genome sequence of this species. 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 (SRR23340274) and assembled genome (JAQSVH000000000).

Introduction

The African Baobab is a large tree species in the dry savannah regions of sub-Saharan Africa. They are an important source of food and shelter for many species of African wildlife, and culturally important for African communities.

Methods

A single captive-bred specimen 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 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.

Results

The genome assembly yielded a total sequence length of 686,996,791.

Data availability

Raw and assembled data is publicly available via GenBank:

Raw genome data

https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR23340274

Assembled genome

https://www.ncbi.nlm.nih.gov/nuccore/JAQSVH000000000

Funding

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

Conflict of Interest Statement

The authors declare they have no conflicts of interests.

Submitted: February 22, 2023 EDT

Accepted: March 05, 2023 EDT

References

Bankevich, Anton, Sergey Nurk, Dmitry Antipov, Alexey A. Gurevich, Mikhail Dvorkin, Alexander S. Kulikov, Valery M. Lesin, et al. 2012. “SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing.” Journal of Computational Biology 19 (5): 455–77. https://doi.org/10.1089/cmb.2012.0021.

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