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).
Keywords: baobab, africa, viridiplantae, genome
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.
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021–1345 Genomic Studies of Eukaryotic Taxa
Footnotes
Conflict of Interest Statement
The authors declare they have no conflicts of interests.
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
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 2021. Zanfona, a genome finishing process for use with paired-end short reads https://github.com/zanfona734/zanfona.
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
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