Abstract
Telfairia occidentalis is a tropical vine grown in West Africa as a leaf vegetable and for its edible seeds. We present the whole genome sequence of this species. Illumina sequencing was performed on a leaf tissue sample from a single cultivated plant. The reads were assembled using a de novo method followed by a series of references from related species for finishing. The raw and assembled data is publicly available via Genbank: Sequence Read Archive (SRR14834394) and Genome Assembly (JAOANK000000000).
Keywords: fluted pumpkin, nigeria, genome
Introduction
Telfairia occidentalis (Cucurbitaceae, Cucurbitales), commonly known as the fluted pumpkin, grows in several countries in West Africa but is mainly cultivated in southeastern Nigeria and it is used primarily in soups and herbal medicines. The cultivated plant is a drought-tolerant, dioecious perennial. The fruit is inedible but the seeds are high in protein and fat. The leaves and seeds are consumed by an estimated 30 to 35 million people indigenous people in Nigeria.
The fruit of this species is quite large. One study documented a range of 16–105 centimetres (6.3–41.3 in) in length, and an average of 9 cm in diameter. Each gourd contains approximately 200 large seeds. The flowers grow in sets of five, with creamy-white and dark red petals, contrasting with the yellow color of the ripe fruit (Okoli and Mgbeogu 1983).
Methods
Leaf tissue from a single 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 et al. 2012) followed by a finishing step using Zanfona (Kieras, O’Neill, and Pirro 2021).
Funding
Funding was provided by Iridian Genomes, grant# IRGEN_RG_2021-1345 Genomic Studies of Eukaryotic Taxa.
Footnotes
Raw genome data
Assembled genome
Results and Data Availability
The genome assembly yielded a total sequence length of 768,820,061 bp.
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. https://github.com/zanfona734/zanfona.
- Okoli Bosa E., and Mgbeogu CM. 1983. “Fluted Pumpkin, Telfairia Occidentalis: West African Vegetable Crop.” Economic Botany 37: 145–49. 10.1007/bf02858775. [DOI] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The genome assembly yielded a total sequence length of 768,820,061 bp.