Third generation sequencing has revolutionized our understanding of genomics, and enabled the in-depth discovery of complex plant genomes. In this project I aimed to assemble and annotate the genome of Z. spina-christi, a native plant to Saudi Arabia, as part of the the Kingdom of Saudi Arabia Native Genome Project established at the Center for Desert Agriculture at KAUST. Initially, a voucher plant was selected from the Al Lith region of Western Saudi Arabia. Fresh leaf tissue was collected for high-molecular weight (HMW) DNA extraction, as well as seed for greenhouse propagation. After HMW DNA extraction, library construction and PacBio HiFi sequencing, I generated a de novo assembly of the Z. spina-christi genome using the Hifiasm assembler, which yielded a 1.9 Gbp long assembly with high levels of duplication. The assembled contigs were scaffolded using an in-house script based on the software RagTag, that yielded a 406 Mbp long scaffold with 331 gaps (85.45% of estimated genome size). A preliminary analysis of the assembly for transposable elements revealed a TE content of 32.36%, with Long Terminal Repeats retrotransposons (LTR-RTs) being the major contributor to the total TE content. Basline annotation was completed using Omicsbox revealing 18,330 functional genes. This work describes the first genomic resource for the desert plant Z. spina-christi. To improve the assembly, I suggest the use of scaffolding using optical mapping, long Nanopore reads and Hi-C data to capture the spatial organization of the genome. Further experimental, genetic and TEs analysis is needed to explore the plant’s resilience to abiotic stresses in extreme environments.
| Identifer | oai:union.ndltd.org:kaust.edu.sa/oai:repository.kaust.edu.sa:10754/679884 |
| Date | 07 1900 |
| Creators | Shuwaikan, Raghad H. |
| Contributors | Wing, Rod Anthony, Biological and Environmental Science and Engineering (BESE) Division, Krattinger, Simon G., Zuccolo, Andrea |
| Source Sets | King Abdullah University of Science and Technology |
| Language | English |
| Detected Language | English |
| Type | Thesis |
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