BOSS mini project on plant genome assembly
Aim:
The study uses several genomic and bioinformatics approaches. In this project, participants will be required to reproduce the genomic analysis carried out in the study. The data will be available from NCBI. You are expected to: Download the sequence data programmatically, carry out DNA sequence pre-processing and de novo assembly and perform genome annotation of the plant of interest.
Chang, Y., Liu, H., Liu, M., Liao, X., Sahu, S. K., Fu, Y., Song, B., Cheng, S., Kariba, R., Muthemba, S., Hendre, P. S., Mayes, S., Ho, W. K., Yssel, A. E. J., Kendabie, P., Wang, S., Li, L., Muchugi, A., Jamnadass, R., … Liu, X. (2018). The draft genomes of five agriculturally important African orphan crops. 8, 1–16. https://doi.org/10.1093/gigascience/giy152
- To determine genome location associated with crucial agronomic traits
- To arrive at similar conclusions as those in the paper?
- Are you able to determine genome location associated with crucial agronomic traits?
- Are you able to arrive at similar conclusions as those in the paper? Why or why not?
- Are the descriptions in the methodology section detailed for reproducibility? If not, what could you have done to improve reproducibility?
This study reported the draft genomes of 5 agriculturally important orphan crops i.e. Vigna subterranean, Lablab purpureus, Faidherbia albida, Sclerocarya birrea and Moringa oleifera. Of the five plants we chose to work with Moringa oleifera which has been observed to have heterozygosity varying from 0.16 to 0.86, with an average of 0.58. it is also diploid with a chromosome number of 2n = 2x = 28 in somatic cells.
- The authors have not provided the library preparation data, which is vital for the de-novo
- Bernice Waweru - Project Lead
- Landi Cofia - Assistant Lead
- Laurah Nyasita Ondari
- Ken Mugambi
- Oscar Mwaura
- Alex Gashanja