1 / 15

Medicago truncatula BAC mth1-13b3

Medicago truncatula BAC mth1-13b3. Courtney Johnson And Majesta Siegfried. Background and Significance.

marsha
Download Presentation

Medicago truncatula BAC mth1-13b3

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Medicago truncatula BAC mth1-13b3 Courtney Johnson And Majesta Siegfried

  2. Background and Significance • Legumes are the second most agriculturally significant crop, making up 27% of the worlds overall primary crop production, and 33% of its dietary protein nitrogen, but in developing countries can reach twice this much. • Medicago truncatula is considered to be a model legume because of its compact genome size, simple Mendelian genetics, short generation time, diploid chromosomes, and self fertilization. Figure 1: Medicago truncatula (www.acnfp.murdoch.edu.au/projects/assets/Medicago)

  3. BAC Information • Name – mth1-13b3 • Location – Linkage group 6 • Marker – R 15L4R • Contig – Singelton • Gene Content Description – Medicago truncatula R gene homologue

  4. Procedure The clone was sequenced using the standard shotgun method. Figure 2: Shotgun sequencing bioinformatics.weizmann.ac.il/courses/BCG /lectures/08_genome/02sequencing/shotgun Figure 3: Gaps were closed using a directed closure approach.

  5. Informatics Strategy 1. Predicting genes using programs such as Genscan and Fgenesh. 2. Determine homology to known genes using BLAST vs the GenBank databases . 3. Comparison to already sequenced data by ClustalW, Pipmaker, and VISTA.

  6. FgeneSH Output

  7. FgeneSH Output Cont.

  8. BLAST Results

  9. Annotation on Genome Browser

  10. Description of Programs Used • ClustalW - A sequence alignment program. • VISTA - A global sequence alignment and percent identity plot program. • Pipmaker - A local sequence alignment and percent identity plot program.

  11. ClustalW Predicted peptide 19, aligned with NBS-LRR Resistance proteins found in other organisms. From this protein comparison Medicago is closest in relation to Glycine and Phaseolus, then Arabidopsis, and finally Lycopersicon.

  12. Pipmaker Significant homology is seen in the exonic regions between Arabidopsis and two genes predicted on this BAC. There appears to be a duplication on chromosomes 2 and 3 in Arabidopsis.

  13. VISTA

  14. VISTA cont. Most of the alignments found using a global alignment are in the intragenic regions and in the introns. Perhaps this is due to repeats.

  15. Conclusion • Sequencing of Medicago truncatula will be useful in studies to improve legume yields. • Sequencing of the Medicago BACs is performed using the standard shotgun method, and closed using directed approaches. • Annotation of BAC mth1-13b3 predicted ~30 genes of which the majority of them appeared to be viral insertions and resistance genes. • Comparative analysis found some significant homology between Medicago and Arabidopsis, but more to other legumes.

More Related