| Titre : | GENOME ASSEMBLY OF ARGANIA SPINOSA | | Type de document : | thèse | | Auteurs : | Abdellah IDRISSI AZAMI, Auteur | | Année de publication : | 2020 | | Langues : | Anglais (eng) | | Mots-clés : | Argania spinosa Morocco Genome assembly Assemblers Annotation Mitogenome Genome Size estimate Argania spinosa Assemblage génome Assembleurs Annotation Mitogenomique Estimation de la taille du génome. | | Résumé : | Argania spinosa is an endemic plant in the mid-western Morocco. Its oil is considered as one of
the most expensive oils in the world thanks to its nutritional value, and medical and therapeutical
effects. Genomic study of the argane tree would make the discovery of the oil and other
metabolite biosynthesis pathways easier which will help in extracting, purifying, and
ameliorating the quality of those metabolites. To achieve this purpose, the whole genome of the
argane tree has been sequenced using Illumina HiSeq Xten, and PacBio RS II technologies, the
genome size estimated using K-mer distribution, then assembled using short-reads, long-reads,
and hybrid assembly strategies using three assemblers, namely Canu, SOAPdenovo 2, and
Masurca. Results showed that hybrid assembly gave the biggest sequence size (423 Mbases), and
the higher N50 value (40 Kbases) among the three assembling approaches. The assembled
genome size was lower than the estimated genome size (630 Mb – 713Mb), which might be due
to the high heterozygosity of the plant and high repetitive regions in the genome. In order to
predict the genes structure and function of different regions in the Argane genome’s, an AB
initio gene prediction was performed, and resulted in the prediction of 115 genes, with 5128
introns, and 6073 exons. This is very low compared to expected 30000-40000 genes, which is
due to the low quality of the input assembly. Seven genes were predicted to be completed, and
annotated using homology search with BLASTp. Three of them code for Photosystems and
RuBisCO, two complexes that leads the light and the dark phases of the photosynthesis process,
two encodes for ribosomal proteins, one codes for RNA polymerase, while the seventh encodes
for the γ-Tocopherol methyltransferase, which is involved in the biosynthesis of the vitamin E.
The mitochondrial genome assembly gave a circular scaffold of 245,326 b, that contains 21
genes mainly involved in the Oxidative Phosphorylation process. Towards full exploitation of
the Genome information for oil biosynthesis pathways discovery, we will enhance the genome
assembly by using other assemblers, as well as combining manual and automated assembly
procedures. | | Numéro (Thèse ou Mémoire) : | MM0452020 | | Président : | Azeddine IBRAHIMI | | Directeur : | Hassan GHAZAL | | Juge : | Abdelhamid EL MOUSSADIK | | Juge : | Noureddine HAMAMOUCH | | Juge : | Fatima GABOUN |
GENOME ASSEMBLY OF ARGANIA SPINOSA [thèse] / Abdellah IDRISSI AZAMI, Auteur . - 2020. Langues : Anglais ( eng) | Mots-clés : | Argania spinosa Morocco Genome assembly Assemblers Annotation Mitogenome Genome Size estimate Argania spinosa Assemblage génome Assembleurs Annotation Mitogenomique Estimation de la taille du génome. | | Résumé : | Argania spinosa is an endemic plant in the mid-western Morocco. Its oil is considered as one of
the most expensive oils in the world thanks to its nutritional value, and medical and therapeutical
effects. Genomic study of the argane tree would make the discovery of the oil and other
metabolite biosynthesis pathways easier which will help in extracting, purifying, and
ameliorating the quality of those metabolites. To achieve this purpose, the whole genome of the
argane tree has been sequenced using Illumina HiSeq Xten, and PacBio RS II technologies, the
genome size estimated using K-mer distribution, then assembled using short-reads, long-reads,
and hybrid assembly strategies using three assemblers, namely Canu, SOAPdenovo 2, and
Masurca. Results showed that hybrid assembly gave the biggest sequence size (423 Mbases), and
the higher N50 value (40 Kbases) among the three assembling approaches. The assembled
genome size was lower than the estimated genome size (630 Mb – 713Mb), which might be due
to the high heterozygosity of the plant and high repetitive regions in the genome. In order to
predict the genes structure and function of different regions in the Argane genome’s, an AB
initio gene prediction was performed, and resulted in the prediction of 115 genes, with 5128
introns, and 6073 exons. This is very low compared to expected 30000-40000 genes, which is
due to the low quality of the input assembly. Seven genes were predicted to be completed, and
annotated using homology search with BLASTp. Three of them code for Photosystems and
RuBisCO, two complexes that leads the light and the dark phases of the photosynthesis process,
two encodes for ribosomal proteins, one codes for RNA polymerase, while the seventh encodes
for the γ-Tocopherol methyltransferase, which is involved in the biosynthesis of the vitamin E.
The mitochondrial genome assembly gave a circular scaffold of 245,326 b, that contains 21
genes mainly involved in the Oxidative Phosphorylation process. Towards full exploitation of
the Genome information for oil biosynthesis pathways discovery, we will enhance the genome
assembly by using other assemblers, as well as combining manual and automated assembly
procedures. | | Numéro (Thèse ou Mémoire) : | MM0452020 | | Président : | Azeddine IBRAHIMI | | Directeur : | Hassan GHAZAL | | Juge : | Abdelhamid EL MOUSSADIK | | Juge : | Noureddine HAMAMOUCH | | Juge : | Fatima GABOUN |
|
Accueil
Affiner la recherche Faire une suggestionGENOME ASSEMBLY OF ARGANIA SPINOSA / Abdellah IDRISSI AZAMI
