Biology subjects

Dudai, N.

Publications and source records attributed to Dudai, N..

3 recordsLinked to original sources

bioRxiv2022

Two independent loss-of-function mutations in anthocyanidin synthase homeologous genes make sweet basil all green

Sweet basil, Ocimum basilicum L., is an important culinary herb grown worldwide. Although basil is green, many landraces, breeding lines and exotic cultivars have purple stems and flowers. This anthocyanins pigmentation is unacceptable in the traditional Italian basil. We used the recently published sweet basil genome to map quantitative trait loci (QTL) for flower and stem color in a bi-parental F2 population. It was found that the pigmentation is governed by a single QTL, harboring an anthocyanidin synthase (ANS) gene. Further analysis revealed that the basil genome harbors two homeologous ANS genes, each carrying a loss-of-function mutation. ObANS1 carries a 1-bp insertion, and ObANS2 carries a missense mutation within the active site. In the purple-flower parent, ANS1 is functional and ANS2 carries a nonsense mutation. The functionality of the active allele was validated by complementation in an Arabidopsis ANS mutant. Moreover, we have restored the functionality of the missense-mutated ANS2 using site-directed activation. We found that the non-functional alleles were expressed to similar levels as the functional allele, suggesting polyploids invest futile effort in expressing non-functional genes, harming their superior redundancy. We show here we can harness basils genomics and genetics to understand the basic mechanism of metabolic traits.

plant biology↗

bioRxiv2021

Dual transcriptional analysis of Peronospora belbahrii and Ocimum basilicum in susceptible interactions

Basil downy mildew, caused by the pathogen Peronospora belbahrii, is a major problem for sweet basil growers worldwide. The genome sequences of both Ocimum basilicum and P. belbahrii were recently completed but extensive transcriptome analysis of this pathosystem has not been completed. RNA sequencing was performed using basil leaf samples collected three and six days after inoculation with sporangia from an Illinois isolate of P. belbahrii and differentially expressed genes were identified. Gene enrichment analysis identified 22 genes that were upregulated at day three, in comparison to mock inoculated leaf samples, that were classified as defense response to oomycetes; among this group were five orthologues of Arabidopsis thaliana DOWNY MILDEW RESISTANCE 6. During the same time interval, many genes contributing to photosynthesis in the infected leaves were downregulated in comparison to control leaf samples. Many more genes were differentially expressed in the inoculated basil leaves at day six, compared to mock inoculated leaves, as the pathogen began to produce sporangiophores. On days three and six, the pathogen produced high transcript levels of secreted glycoside hydrolases, which likely release sugars from the plant cell walls needed for the growth of the pathogen. These results contribute to a better understanding of the infection process of downy mildew and will aid the development of more effective measures for reducing the severity of the disease.

plant biology↗

bioRxiv2018

High-quality assembly of sweet basil genome

Sweet basil, sometimes called the King of Herbs, is well known for its culinary uses, especially in the Italian sauce Pesto. It is also used in traditional medicine, as a source for essential oils and as an ornamental plant. So far, basil was bred by classical and traditional methods due to lack of a reference genome that will allow optimized application of the most up-to-date sequencing techniques. Here, we report on the first completion of the sweet basil genome of the cultivar Perrie, a fresh-cut Genovese-type basil, using several next generation sequencing platforms followed by genome assembly with NRGENEs DeNovoMAGIC assembly tool. We determined that the genome size of sweet basil is 2.13 Gbp and assembled it into 12,212 scaffolds. The high-quality of the assembly is reflected in that more than 90% of the assembly size is composed of only 107 scaffolds. An independent analysis of single copy orthologues genes showed a 93% completeness which reveal also that 74% of them were duplicated, indicating that the sweet basil is a tetraploid organism. A reference genome of sweet basil will enable to develop precise molecular markers for various agricultural important traits such as disease resistance and tolerance to various environmental conditions. We will gain a better understanding of the underlying mechanisms of various metabolic processes such as aroma production and pigment accumulation. Finally, it will save time and money for basil breeders and scientists and ensure higher throughput and robustness in future studies.

genomics↗