Comparative analysis of secondary metabolite clusters synteny in eleven Oryza species and three related species

Sasani, Sahand; Rashidi Monfared, Sajad; Kahrizi, Danial; Khanahmadi, Masoumeh

doi:10.30473/cb.2024.70435.1953

Comparative analysis of secondary metabolite clusters synteny in eleven Oryza species and three related species

Document Type : Research Paper

Authors

¹ Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran

² Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

³ 1. Department of Biotechnology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.

⁴ Academic Center for Education, Culture & Research (ACECR), Kermanshah, Iran

10.30473/cb.2024.70435.1953

Abstract

The rice (Oryza sativa) is part of the Poacea family and is one of the most important crops in the world. In this project, the presence of synteny in the clusters involved in the biosynthesis of secondary metabolites is known in the rice plant with 11 different species of Oryza and 3 related species. Genome sequences of all studied species were received from the NCBI database, and then the genes involved in the biosynthesis of secondary metabolites, which were located in the specific clusters were retrieved from the planti smash database. All genes were selected to align against 13 other species to identify sequences which similar to rice gene clusters using blastn tools. To map the genes of each species with the genome of the same species, gmap software was used. In the last step, gene blocks with synteny were identified using MCScanX software. According to the results, the existence of synteny in the clusters was proven in O. rufipogom, O. punctata and O. sativa indica species. After identifying the common regulatory factors of gene clusters, it is possible to regulate the expression of all gene clusters simultaneously to produce more content for the final products. On the other hand, due to the Co-inheritance of the genes located in each cluster, it could be possible to transfer desirable gene clusters by producing substitution lines that carry that gene cluster.

Keywords

Main Subjects

Bioinformatics

References

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