title: The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae.
abstract: Alkaloid accumulation in plants is activated in response to stress, is limited in distribution and specific alkaloid repertoires are variable across taxa. Rauvolfioideae (Apocynaceae, Gentianales) represents a major center of structural expansion in the monoterpenoid indole alkaloids (MIAs) yielding thousands of unique molecules including highly valuable chemotherapeutics. The paucity of genome-level data for Apocynaceae precludes a deeper understanding of MIA pathway evolution hindering the elucidation of remaining pathway enzymes and the improvement of MIA availability in planta or in vitro. We sequenced the nuclear genome of Rhazya stricta (Apocynaceae, Rauvolfioideae) and present this high quality assembly in comparison with that of coffee (Rubiaceae, Coffea canephora, Gentianales) and others to investigate the evolution of genome-scale features. The annotated Rhazya genome was used to develop the community resource, RhaCyc, a metabolic pathway database. Gene family trees were constructed to identify homologs of MIA pathway genes and to examine their evolutionary history. We found that, unlike Coffea, the Rhazya lineage has experienced many structural rearrangements. Gene tree analyses suggest recent, lineage-specific expansion and diversification among homologs encoding MIA pathway genes in Gentianales and provide candidate sequences with the potential to close gaps in characterized pathways and support prospecting for new MIA production avenues.
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Jamal S M
authors.initials: JS
authors.lastname: Sabir
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.|Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA.
authors.forename: Robert K
authors.initials: RK
authors.lastname: Jansen
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA.
authors.forename: Dhivya
authors.initials: D
authors.lastname: Arasappan
authors.affiliation: Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada.
authors.forename: Virginie
authors.initials: V
authors.lastname: Calderon
authors.affiliation: Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Noutahi
authors.affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, K1N 6N5 Ontario Canada.
authors.forename: Chunfang
authors.initials: C
authors.lastname: Zheng
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA.
authors.forename: Seongjun
authors.initials: S
authors.lastname: Park
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Meshaal J
authors.initials: MJ
authors.lastname: Sabir
authors.affiliation: Department of Biological Sciences, Faculty of Science, University of Jeddah, Jeddah, Saudi Arabia.
authors.forename: Mohammed N
authors.initials: MN
authors.lastname: Baeshen
authors.affiliation: Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Nahid H
authors.initials: NH
authors.lastname: Hajrah
authors.affiliation: King Abdulaziz City for Science and Technology, Riyadh 11442, Saudi Arabia.
authors.forename: Mohammad A
authors.initials: MA
authors.lastname: Khiyami
authors.affiliation: Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Nabih A
authors.initials: NA
authors.lastname: Baeshen
authors.affiliation: Department of Chemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Abdullah Y
authors.initials: AY
authors.lastname: Obaid
authors.affiliation: Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
authors.forename: Abdulrahman L
authors.initials: AL
authors.lastname: Al-Malki
authors.affiliation: Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Ave., Ottawa, K1N 6N5 Ontario Canada.
authors.forename: David
authors.initials: D
authors.lastname: Sankoff
authors.affiliation: Département d'informatique et de recherche opérationnelle, Université de Montréal, CP 6128 succ Centre-Ville, Montréal, H3C 3J7 Québec, Canada.
authors.forename: Nadia
authors.initials: N
authors.lastname: El-Mabrouk
authors.affiliation: Department of Integrative Biology, University of Texas at Austin, Austin, 78712 Texas, USA.
authors.forename: Tracey A
authors.initials: TA
authors.lastname: Ruhlman