Ben Hur Neves de Oliveira1, Andriele Wairich1, Andreia Carina Turchetto-Zolet2, Janette Palma Fett1,3, Felipe Klein Ricachenevsky4,5,6. 1. Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil. 2. Departamento de Genética e Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.323, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil. 3. Departamento de Botânica, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.423, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil. 4. Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.421 CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil. felipecruzalta@gmail.com. 5. Departamento de Botânica, Universidade Federal Do Rio Grande Do Sul, Av. Bento Gonçalves 9500, Building 43.423, CEP, Porto Alegre, Rio Grande do Sul, 91509-900, Brazil. felipecruzalta@gmail.com. 6. Departamento de Biologia, Universidade Federal de Santa Maria, Av. Roraima 1000, Building 16, Room 3254, CEP, Santa Maria, Rio Grande do Sul, 97105-900, Brazil. felipecruzalta@gmail.com.
Abstract
MAIN CONCLUSION: The MIR gene is not an Oryza sativa orphan gene, but an Oryza genus-specific gene that evolved before AA lineage speciation by a complex origination process. Rice (Oryza sativa L.) is a model species and an economically relevant crop. The Oryza genus comprises 25 species, with genomic data available for several Oryza species, making it a model for genetics and evolution. The Mitochondrial Iron-Regulated (MIR) gene was previously implicated in the O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the Oryza sativa complex, which have AA genome type and constitute the primary gene pool for O. sativa breeding. Our data suggest that MIR originated in a stepwise process, in which sequences derived from an exon fragment of the raffinose synthase gene were pseudogenized into non-coding, which in turn originated the MIR gene de novo. All species with a putative functional MIR gene conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, leading to a lack of Fe deficiency responsiveness. Moreover, the MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the genus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact on Fe deficiency response.
MAIN CONCLUSION: The MIR gene is not an Oryza sativa orphan gene, but an Oryza genus-specific gene that evolved before AA lineage speciation by a complex origination process. Rice (Oryza sativa L.) is a model species and an economically relevant crop. The Oryza genus comprises 25 species, with genomic data available for several Oryza species, making it a model for genetics and evolution. The Mitochondrial Iron-Regulated (MIR) gene was previously implicated in the O. sativa Fe deficiency response, and was considered an orphan gene present only in rice. Here we show that MIR is also found in other Oryza species that belong to the Oryza sativa complex, which have AA genome type and constitute the primary gene pool for O. sativa breeding. Our data suggest that MIR originated in a stepwise process, in which sequences derived from an exon fragment of the raffinose synthase gene were pseudogenized into non-coding, which in turn originated the MIR gene de novo. All species with a putative functional MIR gene conserve their regulation by Fe deficiency, with the exception of Oryza barthii. In O. barthii, the MIR coding sequence was translocated to a different chromosomal position and separated from its regulatory region, leading to a lack of Fe deficiency responsiveness. Moreover, the MIR co-expression subnetwork cluster in O. sativa is responsive to Fe deficiency, evidencing the importance of the newly originated gene in Fe uptake. This work establishes that MIR is not an orphan gene as previously proposed, but a de novo originated gene within the genus Oryza. We also showed that MIR is undergoing genomic changes in one species (O. barthii), with an impact on Fe deficiency response.
Entities:
Keywords:
De novo gene origination; Iron deficiency; Orphan gene; Oryza genus; Oryza sativa; Wild rice
Authors: Tanya Barrett; Stephen E Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F Kim; Maxim Tomashevsky; Kimberly A Marshall; Katherine H Phillippy; Patti M Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; Naigong Zhang; Cynthia L Robertson; Nadezhda Serova; Sean Davis; Alexandra Soboleva Journal: Nucleic Acids Res Date: 2012-11-27 Impact factor: 16.971
Authors: David M Goodstein; Shengqiang Shu; Russell Howson; Rochak Neupane; Richard D Hayes; Joni Fazo; Therese Mitros; William Dirks; Uffe Hellsten; Nicholas Putnam; Daniel S Rokhsar Journal: Nucleic Acids Res Date: 2011-11-22 Impact factor: 16.971
Authors: Ricardo José Stein; Guilherme Leitão Duarte; Lívia Scheunemann; Marta Gomes Spohr; Artur Teixeira de Araújo Júnior; Felipe Klein Ricachenevsky; Luis Mauro Gonçalves Rosa; Nilson Ivo Tonin Zanchin; Rinaldo Pires Dos Santos; Janette Palma Fett Journal: Front Plant Sci Date: 2019-06-12 Impact factor: 5.753