1
|
Montenegro JD, Julca I, Chumbe-Nolasco LD, Rodríguez-Pérez LM, Sevilla Panizo R, Medina-Hoyos A, Gutiérrez-Reynoso DL, Guerrero-Abad JC, Amasifuen Guerra CA, García-Serquén AL. Phylogenomic Analysis of the Plastid Genome of the Peruvian Purple Maize Zea mays subsp. mays cv. 'INIA 601'. PLANTS (BASEL, SWITZERLAND) 2022; 11:2727. [PMID: 36297753 PMCID: PMC9612013 DOI: 10.3390/plants11202727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Peru is an important center of diversity for maize; its different cultivars have been adapted to distinct altitudes and water availability and possess an array of kernel colors (red, blue, and purple), which are highly appreciated by local populations. Specifically, Peruvian purple maize is a collection of native landraces selected and maintained by indigenous cultures due to its intense purple color in the seed, bract, and cob. This color is produced by anthocyanin pigments, which have gained interest due to their potential use in the food, agriculture, and pharmaceutical industry. It is generally accepted that the Peruvian purple maize originated from a single ancestral landrace 'Kculli', but it is not well understood. To study the origin of the Peruvian purple maize, we assembled the plastid genomes of the new cultivar 'INIA 601' with a high concentration of anthocyanins, comparing them with 27 cultivars/landraces of South America, 9 Z. mays subsp. parviglumis, and 5 partial genomes of Z. mays subsp. mexicana. Using these genomes, plus four other maize genomes and two outgroups from the NCBI database, we reconstructed the phylogenetic relationship of Z. mays. Our results suggest a polyphyletic origin of purple maize in South America and agree with a complex scenario of domestication with recurrent gene flow from wild relatives. Additionally, we identify 18 plastid positions that can be used as high-confidence genetic markers for further studies. Altogether, these plastid genomes constitute a valuable resource to study the evolution and domestication of Z. mays in South America.
Collapse
Affiliation(s)
- Juan D. Montenegro
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Department of Neurosciences and Developmental Biology, University of Vienna, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Irene Julca
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Lenin D. Chumbe-Nolasco
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lila M. Rodríguez-Pérez
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ricardo Sevilla Panizo
- Departamento de Fitotecnia, Facultad de Agronomía, Universidad Nacional Agraria La Molina, Av. La Molina s/n, Lima 15024, Peru
| | - Alicia Medina-Hoyos
- Estación Experimental Agraria “Baños del Inca”, Instituto Nacional de Innovación Agraria (INIA), Km. 5.5 Carretera Cajamarca–Celendín, Cajamarca 06000, Peru
| | - Dina L. Gutiérrez-Reynoso
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Juan Carlos Guerrero-Abad
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos A. Amasifuen Guerra
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Aura L. García-Serquén
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| |
Collapse
|
2
|
McLay TGB, Murphy DJ, Holmes GD, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ. A genome resource for Acacia, Australia's largest plant genus. PLoS One 2022; 17:e0274267. [PMID: 36240205 PMCID: PMC9565413 DOI: 10.1371/journal.pone.0274267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022] Open
Abstract
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.
Collapse
Affiliation(s)
- Todd G. B. McLay
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Gareth D. Holmes
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Sarah Mathews
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Gillian K. Brown
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Chris J. Jackson
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| |
Collapse
|