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Zhang J, Liu G, Wei J. Assembly and comparative analysis of the first complete mitochondrial genome of Setaria italica. PLANTA 2024; 260:23. [PMID: 38850310 DOI: 10.1007/s00425-024-04386-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/10/2024] [Indexed: 06/10/2024]
Abstract
MAIN CONCLUSION In this study, we assembled the first complete mitochondrial genome of Setaria italica and confirmed the multi-branched architecture. The foxtail millet (Setaria italica) holds significant agricultural importance, particularly in arid and semi-arid regions. It plays a pivotal role in diversifying dietary patterns and shaping planting strategies. Although the chloroplast genome of S. italica has been elucidated in recent studies, the complete mitochondrial genome remains largely unexplored. In this study, we employed PacBio HiFi sequencing platforms to sequence and assemble the complete mitochondrial genome. The mitochondrial genome spans a total length of 446,614 base pairs and harbors a comprehensive set of genetic elements, including 33 unique protein-coding genes (PCGs), encompassing 24 unique mitochondrial core genes and 9 variable genes, along with 20 transfer RNA (tRNA) genes and 3 ribosomal RNA (rRNA) genes. Our analysis of mitochondrial PCGs revealed a pronounced codon usage preference. For instance, the termination codon exhibits a marked preference for UAA, while alanine (Ala) exhibits a preference for GCU, and glutamine (Gln) favors CAA. Notably, the maximum Relative Synonymous Codon Usage (RSCU) values for cysteine (Cys) and phenylalanine (Phe) are both below 1.2, indicating a lack of strong codon usage preference for these amino acids. Phylogenetic analyses consistently place S. italica in close evolutionary proximity to Chrysopogon zizanioides, relative to other Panicoideae plants. Collinearity analysis showed that a total of 39 fragments were identified to display homology with both the mitochondrial and chloroplast genomes. A total of 417 potential RNA-editing sites were discovered across the 33 mitochondrial PCGs. Notably, all these editing events involved the conversion of cytosine (C) to uracil (U). Through the employment of PCR validation coupled with Sanger sequencing for the anticipated editing sites of these codons, RNA-editing events were conclusively identified at two specific loci: nad4L-2 and atp6-1030. The results of this study provide a pivotal foundation for advanced genomic breeding research in foxtail millet. Furthermore, they impart essential insights that will be instrumental for forthcoming investigations into the evolutionary and molecular dynamics of Panicoideae species.
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Affiliation(s)
- Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Guiming Liu
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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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.
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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
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Ma J, Gao Y, Jiang T, Tian F. Excellent Anti-lung Cancer Activity of Populus nigra and Phylogenetic Analysis. J Oleo Sci 2021; 70:1783-1789. [PMID: 34866109 DOI: 10.5650/jos.ess21220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lung cancer has the highest incidence rate among malignant tumors all over the world, and it is also the leading cause of death. In this present research, we aimed to evaluate the anti-cancer activity of the Populus nigra extract against the lung cancer and study the genome evolution of the Populus nigra. Firstly, the inhibitory activity of the Populus nigra extract on the NCI-H292 lung cancer cell viability was determined with Cell Counting Kit-8 (CCK-8) assay. The trans-well assay was conducted and the influence of the Populus nigra extract on the NCI-H292 lung cancer cell migration and invasion ability was determined. In addition to this, the chloroplast (cp) genome of Populus nigra was sequenced with high-throughput Illumina pair-end sequencing, which was a classical useful model for genome evolution assessment. The CCK-8 and trans-well assay indicated the Populus nigra extract exhibited excellent inhibitory activity on the NCI-H292 lung cancer cell viability, migration and invasion ability. The circular cp genome of the Populus nigra was 156,354 bp in size, including a large single-copy (LSC) region of 84,528 bp and a small single-copy (SC) region of 16,564 bp, which were separated by two inverted repeat (IR) regions (38,612 bp each). A total of 132 genes were predicted, including 8 ribosomal RNAs (rRNAs), 37 transfer RNAs (tRNAs), and 90 protein-coding genes (PCGs). Furthermore, phylogenetic analysis revealed that Populus nigra has the closest relationship with Populus alba var. pyramidalis. In addition to Populus alba var. pyramidalis, Populus adenopoda and Populus tomentosa are also has closely relationship with Populus nigra.
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Affiliation(s)
- Jun Ma
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military University
| | - Yang Gao
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military University
| | - Tao Jiang
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military University
| | - Feng Tian
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Military University
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López MG, Fass M, Rivas JG, Carbonell-Caballero J, Vera P, Puebla A, Defacio R, Dopazo J, Paniego N, Hopp HE, Lia VV. Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools. ANNALS OF BOTANY 2021; 128:115-125. [PMID: 33693521 PMCID: PMC8318110 DOI: 10.1093/aob/mcab038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/04/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. METHODS We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. KEY RESULTS Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. CONCLUSIONS Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers.
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Affiliation(s)
- Mariana Gabriela López
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Pcia. Buenos Aires, Argentina
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
- Instituto de Biomedicina de Valencia (IBV-CSIC), c/Jaume Roig 11, 46010, Valencia, Spain
| | - Mónica Fass
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Pcia. Buenos Aires, Argentina
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
| | - Juan Gabriel Rivas
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
| | - José Carbonell-Caballero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr Aiguader 88, 08003 Barcelona, Spain
| | - Pablo Vera
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
| | - Andrea Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
| | - Raquel Defacio
- Estación Experimental Agropecuaria INTA Pergamino, Pergamino Buenos Aires, Argentina
| | - Joaquín Dopazo
- Clinical Bioinformatics Area, Fundación Progreso y Salud, CDCA, Hospital Virgen del Rocío, c/Manuel Siurot s/n, 41013, Sevilla, Spain
| | - Norma Paniego
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Pcia. Buenos Aires, Argentina
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - Verónica Viviana Lia
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Pcia. Buenos Aires, Argentina
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET, Hurlingham, Pcia. Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
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