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Francisconi AF, Marroquín JAM, Cauz-Santos LA, van den Berg C, Martins KKM, Costa MF, Picanço-Rodrigues D, de Alencar LD, Zanello CA, Colombo CA, Hernández BGD, Amaral DT, Lopes MTG, Veasey EA, Zucchi MI. Complete chloroplast genomes of six neotropical palm species, structural comparison, and evolutionary dynamic patterns. Sci Rep 2023; 13:20635. [PMID: 37996522 PMCID: PMC10667357 DOI: 10.1038/s41598-023-44631-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/10/2023] [Indexed: 11/25/2023] Open
Abstract
The Arecaceae family has a worldwide distribution, especially in tropical and subtropical regions. We sequenced the chloroplast genomes of Acrocomia intumescens and A. totai, widely used in the food and energy industries; Bactris gasipaes, important for palm heart; Copernicia alba and C. prunifera, worldwide known for wax utilization; and Syagrus romanzoffiana, of great ornamental potential. Copernicia spp. showed the largest chloroplast genomes (C. prunifera: 157,323 bp and C. alba: 157,192 bp), while S. romanzoffiana and B. gasipaes var. gasipaes presented the smallest (155,078 bp and 155,604 bp). Structurally, great synteny was detected among palms. Conservation was also observed in the distribution of single sequence repeats (SSR). Copernicia spp. presented less dispersed repeats, without occurrence in the small single copy (SSC). All RNA editing sites were C (cytidine) to U (uridine) conversions. Overall, closely phylogenetically related species shared more sites. Almost all nodes of the phylogenetic analysis showed a posterior probability (PP) of 1.0, reaffirming the close relationship between Acrocomia species. These results elucidate the conservation among palm chloroplast genomes, but point to subtle structural changes, providing support for the evolutionary dynamics of the Arecaceae family.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Jonathan Andre Morales Marroquín
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Luiz Augusto Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Av. Transnordestina S/N-Novo Horizonte, Feira de SantanaFeira de Santana, Bahia, CEP 44036-900, Brazil
| | - Kauanne Karolline Moreno Martins
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Marcones Ferreira Costa
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
- Universidade Federal do Piauí, BR-343 Km 3.5, Floriano, Piauí, CEP 64808-605, Brazil
| | - Doriane Picanço-Rodrigues
- Departamento de Biologia, Universidade Federal do Amazonas, Avenida Gen. Rodrigo Octávio Jordão Ramos, 3000-Coroado I-Campus Universitário-Senador Arthur Virgílio Filho-Setor Sul, Bloco H, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Luciano Delmodes de Alencar
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Cesar Augusto Zanello
- Programa de Pós-Gradução em Genética e Biologia Molecular, Universidade Estadual de Campinas, R. Monteiro Lobato, 255-Barão Geraldo, Campinas, São Paulo, CEP 13083-862, Brazil
| | - Carlos Augusto Colombo
- Instituto Agronômico, Av. Theodureto de Almeida Camargo, 1500, Campinas, São Paulo, CEP 13075-630, Brazil
| | | | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal do ABC, Avenida dos Estados, 5001, Santo André, São Paulo, CEP 09040-040, Brazil
| | - Maria Teresa Gomes Lopes
- Faculdade de Ciências Agrárias, Universidade Federal do Amazonas, Avenida Rodrigo Otávio Ramos, 3000-Bairro Coroado, Manaus, Amazonas, CEP 69077-000, Brazil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Avenida Pádua Dias, 11-Bairro São Dimas, Piracicaba, São Paulo, CEP 13418-900, Brazil
| | - Maria Imaculada Zucchi
- Agência Paulista de Tecnologia dos Agronegócios (APTA), Polo Centro Sul, Rodovia SP 127 Km 30, CP 28, Piracicaba, São Paulo, CEP 13400-970, Brazil.
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Kramer YV, Clement CR, de Carvalho JC, Fernandes AV, da Silva CVA, Koolen HHF, Aguiar JPL, Nunes-Nesi A, Ramos MV, Araújo WL, Gonçalves JFDC. Understanding the Technical-Scientific Gaps of Underutilized Tropical Species: The Case of Bactris gasipaes Kunth. PLANTS (BASEL, SWITZERLAND) 2023; 12:337. [PMID: 36679052 PMCID: PMC9867503 DOI: 10.3390/plants12020337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/30/2022] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
The extraction and commercialization of palm hearts is the most profitable activity involving the peach palm (Bactris gasipaes), while consumption of its fruits is limited to Amazonian communities. The excessive attention paid to the implementation of germplasm banks contributed to the lack of development of high-performance varieties, limiting the production and consumption of peach palm fruits and by-products. In addition, with the fragmentation of the Amazonian rainforest, wild populations are in danger of extinction. The species domestication, initiated by Native Amazonians, generated a large variety of peach palm populations, as evidenced by the diversity in fruit sizes and quality. Some advances in agronomic traits also took place. However, more research needs to be conducted to understand the implications of climatic changes on plant physiological performance. Indeed, the key point is that the exploitation of the full potential of B. gasipaes has not been completely exploited. Therefore, understanding the state-of-the-art research on the peach palm with a focus on its underutilized resources is essential for expanding plantations and, consequently, promoting the market expansion of the peach palm as a fruit crop.
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Affiliation(s)
- Yasmin Verçosa Kramer
- Plant Physiology Graduate Program, Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Avenida PH Rolfs, s/n, Viçosa 36570-900, Brazil
| | - Charles Roland Clement
- Department of Technology and Innovation, National Institute for Amazonian Research (MCTI-INPA), Avenida André Araújo, 2936, Aleixo, Manaus 69011-970, Brazil
| | - Josiane Celerino de Carvalho
- Laboratory of Plant Physiology and Biochemistry, National Institute for Amazonian Research (MCTI-INPA), André Araújo Avenue, 2936, Aleixo, Manaus 69011-970, Brazil
| | - Andreia Varmes Fernandes
- Laboratory of Plant Physiology and Biochemistry, National Institute for Amazonian Research (MCTI-INPA), André Araújo Avenue, 2936, Aleixo, Manaus 69011-970, Brazil
| | - Carlos Vinicius Azevedo da Silva
- Grupo de Pesquisas em Metabolômica e Espectrometria de Massas, Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Avenida Carvalho Leal, 1777, Cachoeirinha, Manaus 69065-000, Brazil
| | - Hector Henrique Ferreira Koolen
- Grupo de Pesquisas em Metabolômica e Espectrometria de Massas, Escola Superior de Ciências da Saúde, Universidade do Estado do Amazonas, Avenida Carvalho Leal, 1777, Cachoeirinha, Manaus 69065-000, Brazil
| | - Jaime Paiva Lopes Aguiar
- Coordination Society of Environment and Health and Laboratory of Physical Chemistry of Food, National Institute for Amazonian Research (MCTI-INPA), Avenida André Araújo, 2936, Aleixo, Manaus 69011-970, Brazil
| | - Adriano Nunes-Nesi
- Plant Physiology Graduate Program, Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Avenida PH Rolfs, s/n, Viçosa 36570-900, Brazil
| | - Marcio Viana Ramos
- Departamento de Bioquímica E Biologia Molecular, Centro de Ciências, Universidade Federal do Ceará (UFC), Campus do Pici, Benfica, Fortaleza 60020-181, Brazil
| | - Wagner L. Araújo
- Plant Physiology Graduate Program, Departamento de Biologia Vegetal, Universidade Federal de Viçosa (UFV), Avenida PH Rolfs, s/n, Viçosa 36570-900, Brazil
| | - José Francisco de Carvalho Gonçalves
- Laboratory of Plant Physiology and Biochemistry, National Institute for Amazonian Research (MCTI-INPA), André Araújo Avenue, 2936, Aleixo, Manaus 69011-970, Brazil
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Buitrago Acosta MC, Montúfar R, Guyot R, Mariac C, Tranbarger TJ, Restrepo S, Couvreur TLP. Bactris gasipaes Kunth var. gasipaes complete plastome and phylogenetic analysis. Mitochondrial DNA B Resour 2022; 7:1540-1544. [PMID: 36046105 PMCID: PMC9423826 DOI: 10.1080/23802359.2022.2109437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bactris gasipaes var. gasipaes (Arecaceae, Palmae) is an economically and socially important plant species for populations across tropical South and Central America. It has been domesticated from its wild variety, B. gasipaes var. chichagui, since pre-Columbian times. In this study, we sequenced the plastome of the cultivated variety, B. gasipaes Kunth var. gasipaes and compared it with the published plastome of the wild variety. The chloroplast sequence obtained was 156,580 bp. The cultivated chloroplast sequence was conserved compared to the wild type sequence with 99.8% of nucleotide identity. We did, however, identify multiple Single Nucleotide Variants (SNVs), insertions, microsatellites and a resolved region of missing nucleotides. A SNV in one of the core barcode markers (matK) was detected between the wild and cultivated accessions. Phylogenetic analysis was carried out across the Arecaceae family and compared to previous reports, resulting in an identical topology. This study is a step forward in understanding the genome evolution of this species.
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Affiliation(s)
| | - Rommel Montúfar
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Romain Guyot
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
- Department of Electronics and Automation, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Cedric Mariac
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | | | - Silvia Restrepo
- Laboratorio de Micología y Fitopatología, Universidad de los Andes, Bogotá, Colombia
| | - Thomas L. P. Couvreur
- Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
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Francisconi AF, Cauz-Santos LA, Morales Marroquín JA, van den Berg C, Alves-Pereira A, Delmondes de Alencar L, Picanço-Rodrigues D, Zanello CA, Ferreira Costa M, Gomes Lopes MT, Veasey EA, Zucchi MI. Complete chloroplast genomes and phylogeny in three Euterpe palms (E. edulis, E. oleracea and E. precatoria) from different Brazilian biomes. PLoS One 2022; 17:e0266304. [PMID: 35901127 PMCID: PMC9333295 DOI: 10.1371/journal.pone.0266304] [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: 03/15/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
Abstract
The Brazilian palm fruits and hearts-of-palm of Euterpe edulis, E. oleracea and E. precatoria are an important source for agro-industrial production, due to overexploitation, conservation strategies are required to maintain genetic diversity. Chloroplast genomes have conserved sequences, which are useful to explore evolutionary questions. Besides the plastid DNA, genome skimming allows the identification of other genomic resources, such as single nucleotide polymorphisms (SNPs), providing information about the genetic diversity of species. We sequenced the chloroplast genome and identified gene content in the three Euterpe species. We performed comparative analyses, described the polymorphisms among the chloroplast genome sequences (repeats, indels and SNPs) and performed a phylogenomic inference based on 55 palm species chloroplast genomes. Finally, using the remaining data from genome skimming, the nuclear and mitochondrial reads, we identified SNPs and estimated the genetic diversity among these Euterpe species. The Euterpe chloroplast genomes varied from 159,232 to 159,275 bp and presented a conserved quadripartite structure with high synteny with other palms. In a pairwise comparison, we found a greater number of insertions/deletions (indels = 93 and 103) and SNPs (284 and 254) between E. edulis/E. oleracea and E. edulis/E. precatoria when compared to E. oleracea/E. precatoria (58 indels and 114 SNPs). Also, the phylogeny indicated a closer relationship between E. oleracea/E. precatoria. The nuclear and mitochondrial genome analyses identified 1,077 SNPs and high divergence among species (FST = 0.77), especially between E. edulis and E. precatoria (FST = 0.86). These results showed that, despite the few structural differences among the chloroplast genomes of these Euterpe palms, a differentiation between E. edulis and the other Euterpe species can be identified by point mutations. This study not only brings new knowledge about the evolution of Euterpe chloroplast genomes, but also these new resources open the way for future phylogenomic inferences and comparative analyses within Arecaceae.
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Affiliation(s)
- Ana Flávia Francisconi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
| | | | | | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brasil
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Alessandro Alves-Pereira
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Luciano Delmondes de Alencar
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | | | - Cesar Augusto Zanello
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
| | - Marcones Ferreira Costa
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Campus Amílcar Ferreira Sobral, Universidade Federal do Piauí, Floriano, Piauí, Brasil
| | - Maria Teresa Gomes Lopes
- Departamento de Produção Animal e Vegetal, Universidade Federal do Amazonas, Manaus, Amazonas, Brasil
| | - Elizabeth Ann Veasey
- Departamento de Genética, Universidade de São Paulo, Piracicaba, São Paulo, Brasil
| | - Maria Imaculada Zucchi
- Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Estadual de Campinas, Campinas, São Paulo, Brasil
- Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, São Paulo, Brasil
- * E-mail: (MIZ); (AFF)
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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Dias MC, Clement CR, Fraga HPDF, Silva RSD, Rodrigues DP, Vieira LDN. The complete plastid genome of Bactris riparia (Arecaceae) and a comparative analysis in Bactridinae (Cocoseae, Arecaceae). Genet Mol Biol 2022; 45:e20210305. [DOI: 10.1590/1678-4685-gmb-2021-0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 09/24/2022] [Indexed: 11/09/2022] Open
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