1
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González-Trillo AC, Reyes López MÁ, Almaraz-Abarca N, Herrera-Arrieta Y, Gutiérrez-Velázquez MV, Barraza Salas M, Monreal-García HM, Torres-Ricario R. Characterization of the complete chloroplast genome sequence of Agave durangensis (Asparagales: Asparagaceae: Agavoideae). Mitochondrial DNA B Resour 2024; 9:536-540. [PMID: 38655148 PMCID: PMC11036899 DOI: 10.1080/23802359.2024.2338546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 03/31/2024] [Indexed: 04/26/2024] Open
Abstract
Agave durangensis commonly known as agave cenizo, is an endemic Agave species in Mexico used for mescal production, yet its taxonomic delimitation is still controversial. This study aimed to enhance taxonomic clarity by characterizing its chloroplast genome. Chloroplast DNA was isolated from 2-year-old A. durangensis leaves. The complete chloroplast genome size was 156,441 bp, comprising a large single-copy region (LSC), a pair of inverted repeat regions (IR), and a small single-copy region (SSC). Annotation revealed 87 protein-coding genes, 38 tRNAs, and 8 rRNAs, with notable gene inversions. Phylogenetic analysis suggests, A. durangensis forms a separate lineage within the Agave genus.
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Affiliation(s)
| | | | | | | | | | - Marcelo Barraza Salas
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Durango, Mexico
| | - Hugo Manuel Monreal-García
- Instituto Politécnico Nacional CIIDIR Unidad Durango, Durango, Durango, Mexico
- Centro de Biotecnología Genómica, Instituto Politécnico Nacional, Reynosa, Tamaulipas, Mexico
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango, Durango, Durango, Mexico
| | - Rene Torres-Ricario
- Instituto Politécnico Nacional CIIDIR Unidad Durango, Durango, Durango, Mexico
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Kan J, Zhang S, Wu Z, Bi D. Exploring Plastomic Resources in Sempervivum (Crassulaceae): Implications for Phylogenetics. Genes (Basel) 2024; 15:441. [PMID: 38674377 PMCID: PMC11049882 DOI: 10.3390/genes15040441] [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: 03/01/2024] [Revised: 03/29/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024] Open
Abstract
The plastid organelle is vital for photosynthesis and energy production. Advances in sequencing technology have enabled the exploration of plastomic resources, offering insights into plant evolution, diversity, and conservation. As an important group of horticultural ornamentals in the Crassulaceae family, Sempervivum plants are known for their unique rosette-like structures and reproduction through offsets. Despite their popularity, the classification status of Sempervivum remains uncertain, with only a single plastome sequence currently available. Furthermore, codon usage bias (CUB) is a widespread phenomenon of the unbalanced usage of synonymous codons in the coding sequence (CDS). However, due to the limited available plastid data, there has been no research that focused on the CUB analysis among Sempervivum until now. To address these gaps, we sequenced and released the plastomes of seven species and one subspecies from Sempervivum, revealing several consistent patterns. These included a shared 110 bp extension of the rps19 gene, 14 hypervariable regions (HVRs) with distinct nucleotide diversity (π: 0.01173 to 0.02702), and evidence of selective pressures shaping codon usage. Notably, phylogenetic analysis robustly divided the monophyletic clade into two sections: Jovibarba and Sempervivum. In conclusion, this comprehensive plastomic resource provides valuable insights into Sempervivum evolution and offers potential molecular markers for DNA barcoding.
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Affiliation(s)
- Junhu Kan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Shuo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; (J.K.); (S.Z.)
| | - De Bi
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215000, China
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Wang H, Zhang Y, Zhang L, Wang J, Guo H, Zong J, Chen J, Li D, Li L, Liu J, Li J. Molecular Characterization and Phylogenetic Analysis of Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] Based on the Complete Chloroplast Genome Sequence. Curr Issues Mol Biol 2024; 46:1635-1650. [PMID: 38392224 PMCID: PMC10888139 DOI: 10.3390/cimb46020106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/07/2024] [Accepted: 02/10/2024] [Indexed: 02/24/2024] Open
Abstract
Centipedegrass (Eremochloa ophiuroides) is an important warm-season grass plant used as a turfgrass as well as pasture grass in tropical and subtropical regions, with wide application in land surface greening and soil conservation in South China and southern United States. In this study, the complete cp genome of E. ophiuroides was assembled using high-throughput Illumina sequencing technology. The circle pseudomolecule for E. ophiuroides cp genome is 139,107 bp in length, with a quadripartite structure consisting of a large single copyregion of 82,081 bp and a small single copy region of 12,566 bp separated by a pair of inverted repeat regions of 22,230 bp each. The overall A + T content of the whole genome is 61.60%, showing an asymmetric nucleotide composition. The genome encodes a total of 131 gene species, composed of 20 duplicated genes within the IR regions and 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA genes, and 4 ribosome RNA genes. The complete cp genome sequence contains 51 long repeats and 197 simple sequence repeats, and a high degree of collinearity among E. ophiuroide and other Gramineae plants was disclosed. Phylogenetic analysis showed E. ophiuroides, together with the other two Eremochloa species, is closely related to Mnesithea helferi within the subtribe Rottboelliinae. These findings will be beneficial for the classification and identification of the Eremochloa taxa, phylogenetic resolution, novel gene discovery, and functional genomic studies for the genus Eremochloa.
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Affiliation(s)
- Haoran Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Yuan Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Zhang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingjing Wang
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Hailin Guo
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Junqin Zong
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jingbo Chen
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Dandan Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Ling Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianxiu Liu
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
| | - Jianjian Li
- The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing Botanical Garden, Mem. Sun Yat-Sen, Nanjing 210014, China
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4
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Kim JH, Kim J. Comprehensive analysis of the chloroplast genome and phylogenetic relationships of Sasa quelpaertensis Nakai. Mitochondrial DNA B Resour 2024; 9:88-93. [PMID: 38222981 PMCID: PMC10786426 DOI: 10.1080/23802359.2023.2301017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/16/2024] Open
Abstract
Jeju-Joritdae (Sasa quelpaertensis Nakai) is a broad-leaved bamboo grass endemic to Mount Halla, Jeju Island, South Korea. In this study, we report the complete chloroplast genome sequence of S. quelpaertensis. Its chloroplast genome is 139,730 bp in size and consists of a large single-copy (LSC, 83,351 bp) region, one small single-copy (SSC, 12,788 bp) region, and two inverted repeats (IRs, 21,796 bp each). The chloroplast genome of S. quelpaertensis encodes 131 genes, including 86 protein-coding, 37 tRNA, and 8 rRNA genes. The overall GC content of the S. quelpaertensis chloroplast genome is 38.86%. Phylogenetic analysis using the chloroplast genome sequence showed that S. quelpaertensis is closely related to Sasa veitchii and Sasella kogasensis. These findings provide valuable genomic resources for future studies of the Sasa genus in South Korea and other countries encompassing its distribution area.
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Affiliation(s)
- Jin Hee Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
| | - Jeongsik Kim
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
- Faculty of Science Education, Jeju National University, Jeju, Republic of Korea
- Interdisciplinary Graduate Program in Advanced Convergence Technology & Science, Jeju National University, Jeju, Republic of Korea
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5
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Zhou Q, Ding X, Wang H, Farooq Z, Wang L, Yang S. A novel in-situ-process technique constructs whole circular cpDNA library. PLANT METHODS 2024; 20:2. [PMID: 38172924 PMCID: PMC10763311 DOI: 10.1186/s13007-023-01126-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND The chloroplast genome (cp genome) is directly related to the study and analysis of molecular phylogeny and evolution of plants in the phylogenomics era. The cp genome, whereas, is highly plastic and exists as a heterogeneous mixture of sizes and physical conformations. It is advantageous to purify/enrich the circular chloroplast DNA (cpDNA) to reduce sequence complexity in cp genome research. Large-insert, ordered DNA libraries are more practical for genomics research than conventional, unordered ones. From this, a technique of constructing the ordered BAC library with the goal-insert cpDNA fragment is developed in this paper. RESULTS This novel in-situ-process technique will efficiently extract circular cpDNA from crops and construct a high-quality cpDNA library. The protocol combines the in-situ chloroplast lysis for the high-purity circular cpDNA with the in-situ substitute/ligation for the high-quality cpDNA library. Individually, a series of original buffers/solutions and optimized procedures for chloroplast lysis in-situ is different than bacterial lysis in-situ; the in-situ substitute/ligation that reacts on the MCE membrane is suitable for constructing the goal-insert, ordered cpDNA library while preventing the large-insert cpDNA fragment breakage. The goal-insert, ordered cpDNA library is arrayed on the microtiter plate by three colonies with the definite cpDNA fragment that are homologous-corresponds to the whole circular cpDNA of the chloroplast. CONCLUSION The novel in-situ-process technique amply furtherance of research in genome-wide functional analysis and characterization of chloroplasts, such as genome sequencing, bioinformatics analysis, cloning, physical mapping, molecular phylogeny and evolution.
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Affiliation(s)
- Qiang Zhou
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xianlong Ding
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Hongjie Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Zunaira Farooq
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Liang Wang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Shouping Yang
- Key Laboratory of Biology and Genetics Improvement of Soybean, Ministry of Agriculture of the People's Republic of China, Zhongshan Biological Breeding Laboratory (ZSBBL), National Innovation Platform for Soybean Breeding and Industry-Education Integration, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Soybean Research Institute, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
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6
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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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7
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Shioya N, Ogiso-Tanaka E, Watanabe M, Anai T, Hoshino T. Development of a High-Quality/Yield Long-Read Sequencing-Adaptable DNA Extraction Method for Crop Seeds. PLANTS (BASEL, SWITZERLAND) 2023; 12:2971. [PMID: 37631182 PMCID: PMC10457885 DOI: 10.3390/plants12162971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
Genome sequencing is important for discovering critical genes in crops and improving crop breeding efficiency. Generally, fresh, young leaves are used for DNA extraction from plants. However, seeds, the storage form, are more efficient because they do not require cultivation and can be ground at room temperature. Yet, only a few DNA extraction kits or methods suitable for seeds have been developed to date. In this study, we introduced an improved (IMP) Boom method that is relatively low-cost, simple to operate, and yields high-quality DNA that can withstand long-read sequencing. The method successfully extracted approximately 8 µg of DNA per gram of seed weight from soybean seeds at an average concentration of 48.3 ng/µL, approximately 40-fold higher than that extracted from seeds using a common extraction method kit. The A260/280 and A260/230 values of the DNA were 1.90 and 2.43, respectively, which exceeded the respective quality thresholds of 1.8 and 2.0. The DNA also had a DNA integrity number value (indicating the degree of DNA degradation) of 8.1, higher than that obtained using the kit and cetyltrimethylammonium bromide methods. Furthermore, the DNA showed a read length N50 of 20.96 kbp and a maximum read length of 127.8 kbp upon long-read sequencing using the Oxford Nanopore sequencer, with both values being higher than those obtained using the other methods. DNA extracted from seeds using the IMP Boom method showed an increase in the percentage of the nuclear genome with a decrease in the relative ratio of chloroplast DNA. These results suggested that the proposed IMP Boom method can extract high-quality and high-concentration DNA that can be used for long-read sequencing, which cannot be achieved from plant seeds using other conventional DNA extraction methods. The IMP Boom method could also be adapted to crop seeds other than soybeans, such as pea, okra, maize, and sunflower. This improved method is expected to improve the efficiency of various crop-breeding operations, including seed variety determination, testing of genetically modified seeds, and marker-assisted selection.
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Affiliation(s)
- Naohiro Shioya
- Laboratory of Crop Breeding, Graduate School of Agricultural Sciences, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
| | - Eri Ogiso-Tanaka
- Center for Molecular Biodiversity Research, National Museum of Nature and Science, 4-1-1 Amakubo, Tsukuba 305-0005, Ibaraki, Japan
| | - Masanori Watanabe
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
| | - Toyoaki Anai
- Laboratory of Agroecology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka 819-0395, Fukuoka, Japan;
| | - Tomoki Hoshino
- Laboratory of Crop Breeding, Graduate School of Agricultural Sciences, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka 997-8555, Yamagata, Japan;
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8
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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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9
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Li F, Xie X, Huang R, Tian E, Li C, Chao Z. Chloroplast genome sequencing based on genome skimming for identification of Eriobotryae Folium. BMC Biotechnol 2021; 21:69. [PMID: 34895202 PMCID: PMC8666020 DOI: 10.1186/s12896-021-00728-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 12/06/2021] [Indexed: 12/02/2022] Open
Abstract
Background Whole chloroplast genome (cpDNA) sequence is becoming widely used in the phylogenetic studies of plant and species identification, but in most cases the cpDNA were acquired from silica gel dried fresh leaves. So far few reports have been available to describe cpDNA acquisition from crude drugs derived from plant materials, the DNA of which usually was seriously damaged during their processing. In this study, we retrieved cpDNA from the commonly used crude drug Eriobotryae Folium (Pipaye in Chinese, which is the dried leaves of Eriobotrya japonica, PPY) using genome skimming technique. Results We successfully recovered cpDNA sequences and rDNA sequences from the crude drug PPY, and bioinformatics analysis showed a high overall consistency between the cpDNA obtained from the crude drugs and fresh samples. In the ML tree, each species formed distinct monophyletic clades based on cpDNA sequence data, while the phylogenetic relationships between Eriobotrya species were poorly resolved based on ITS and ITS2. Conclusion Our results demonstrate that both cpDNA and ITS/ITS2 are effective for identifying PPY and its counterfeits derived from distantly related species (i.e. Dillenia turbinata and Magnolia grandiflora), but cpDNA is more effective for distinguishing the counterfeits derived from the close relatives of Eriobotrya japonica, suggesting the potential of genome skimming for retrieving cpDNA from crude drugs used in Traditional Chinese Medicine for their identification. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00728-0.
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Affiliation(s)
- Fang Li
- Department of Pharmacy, Zhujiang Hospital, Southern Medical University, Guangzhou, 510282, China.,Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Xuena Xie
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Rong Huang
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Enwei Tian
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Chan Li
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Zhi Chao
- Faculty of Medicinal Plants and Pharmacognosy, School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China. .,Guangdong Provincial Key Laboratory of Chinese Medicine Pharmaceutics, Guangzhou, 510515, China.
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10
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Cauz-Santos LA, da Costa ZP, Callot C, Cauet S, Zucchi MI, Bergès H, van den Berg C, Vieira MLC. A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes. Genome Biol Evol 2021; 12:1841-1857. [PMID: 32722748 PMCID: PMC7586853 DOI: 10.1093/gbe/evaa155] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
Chloroplast genomes (cpDNA) in angiosperms are usually highly conserved. Although rearrangements have been observed in some lineages, such as Passiflora, the mechanisms that lead to rearrangements are still poorly elucidated. In the present study, we obtained 20 new chloroplast genomes (18 species from the genus Passiflora, and Dilkea retusa and Mitostemma brevifilis from the family Passifloraceae) in order to investigate cpDNA evolutionary history in this group. Passiflora cpDNAs vary in size considerably, with ∼50 kb between shortest and longest. Large inverted repeat (IR) expansions were identified, and at the extreme opposite, the loss of an IR was detected for the first time in Passiflora, a rare event in angiosperms. The loss of an IR region was detected in Passiflora capsularis and Passiflora costaricensis, a species in which occasional biparental chloroplast inheritance has previously been reported. A repertory of rearrangements such as inversions and gene losses were detected, making Passiflora one of the few groups with complex chloroplast genome evolution. We also performed a phylogenomic study based on all the available cp genomes and our analysis implies that there is a need to reconsider the taxonomic classifications of some species in the group.
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Affiliation(s)
- Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
| | - Caroline Callot
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Stéphane Cauet
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Maria Imaculada Zucchi
- Polo Regional de Desenvolvimento Tecnológico do Centro Sul, Agência Paulista de Tecnologia dos Agronegócios, Piracicaba, SP, Brazil
| | - Hélène Bergès
- Centre National de Ressources Génomiques Végétales, INRA, Auzeville, Castanet-Tolosan, France
| | - Cássio van den Berg
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil.,Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, BA, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz," Universidade de São Paulo, Piracicaba, SP, Brazil
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11
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Liu XJ, Sun J, Huang Y, Li C, Zheng P, Yuan Y, Chen H, Jan M, Zheng H, Du H, Tu J. Osj10gBTF3-Mediated Import of Chloroplast Protein Is Essential for Pollen Development in Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:713544. [PMID: 34421965 PMCID: PMC8377413 DOI: 10.3389/fpls.2021.713544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Chloroplasts are crucial organelles for the generation of fatty acids and starch required for plant development. Nascent polypeptide-associated complex (NAC) proteins have been implicated in development as transcription factors. However, their chaperone roles in chloroplasts and their relationship with pollen development in plants remain to be elucidated. Here, we demonstrated that Osj10gBTF3, a NAC protein, regulates pollen and chloroplast development in rice by coordinating with a Hsp90 family chaperone OsHSP82 to mediate chloroplast import. Knockout of Osj10gBTF3 affects pollen and chloroplast development and significantly reduces the accumulation of fertility-related chloroplast protein OsPPR676. Both Osj10gBTF3 and OsHSP82 interact with OsPPR676. Interestingly, the interaction between OsHSP82 and OsPPR676 is only found in the cytoplasm, while the interaction between Osj10gBTF3 and OsPPR676 also occurs inside the chloroplast. The chloroplast stroma chaperone OsCpn60 can also be co-precipitated with Osj10gBTF3, but not with OsHSP82. Further investigation indicates that Osj10gBTF3 enters the chloroplast stroma possibly through the inner chloroplast membrane channel protein Tic110 and then recruits OsCpn60 for the folding or assembly of OsPPR676. Our results reveal a chaperone role of Osj10gBTF3 in chloroplast import different from Hsp90 and provide a link between chloroplast transport and pollen development in rice.
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Affiliation(s)
- Xue-jiao Liu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Jiaqi Sun
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Yuqing Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Chao Li
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Peng Zheng
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Yue Yuan
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Hao Chen
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehmood Jan
- Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Huanquan Zheng
- Department of Biology, McGill University, Montreal, QC, Canada
| | - Hao Du
- Institute of Crop Science, Zhejiang University, Hangzhou, China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jumin Tu
- Institute of Crop Science, Zhejiang University, Hangzhou, China
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12
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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13
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Teske D, Peters A, Möllers A, Fischer M. Genomic Profiling: The Strengths and Limitations of Chloroplast Genome-Based Plant Variety Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14323-14333. [PMID: 32917087 DOI: 10.1021/acs.jafc.0c03001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Genomic profiling is a suitable tool for variety authentication and has applications in both operational quality and regulatory raw material control. It can be used to differentiate species or varieties and to identify admixtures as well as field contaminants. To establish a molecular profile, reliable and very accurate sequence data are required. As a result of the influence of the pollinator plant, nuclear genome-based authentication is in most cases not suitable for a direct application on the fruit. Sequences must be used that come exclusively from the localized mother plant. Parts of the fruit of maternal origin, e.g., components derived from the blossom, are suitable as a basis for this. Alternatively, DNA from cell organelles that are maternally inherited, such as mitochondria or chloroplasts, can be used. The latter will be discussed in this review in closer detail. Although individual gene segments on the chloroplast genome are already used for species differentiation in barcoding studies on plants, little is known about the usefulness of the entire chloroplast genome for intraspecies differentiation in general and for differentiation between modern varieties in particular. Results from the literature as well as from our own work suggest that chloroplast genome sequences are indeed very well-suited for the differentiation of old varieties. On the other hand, they are less or not suitable for the genetic differentiation of modern cultivars, because they are often too closely related.
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Affiliation(s)
- Doreen Teske
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alina Peters
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Alexander Möllers
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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14
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Liu H, Ren D, Jiang L, Li X, Yao Y, Mi L, Chen W, Mo A, Jiang N, Yang J, Chen P, Ma H, Luo X, Lu P. A Natural Variation in PLEIOTROPIC DEVELOPMENTAL DEFECTS Uncovers a Crucial Role for Chloroplast tRNA Modification in Translation and Plant Development. THE PLANT CELL 2020; 32:2345-2366. [PMID: 32327539 PMCID: PMC7346568 DOI: 10.1105/tpc.19.00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 03/30/2020] [Accepted: 04/15/2020] [Indexed: 05/28/2023]
Abstract
The modification of tRNA is important for accurate, efficient protein translation. A number of tRNA-modifying enzymes were found to influence various developmental processes in distinct organisms. However, few genetic or molecular studies have focused on genes encoding tRNA-modifying enzymes in green plant organelles. Here, we discovered that PDD OL , a natural variation allele of PLEIOTROPIC DEVELOPMENTAL DEFECTS (PDD), leads to pleiotropic developmental defects in a near-isogenic line (NIL) generated by introgressing the wild rice Oryza longistaminata into the rice (Oryza sativa) cv 187R. Map-based cloning revealed that PDD encodes an evolutionarily conserved tRNA-modifying GTPase belonging to the tRNA modification E family. The function of PDD was further confirmed by genetic complementation experiments and mutant analysis. PDD mRNA is primarily expressed in leaves, and PDD is localized to chloroplasts. Biochemical analyses indicated that PDD187R forms homodimers and has strong GTPase activity, whereas PDDOL fails to form homodimers and has weak GTPase activity. Liquid chromatography-coupled tandem quadrupole mass spectrometry revealed that PDD is associated with the 5-methylaminomethyl-2-thiouridine modification of chloroplast tRNA. Furthermore, compared to 187R, NIL-PDD OL has severely reduced levels of proteins involved in photosynthesis and ribosome biogenesis but increased levels of plastid-encoded RNA polymerase subunits. Finally, we demonstrate that the defect due to PDD OL alters chloroplast gene expression, thereby affecting communication between the chloroplast and the nucleus.
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Affiliation(s)
- Hui Liu
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ding Ren
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
| | - Ling Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiaojing Li
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yuan Yao
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Limin Mi
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Wanli Chen
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Aowei Mo
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ning Jiang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinshui Yang
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Chen
- Biomass and Bioenergy Research Centre, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Xiaojin Luo
- School of Life Sciences, Fudan University, Shanghai 200433, China
- MOE Engineering Research Center of Gene Technology, Fudan University, Shanghai 200433, China
| | - Pingli Lu
- School of Life Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
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15
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Scheunert A, Dorfner M, Lingl T, Oberprieler C. Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing. PLoS One 2020; 15:e0226234. [PMID: 32208422 PMCID: PMC7092973 DOI: 10.1371/journal.pone.0226234] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/28/2020] [Indexed: 12/13/2022] Open
Abstract
The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore long reads are additionally employed in hybrid approaches to enable assembly across the highly similar inverted repeats of a chloroplast genome. Unlike for PacBio, plastome assemblies based solely on Nanopore reads are rarely found, due to their high error rate and non-random error profile. However, the actual quality decline connected to their use has rarely been quantified. Furthermore, no study has employed reference-based assembly using Nanopore reads, which is common with Illumina data. Using Leucanthemum Mill. as an example, we compared the sequence quality of seven chloroplast genome assemblies of the same species, using combinations of two sequencing platforms and three analysis pipelines. In addition, we assessed the factors which might influence Nanopore assembly quality during sequence generation and bioinformatic processing. The consensus sequence derived from de novo assembly of Nanopore data had a sequence identity of 99.59% compared to Illumina short-read de novo assembly. Most of the errors detected were indels (81.5%), and a large majority of them is part of homopolymer regions. The quality of reference-based assembly is heavily dependent upon the choice of a close-enough reference. When using a reference with 0.83% sequence divergence from the studied species, mapping of Nanopore reads results in a consensus comparable to that from Nanopore de novo assembly, and of only slightly inferior quality compared to a reference-based assembly with Illumina data. For optimal de novo assembly of Nanopore data, appropriate filtering of contaminants and chimeric sequences, as well as employing moderate read coverage, is essential. Based on these results, we conclude that Nanopore long reads are a suitable alternative to Illumina short reads in plastome phylogenomics. Few errors remain in the finalized assembly, which can be easily masked in phylogenetic analyses without loss in analytical accuracy. The easily applicable and cost-effective technology might warrant more attention by researchers dealing with plant chloroplast genomes.
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Affiliation(s)
- Agnes Scheunert
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Marco Dorfner
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Thomas Lingl
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
| | - Christoph Oberprieler
- Evolutionary and Systematic Botany Group, Institute of Plant Sciences, University of Regensburg, Regensburg, Germany
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16
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Kitajima-Koga A, Baslam M, Hamada Y, Ito N, Taniuchi T, Takamatsu T, Oikawa K, Kaneko K, Mitsui T. Functional Analysis of Rice Long-Chain Acyl-CoA Synthetase 9 ( OsLACS9) in the Chloroplast Envelope Membrane. Int J Mol Sci 2020; 21:E2223. [PMID: 32210132 PMCID: PMC7139535 DOI: 10.3390/ijms21062223] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/17/2020] [Accepted: 03/19/2020] [Indexed: 02/04/2023] Open
Abstract
The long-chain acyl-CoA synthetases (LACSs) are involved in lipid synthesis, fatty acid catabolism, and the transport of fatty acids between subcellular compartments. These enzymes catalyze the critical reaction of fatty acyl chains to fatty acyl-CoAs for the triacylglycerol biosynthesis used as carbon and energy reserves. In Arabidopsis, LACSs are encoded by a family of nine genes, with LACS9 being the only member located in the chloroplast envelope membrane. However, the comprehensive role of LACS9 and its contribution to plant metabolism have not been explored thoroughly. In this study, we report on the identification and characterization of LACS9 mutants in rice plants. Our results indicate that the loss-of-function mutations in OsLACS9 affect the architecture of internodes resulting in dwarf plants with large starch granules in the chloroplast, showing the suppression of starch degradation. Moreover, the plastid localization of α-amylase I-1 (AmyI-1)-a key enzyme involved in starch breakdown in plastids-was suppressed in the lacs9 mutant line. Immunological and confocal laser scanning microscopy analyses showed that OsLACS9-GFP is located in the chloroplast envelope in green tissue. Microscopic analysis showed that OsLACS9s interact with each other in the plastid envelope membrane. Furthermore, OsLACS9 is also one of the proteins transported to plastids without a transit peptide or involvement of the Toc/Tic complex system. To identify the plastid-targeting signal of OsLACS9, the transient expression and localization of a series of N-terminal truncated OsLACS9-green fluorescent protein (GFP) fusion proteins were examined. Truncation analyses identified the N-terminal 30 amino acid residues to be required for OsLACS9 plastid localization. Overall, the data in this study provide an advanced understanding of the function of OsLACS9 and its role in starch degradation and plant growth.
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Affiliation(s)
- Aya Kitajima-Koga
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Yuuki Hamada
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Namiko Ito
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Tomoko Taniuchi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Takeshi Takamatsu
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Kazusato Oikawa
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Kentaro Kaneko
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
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Isolation of Intact Chloroplast for Sequencing Plastid Genomes of Five Festuca Species. PLANTS 2019; 8:plants8120606. [PMID: 31847311 PMCID: PMC6963596 DOI: 10.3390/plants8120606] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/08/2019] [Accepted: 12/12/2019] [Indexed: 12/02/2022]
Abstract
Isolation of good quality chloroplast DNA (cpDNA) is a challenge in different plant species, although several methods for isolation are known. Attempts were undertaken to isolate cpDNA from Festuca grass species by using available standard protocols; however, they failed due to difficulties separating intact chloroplasts from the polysaccharides, oleoresin, and contaminated nuclear DNA that are present in the crude homogenate. In this study, we present a quick and inexpensive protocol for isolating intact chloroplasts from seven grass varieties/accessions of five Festuca species using a single layer of 30% Percoll solution. This protocol was successful in isolating high quality cpDNA with the least amount of contamination of other DNA. We performed Illumina MiSeq paired-end sequencing (2 × 300 bp) using 200 ng of cpDNA of each variety/accession. Chloroplast genome mapping showed that 0.28%–11.37% were chloroplast reads, which covered 94%–96% of the reference plastid genomes of the closely related grass species. This improved method delivered high quality cpDNA from seven grass varieties/accessions of five Festuca species and could be useful for other grass species with similar genome complexity.
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Optimized Nuclear Pellet Method for Extracting Next-Generation Sequencing Quality Genomic DNA from Fresh Leaf Tissue. Methods Protoc 2019; 2:mps2020054. [PMID: 31242613 PMCID: PMC6632156 DOI: 10.3390/mps2020054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/20/2019] [Accepted: 06/21/2019] [Indexed: 01/10/2023] Open
Abstract
Next-generation sequencing (NGS) is a revolutionary advancement allowing large-scale discovery of functional molecular markers that has many applications, including plant breeding. High-quality genomic DNA (gDNA) is a prerequisite for successful NGS library preparation and sequencing; however, few reliable protocols to obtain such plant gDNA exist. A previously reported nuclear pellet (NP) method enables extraction of high-yielding gDNA from fresh leaf tissue of maize (Zea mays L.), but the quality does not meet the stringent requirements of NGS. In this study, we optimized the NP method for whole-genome sequencing of rice (Oryza sativa L.) through the integration of simple purification steps. The optimized NP method relied on initial nucleus enrichment, cell lysis, extraction, and subsequent gDNA purification buffers. The purification steps used proteinase K, RNase A, phenol/chloroform/isoamyl alcohol (25:24:1), and chloroform/isoamyl alcohol (24:1) treatments for protein digestion and RNA, protein, and phenol removal, respectively. Our data suggest that this optimized NP method allowed extraction of consistently high-yielding and high-quality undegraded gDNA without contamination by protein and RNA. Moreover, the extracted gDNA fulfilled the quality metrics of NGS library preparation for the Illumina HiSeq X Ten platform by the TruSeq DNA PCR-Free Library Prep Kit (Illumina). We provide a reliable step-by-step guide to the extraction of high-quality gDNA from fresh leaf tissues of rice for molecular biologists with limited resources.
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Inomata T, Baslam M, Masui T, Koshu T, Takamatsu T, Kaneko K, Pozueta-Romero J, Mitsui T. Proteomics Analysis Reveals Non-Controlled Activation of Photosynthesis and Protein Synthesis in a Rice npp1 Mutant under High Temperature and Elevated CO₂ Conditions. Int J Mol Sci 2018; 19:ijms19092655. [PMID: 30205448 PMCID: PMC6165220 DOI: 10.3390/ijms19092655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 08/30/2018] [Accepted: 09/03/2018] [Indexed: 11/26/2022] Open
Abstract
Rice nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) catalyzes the hydrolytic breakdown of the pyrophosphate and phosphodiester bonds of a number of nucleotides including ADP-glucose and ATP. Under high temperature and elevated CO2 conditions (HT + ECO2), the npp1 knockout rice mutant displayed rapid growth and high starch content phenotypes, indicating that NPP1 exerts a negative effect on starch accumulation and growth. To gain further insight into the mechanisms involved in the NPP1 downregulation induced starch overaccumulation, in this study we conducted photosynthesis, leaf proteomic, and chloroplast phosphoproteomic analyses of wild-type (WT) and npp1 plants cultured under HT + ECO2. Photosynthesis in npp1 leaves was significantly higher than in WT. Additionally, npp1 leaves accumulated higher levels of sucrose than WT. The proteomic analyses revealed upregulation of proteins related to carbohydrate metabolism and the protein synthesis system in npp1 plants. Further, our data indicate the induction of 14-3-3 proteins in npp1 plants. Our finding demonstrates a higher level of protein phosphorylation in npp1 chloroplasts, which may play an important role in carbohydrate accumulation. Together, these results offer novel targets and provide additional insights into carbohydrate metabolism regulation under ambient and adverse conditions.
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Affiliation(s)
- Takuya Inomata
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Marouane Baslam
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Takahiro Masui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Tsutomu Koshu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Takeshi Takamatsu
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
| | - Kentaro Kaneko
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
| | - Javier Pozueta-Romero
- Instituto de Agrobiotecnología (CSIC, UPNA, Gobierno de Navarra), Mutiloako Etorbidea Zenbaki Gabe, 31192 Mutiloabeti, Nafarroa, Spain.
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Niigata 950-2181, Japan.
- Department of Biochemistry, Niigata University, Niigata 950-218, Japan.
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Ge J, Cai L, Bi GQ, Chen G, Sun W. Characterization of the Complete Chloroplast Genomes of Buddleja colvilei and B. sessilifolia: Implications for the Taxonomy of Buddleja L. Molecules 2018; 23:E1248. [PMID: 29882896 PMCID: PMC6100213 DOI: 10.3390/molecules23061248] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 05/19/2018] [Accepted: 05/21/2018] [Indexed: 11/17/2022] Open
Abstract
Buddleja colvilei Hook.f. & Thomson (Scrophulariaceae) is a threatened alpine plant with a distribution throughout the Himalayas, also used as an ornamental plant. The name Buddleja sessilifolia B.S. Sun ex S.Y. Pao was assigned in 1983 to a plant distributed throughout the Gaoligong Mountains, but the name was later placed in synonymy with B. colvilei in the Flora of China. In this study we sequenced the complete chloroplast (cp) genomes of two individuals of B. colvilei and three individuals of B. sessilifolia from across the range. Both molecular and morphological analysis support the revision of B. sessilifolia. The phylogenetic analysis constructed with the whole cp genomes, the large single-copy regions (LSC), small single-copy regions (SSC), inverted repeat (IR) and the nuclear genes 18S/ITS1/5.8S/ITS2/28S all supported B. sessilifolia as a distinct species. Additionally, coalescence-based species delimitation methods (bGMYC, bPTP) using the whole chloroplast datasets also supported B. sessilifolia as a distinct species. The results suggest that the B. sessilifolia lineage was early diverging among the Asian Buddleja species. Overall gene contents were similar and gene arrangements were found to be highly conserved in the two species, however, fixed differences were found between the two species. A total of 474 single nucleotide polymorphisms (SNPs) were identified between the two species. The Principal Coordinate Analysis of the morphological characters resolved two groups and supported B. sessilifolia as a distinct species. Discrimination of B. colvilei and B. sessilifolia using morphological characters and the redescription of B. sessilifolia are detailed here.
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Affiliation(s)
- Jia Ge
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Gui-Qi Bi
- Key Laboratory of Marine Genetics and Breeding (OUC), Ministry of Education, Qingdao 266100, China.
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China.
| | - Gao Chen
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming 650201, China.
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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