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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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Bandaranayake PCG, Naranpanawa N, Chandrasekara CHWMRB, Samarakoon H, Lokuge S, Jayasundara S, Bandaranayake AU, Pushpakumara DKNG, Wijesundara DSA. Chloroplast genome, nuclear ITS regions, mitogenome regions, and Skmer analysis resolved the genetic relationship among Cinnamomum species in Sri Lanka. PLoS One 2023; 18:e0291763. [PMID: 37729154 PMCID: PMC10511092 DOI: 10.1371/journal.pone.0291763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/05/2023] [Indexed: 09/22/2023] Open
Abstract
Cinnamomum species have gained worldwide attention because of their economic benefits. Among them, C. verum (synonymous with C. zeylanicum Blume), commonly known as Ceylon Cinnamon or True Cinnamon is mainly produced in Sri Lanka. In addition, Sri Lanka is home to seven endemic wild cinnamon species, C. capparu-coronde, C. citriodorum, C. dubium, C. litseifolium, C. ovalifolium, C. rivulorum and C. sinharajaense. Proper identification and genetic characterization are fundamental for the conservation and commercialization of these species. While some species can be identified based on distinct morphological or chemical traits, others cannot be identified easily morphologically or chemically. The DNA barcoding using rbcL, matK, and trnH-psbA regions could not also resolve the identification of Cinnamomum species in Sri Lanka. Therefore, we generated Illumina Hiseq data of about 20x coverage for each identified species and a C. verum sample (India) and assembled the chloroplast genome, nuclear ITS regions, and several mitochondrial genes, and conducted Skmer analysis. Chloroplast genomes of all eight species were assembled using a seed-based method.According to the Bayesian phylogenomic tree constructed with the complete chloroplast genomes, the C. verum (Sri Lanka) is sister to previously sequenced C. verum (NC_035236.1, KY635878.1), C. dubium and C. rivulorum. The C. verum sample from India is sister to C. litseifolium and C. ovalifolium. According to the ITS regions studied, C. verum (Sri Lanka) is sister to C. verum (NC_035236.1), C. dubium and C. rivulorum. Cinnamomum verum (India) shares an identical ITS region with C. ovalifolium, C. litseifolium, C. citriodorum, and C. capparu-coronde. According to the Skmer analysis C. verum (Sri Lanka) is sister to C. dubium and C. rivulorum, whereas C. verum (India) is sister to C. ovalifolium, and C. litseifolium. The chloroplast gene ycf1 was identified as a chloroplast barcode for the identification of Cinnamomum species. We identified an 18 bp indel region in the ycf1 gene, that could differentiate C. verum (India) and C. verum (Sri Lanka) samples tested.
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Affiliation(s)
| | - Nathasha Naranpanawa
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
- Postgraduate Institute of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | | | - Hiruna Samarakoon
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Lokuge
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - S. Jayasundara
- Faculty of Agriculture, Agricultural Biotechnology Centre, University of Peradeniya, Peradeniya, Sri Lanka
| | - Asitha U. Bandaranayake
- Faculty of Engineering, Department of Computer Engineering, University of Peradeniya, Peradeniya, Sri Lanka
| | - D. K. N. G. Pushpakumara
- Faculty of Agriculture, Department of Crop Science, University of Peradeniya, Peradeniya, Sri Lanka
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Du Q, Li J, Wang L, Chen H, Jiang M, Chen Z, Jiang C, Gao H, Wang B, Liu C. Complete chloroplast genomes of two medicinal Swertia species: the comparative evolutionary analysis of Swertia genus in the Gentianaceae family. PLANTA 2022; 256:73. [PMID: 36083348 DOI: 10.1007/s00425-022-03987-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
The complete chloroplast genome of Swertia kouitchensis has been sequenced and assembled, compared with that of S. bimaculata to determine the evolutionary relationships among species of the Swertia in the Gentianaceae family. Swertia kouitchensis and S. bimaculata are from the Gentianaceae family. The complete chloroplast genome of S. kouitchensis was newly assembled, annotated, and analyzed by Illumina Hiseq 2500 platform. The chloroplast genomes of the two species encoded a total of 133, 134 genes, which included 88-89 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA genes. One intron was contained in each of the eight protein-coding genes and eight tRNA-coding genes, whereas two introns were found in two genes (ycf3 and clpP). The most abundant codon of the two species was for isoleucine, and the least abundant codon was for cysteine. The number of microsatellite repeat sequences was twenty-eight and thirty-two identified in the chloroplast genomes of S. kouitchensis and S. bimaculata, respectively. A total of 1127 repeat sequences were identified in all the 23 Swertia chloroplast genomes, and they fell into four categories. Furthermore, five divergence hotspot regions can be applied to discriminate these 23 Swertia species through genomes comparison. One pair of genus-specific DNA barcodes primer has been accurately identified. Therefore, the diverse regions cloned by a specific primer may become an effective and powerful molecular marker for the identification of Swertia genus. Moreover, four genes (ccsA, ndhK, rpoC1, and rps12) were positive selective pressure. The phylogenetic tree showed that the 23 Swertia species were clustered into a large clade including four evident subbranches, whereas the two species of S. kouitchensis and S. bimaculata were separately clustered into the diverse but correlated species group.
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Affiliation(s)
- Qing Du
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China.
- College of Pharmacy, Key Laboratory of Medicinal Plant Resources of Qinghai-Tibetan Plateau in Qinghai Province, Qinghai Minzu University, No.3, Bayi Mid-road, Chengdong District, Xining City, Qinghai Province, 810007, People's Republic of China.
- Fresh Sky-Right (Beijing) International Science and Technology Co., Ltd, No.59, Banjing Road, Haidian District, Beijing, 100097, People's Republic of China.
| | - Jing Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China
| | - Liqiang Wang
- College of Pharmacy, Heze University, No.2269, University Road, Mudan District, Heze City, Shandong Province, 274015, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), No. 3501, University Road, Changqing District, Jinan City, Shandong Province, 250399, People's Republic of China
| | - Zhuoer Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China
| | - Chuanbei Jiang
- Genepioneer Biotechnologies Inc, No. 9, Weidi Road, Qixia District, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Haidong Gao
- Genepioneer Biotechnologies Inc, No. 9, Weidi Road, Qixia District, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Bin Wang
- Xiangnan University, No. 889, Chenzhou dadao, Chenzhou City, Hunan Province, 423000, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, No. 151, Malianwa North Road, Hai Dian District, Beijing, 100193, People's Republic of China.
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Dalla Costa TP, Silva MC, de Santana Lopes A, Gomes Pacheco T, de Oliveira JD, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The plastome of Melocactus glaucescens Buining & Brederoo reveals unique evolutionary features and loss of essential tRNA genes. PLANTA 2022; 255:57. [PMID: 35113261 DOI: 10.1007/s00425-022-03841-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The plastome of Melocactus glaucescens shows unique rearrangements, IR expansion, and unprecedented gene losses in Cactaceae. Our data indicate tRNA import from the cytosol to the plastids in this species. Cactaceae represents one of the richest families in keystone species of arid and semiarid biomes. This family shows various specific features comprehending morphology, anatomy, and metabolism, which allow them to grow under unfavorable environmental conditions. The subfamily Cactoideae contains the most divergence of species, which are highly variable in growth habit and morphology. This subfamily includes the endangered species Melocactus glaucescens (tribe Cereeae), which is a cactus endemic to the biome Caatinga in Brazil. Aiming to analyze the plastid evolution and develop molecular markers, we sequenced and analyzed in detail the plastome of M. glaucescens. Our analyses revealed that the M. glaucescens plastome is the most divergent among the species of the family Cactaceae sequenced so far. We characterized here unique rearrangements, expanded IRs containing an unusual set of genes, and several gene losses. Some genes related to the ndh complex were lost during the plastome evolution, while others have lost their functionality. Additionally, the loss of three tRNA genes (trnA-UGC, trnV-UAC, and trnV-GAC) suggests tRNA import from the cytosol to the plastids in M. glaucescens. Moreover, we identified high gene divergence, several putative positive signatures, and possible unique RNA-editing sites. Furthermore, we mapped 169 SSRs in the plastome of M. glaucescens, which are helpful to access the genetic diversity of natural populations and conservation strategies. Finally, our data provide new insights into the evolution of plastids in Cactaceae, which is an outstanding lineage adapted to extreme environmental conditions and a notorious example of the atypical evolution of plastomes.
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Affiliation(s)
- Tanara P Dalla Costa
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Maria C Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José D de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Valter A de Baura
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Du Q, Jiang M, Sun S, Wang L, Liu S, Jiang C, Gao H, Chen H, Li Y, Wang B, Liu C. The complete chloroplast genome sequence of Clerodendranthus spicatus, a medicinal plant for preventing and treating kidney diseases from Lamiaceae family. Mol Biol Rep 2022; 49:3073-3083. [PMID: 35059973 DOI: 10.1007/s11033-022-07135-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/10/2022] [Indexed: 12/25/2022]
Abstract
BACKGROUND Clerodendranthus spicatus (Thunb.) C. Y. Wu ex H. W. Li is one of the most important medicines for the treatment of nephrology in the southeast regions of China. To understand the taxonomic classification of Clerodendranthus species and identify species discrimination markers, we sequenced and characterized its chloroplast genome in the current study. METHODS AND RESULTS Total genomic DNA were isolated from dried leaves of C. spicatus and sequenced using an Illumina sequencing platform. The data were assembled and annotated by the NOVOPlasty software and CpGAVAS2 web service. The complete chloroplast genome of C. spicatus was 152,155 bp, including a large single-copy region of 83,098 bp, a small single-copy region of 17,665 bp, and a pair of inverted repeat regions of 25,696 bp. The Isoleucine codons are the most abundant, accounting for 4.17% of all codons. The codons of AUG, UUA, and AGA demonstrated a high degree of usage bias. Twenty-eight simple sequence repeats, thirty-six tandem repeats, and forty interspersed repeats were identified. The distribution of the specific rps19, ycf1, rpl2, trnH, psbA genes were analyzed. Analysis of the genetic distance of the intergenic spacer regions shows that ndhG-ndhI, accD-psaI, rps15-ycf1, rpl20-clpP, ccsA-ndhD regions have high K2p values. Phylogenetic analysis showed that C. spicatu is closely related to two Lamiaceae species, Tectona grandis, and Glechoma longituba. CONCLUSIONS In this study, we sequenced and characterized the chloroplast genome of C. spicatus. Phylogenomic analysis has identified species closely related to C. spicatus, which represent potential candidates for the development of drugs improving renal functions.
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Affiliation(s)
- Qing Du
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,College of Pharmacy, Qinghai Provincial Key Laboratory of Phytochemistry of Qinghai Tibet Plateau, Qinghai Minzu University, Xining, Qinghai, 810007, People's Republic of China.,Fresh Sky-Right (Beijing) International Science and Technology Co. Ltd, Beijing, 100187, People's Republic of China
| | - Mei Jiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.,School of Pharmaceutical Sciences, Qilu University of Technology, Shandong Academy of Sciences, Jinan, Shandong, 250353, People's Republic of China
| | - Sihui Sun
- College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People's Republic of China
| | - Liqiang Wang
- College of Pharmacy, Heze University, Heze, Shandong, 274015, People's Republic of China
| | - Shengyu Liu
- Institute of Medical Information & Library, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Chuanbei Jiang
- Genepioneer Biotechnologies Inc., Nanjing, Jiangsu, 210023, People's Republic of China
| | - Haidong Gao
- Genepioneer Biotechnologies Inc., Nanjing, Jiangsu, 210023, People's Republic of China
| | - Haimei Chen
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China
| | - Yong Li
- College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People's Republic of China
| | - Bin Wang
- College of Pharmacy, Xiangnan University, Chenzhou, Hunan, 423000, People's Republic of China.
| | - Chang Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, People's Republic of China.
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Shestibratov KA, Baranov OY, Mescherova EN, Kiryanov PS, Panteleev SV, Mozharovskaya LV, Krutovsky KV, Padutov VE. Structure and Phylogeny of the Curly Birch Chloroplast Genome. Front Genet 2021; 12:625764. [PMID: 34671379 PMCID: PMC8521055 DOI: 10.3389/fgene.2021.625764] [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: 11/03/2020] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Curly birch [Betula pendula var. carelica (Merckl.) Hämet-Ahti] is a relatively rare variety of silver birch (B. pendula Roth) that occurs mainly in Northern Europe and northwest part of Russia (Karelia). It is famous for the beautiful decorative texture of wood. Abnormal xylogenesis underlying this trait is heritable, but its genetic mechanism has not yet been fully understood. The high number of potentially informative genetic markers can be identified through sequencing nuclear and organelle genomes. Here, the de novo assembly, complete nucleotide sequence, and annotation of the chloroplast genome (plastome) of curly birch are presented for the first time. The complete plastome length is 160,523 bp. It contains 82 genes encoding structural and enzymatic proteins, 37 transfer RNAs (tRNAs), and eight ribosomal RNAs (rRNAs). The chloroplast DNA (cpDNA) is AT-rich containing 31.5% of A and 32.5% of T nucleotides. The GC-rich regions represent inverted repeats IR1 and IR2 containing genes of rRNAs (5S, 4.5S, 23S, and 16S) and tRNAs (trnV, trnI, and trnA). A high content of GC was found in rRNA (55.2%) and tRNA (53.2%) genes, but only 37.0% in protein-coding genes. In total, 384 microsatellite or simple sequence repeat (SSR) loci were found, mostly with mononucleotide motifs (92% of all loci) and predominantly A or T motifs (94% of all mononucleotide motifs). Comparative analysis of cpDNA in different plant species revealed high structural and functional conservatism in organization of the angiosperm plastomes, while the level of differences depends on the phylogenetic relationship. The structural and functional organization of plastome in curly birch was similar to cpDNA in other species of woody plants. Finally, the identified cpDNA sequence variation will allow to develop useful genetic markers.
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Affiliation(s)
- Konstantin A Shestibratov
- Forest Biotechnology Group, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia.,Forestry Faculty, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia
| | - Oleg Yu Baranov
- Laboratory of Genomics and Bioinformatics, Forest Research Institute, National Academy of Sciences of Belarus, Gomel, Belarus
| | - Eugenia N Mescherova
- Forest Biotechnology Group, Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Russia
| | - Pavel S Kiryanov
- Laboratory of Genomics and Bioinformatics, Forest Research Institute, National Academy of Sciences of Belarus, Gomel, Belarus
| | - Stanislav V Panteleev
- Laboratory of Genomics and Bioinformatics, Forest Research Institute, National Academy of Sciences of Belarus, Gomel, Belarus
| | - Ludmila V Mozharovskaya
- Laboratory of Genomics and Bioinformatics, Forest Research Institute, National Academy of Sciences of Belarus, Gomel, Belarus
| | - Konstantin V Krutovsky
- Forestry Faculty, G. F. Morozov Voronezh State University of Forestry and Technologies, Voronezh, Russia.,Department of Forest Genetics and Forest Tree Breeding, George-August University of Göttingen, Göttingen, Germany.,Laboratory of Population Genetics, N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Vladimir E Padutov
- Department of Genetics, Tree Breeding and Biotechnology, Forest Research Institute, National Academy of Sciences of Belarus, Gomel, Belarus
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Santos da Silva R, Roland Clement C, Balsanelli E, de Baura VA, Maltempi de Souza E, Pacheco de Freitas Fraga H, do Nascimento Vieira L. The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae). PLoS One 2021; 16:e0256373. [PMID: 34428237 PMCID: PMC8384209 DOI: 10.1371/journal.pone.0256373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/04/2021] [Indexed: 11/18/2022] Open
Abstract
The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.
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Affiliation(s)
| | - Charles Roland Clement
- Coordenação de Tecnologia e Inovação, Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
- Departamento de Bioquímica e Biologia Molecular, GoGenetic, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
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8
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Scobeyeva VA, Artyushin IV, Krinitsina AA, Nikitin PA, Antipin MI, Kuptsov SV, Belenikin MS, Omelchenko DO, Logacheva MD, Konorov EA, Samoilov AE, Speranskaya AS. Gene Loss, Pseudogenization in Plastomes of Genus Allium ( Amaryllidaceae), and Putative Selection for Adaptation to Environmental Conditions. Front Genet 2021; 12:674783. [PMID: 34306019 PMCID: PMC8296844 DOI: 10.3389/fgene.2021.674783] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/15/2021] [Indexed: 01/07/2023] Open
Abstract
Amaryllidaceae is a large family with more than 1,600 species, belonging to 75 genera. The largest genus—Allium—is vast, comprising about a thousand species. Allium species (as well as other members of the Amaryllidaceae) are widespread and diversified, they are adapted to a wide range of habitats from shady forests to open habitats like meadows, steppes, and deserts. The genes present in chloroplast genomes (plastomes) play fundamental roles for the photosynthetic plants. Plastome traits could thus be associated with geophysical abiotic characteristics of habitats. Most chloroplast genes are highly conserved and are used as phylogenetic markers for many families of vascular plants. Nevertheless, some studies revealed signatures of positive selection in chloroplast genes of many plant families including Amaryllidaceae. We have sequenced plastomes of the following nine Allium (tribe Allieae of Allioideae) species: A. zebdanense, A. moly, A. victorialis, A. macleanii, A. nutans, A. obliquum, A. schoenoprasum, A. pskemense, A. platyspathum, A. fistulosum, A. semenovii, and Nothoscordum bivalve (tribe Leucocoryneae of Allioideae). We compared our data with previously published plastomes and provided our interpretation of Allium plastome genes’ annotations because we found some noteworthy inconsistencies with annotations previously reported. For Allium species we estimated the integral evolutionary rate, counted SNPs and indels per nucleotide position as well as compared pseudogenization events in species of three main phylogenetic lines of genus Allium to estimate whether they are potentially important for plant physiology or just follow the phylogenetic pattern. During examination of the 38 species of Allium and the 11 of other Amaryllidaceae species we found that rps16, rps2, infA, ccsA genes have lost their functionality multiple times in different species (regularly evolutionary events), while the pseudogenization of other genes was stochastic events. We found that the “normal” or “pseudo” state of rps16, rps2, infA, ccsA genes correlates well with the evolutionary line of genus the species belongs to. The positive selection in various NADH dehydrogenase (ndh) genes as well as in matK, accD, and some others were found. Taking into account known mechanisms of coping with excessive light by cyclic electron transport, we can hypothesize that adaptive evolution in genes, coding subunits of NADH-plastoquinone oxidoreductase could be driven by abiotic factors of alpine habitats, especially by intensive light and UV radiation.
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Affiliation(s)
- Victoria A Scobeyeva
- Department of Evolution, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ilya V Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anastasiya A Krinitsina
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Pavel A Nikitin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim I Antipin
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergei V Kuptsov
- Botanical Garden, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim S Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Denis O Omelchenko
- Laboratory of Plant Genomics, Institute for Information Transmission Problems, Moscow, Russia
| | - Maria D Logacheva
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Evgenii A Konorov
- Laboratory of Animal Genetics, Vavilov Institute of General Genetics, Russian Academy of Science (RAS), Moscow, Russia
| | - Andrey E Samoilov
- Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna S Speranskaya
- Department of Higher Plants, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Group of Genomics and Postgenomic Technologies, Central Research Institute of Epidemiology, Moscow, Russia
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9
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An J, Miao X, Wang L, Li X, Liu X, Gao H. Visualizing the Integrity of Chloroplast Envelope by Rhodamine and Nile Red Staining. FRONTIERS IN PLANT SCIENCE 2021; 12:668414. [PMID: 33981327 PMCID: PMC8107281 DOI: 10.3389/fpls.2021.668414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Chloroplasts are essential organelles in plant cells with many important functions. Chloroplasts isolated by Percoll density gradient centrifugation are widely used in the study of chloroplasts. The intactness of isolated chloroplasts is necessary for many of the experiments. In the past, those isolated chloroplasts were either simply believed to be intact or had to be analyzed by indirect biochemical methods. Here we show a new method to check the intactness of isolated chloroplasts by staining their envelope with fluorescent dyes, Rhodamine or Nile red, and then observing them with a fluorescence microscope. With this method, broken chloroplasts and intact chloroplasts can be distinguished easily and their integrity can be checked in a few minutes. Results of this method agreed well with those of biochemical methods. Moreover, we have also found that sometimes the middle layer chloroplasts from the Percoll gradient centrifugation could be mostly broken, which could cause mistakes in the experiment. With our method, this problem can be easily found. This chloroplast envelope staining method can be used in the preparation of isolated chloroplasts to ensure the intactness.
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Affiliation(s)
- Jinjie An
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xin Miao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lulu Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaomin Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongbo Gao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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10
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de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, do Nascimento Vieira L, Guerra MP, Pacca Luna Mattar E, de Baura VA, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Plastid genome evolution in Amazonian açaí palm (Euterpe oleracea Mart.) and Atlantic forest açaí palm (Euterpe edulis Mart.). PLANT MOLECULAR BIOLOGY 2021; 105:559-574. [PMID: 33386578 DOI: 10.1007/s11103-020-01109-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 12/15/2020] [Indexed: 06/12/2023]
Abstract
The plastomes of E. edulis and E. oleracea revealed several molecular markers useful for genetic studies in natural populations and indicate specific evolutionary features determined by vicariant speciation. Arecaceae is a large and diverse family occurring in tropical and subtropical ecosystems worldwide. E. oleracea is a hyperdominant species of the Amazon forest, while E. edulis is a keystone species of the Atlantic forest. It has reported that E. edulis arose from vicariant speciation after the emergence of the belt barrier of dry environment (Cerrado and Caatinga biomes) between Amazon and Atlantic forests, isolating the E. edulis in the Atlantic forest. We sequenced the complete plastomes of E. edulis and E. oleracea and compared them concerning plastome structure, SSRs, tandem repeats, SNPs, indels, hotspots of nucleotide polymorphism, codon Ka/Ks ratios and RNA editing sites aiming to investigate evolutionary traits possibly affected by distinct environments. Our analyses revealed 303 SNPs, 91 indels, and 82 polymorphic SSRs among both species. Curiously, the narrow correlation among localization of repetitive sequences and indels strongly suggests that replication slippage is involved in plastid DNA mutations in Euterpe. Moreover, most non-synonymous substitutions represent amino acid variants in E. edulis that evolved specifically or in a convergent manner across the palm phylogeny. Amino acid variants observed in several plastid proteins in E. edulis were also identified as positive signatures across palm phylogeny. The higher incidence of specific amino acid changes in plastid genes of E. edulis in comparison with E. oleracea probably configures adaptive genetic variations determined by vicariant speciation. Our data indicate that the environment generates a selective pressure on the plastome making it more adapted to specific conditions.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | | | - Valter Antonio de Baura
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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11
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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: 16] [Impact Index Per Article: 4.0] [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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12
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de Souza Magnabosco JW, de Freitas Fraga HP, da Silva RS, Rogalski M, de Souza EM, Guerra MP, Vieira LDN. Characterization of the complete plastid genome of Butia eriospatha (Arecaceae). Genet Mol Biol 2020; 43:e20200023. [PMID: 32926069 PMCID: PMC7488953 DOI: 10.1590/1678-4685-gmb-2020-0023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 07/10/2020] [Indexed: 11/21/2022] Open
Abstract
Butia eriospatha is an endemic palm species from the Atlantic Rainforest in Brazil, a biodiversity hotspot. This species is currently listed in the IUCN red list as vulnerable and lacks specific plastid markers for population genetics studies. In addition, the evolutionary relationship within the genus Butia is not yet well resolved. Here, we sequenced and characterized the complete plastid genome (plastome) sequence of B. eriospatha. The complete plastome sequence is 154,048 bp in length, with the typical quadripartite structure. This plastome length and genes content is consistent with other six species from tribe Cocoseae. However, the Inverted Repeat (IR) borders show some variation among the analyzed species from this tribe. Species from the Bactridinae (Astrocaryum and Acrocomia) and Elaeidinae (Elaeis) subtribes present the rps19 gene completely duplicated in the IR region. In contrast, all plastomes sequenced from the subtribe Attaleinae (Butia, Cocos, Syagrus) present one complete CDS of rps19 and one partial copy of rps19. The difference in the IR/LSC junctions between Attaleinae and the sister clades Bactridinae + Elaeidinae might be considered an evolutionary signal and the plastome sequence of B. eriopatha may be used in future studies of population genetics and phylogeny.
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Affiliation(s)
| | | | - Raquel Santos da Silva
- Universidade Federal do Paraná, Programa de Pós-graduação em Botânica, Curitiba, Paraná, Brazil
| | - Marcelo Rogalski
- Universidade Federal de Viçosa, Programa de Pós-graduação em Fisiologia Vegetal, Viçosa, MG, Brazil
| | - Emanuel Maltempi de Souza
- Universidade Federal do Paraná, Programa de Pós-graduação em Bioquímica e Biologia Molecular, Curitiba, PR, Brazil
| | - Miguel Pedro Guerra
- Universidade Federal de Santa Catarina, Programa de Pós-graduação em Recursos Genéticos Vegetais, Florianópolis, SC, Brazil
- Universidade Federal de Santa Catarina, Programa de Pós-Graduação em Ecossistemas Agrícolas e Naturais, Curitibanos, SC, Brazil
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13
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Pacheco TG, Lopes ADS, Welter JF, Yotoko KSC, Otoni WC, Vieira LDN, Guerra MP, Nodari RO, Balsanelli E, Pedrosa FDO, de Souza EM, Rogalski M. Plastome sequences of the subgenus Passiflora reveal highly divergent genes and specific evolutionary features. PLANT MOLECULAR BIOLOGY 2020; 104:21-37. [PMID: 32533420 DOI: 10.1007/s11103-020-01020-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Fátima Welter
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Karla Suemy Clemente Yotoko
- Laboratório de Bioinformática e Evolução, Departamento de Biologia Geral, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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14
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Gomes Pacheco T, Morais da Silva G, de Santana Lopes A, de Oliveira JD, Rogalski JM, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. Phylogenetic and evolutionary features of the plastome of Tropaeolum pentaphyllum Lam. (Tropaeolaceae). PLANTA 2020; 252:17. [PMID: 32666132 DOI: 10.1007/s00425-020-03427-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/08/2020] [Indexed: 06/11/2023]
Abstract
Complete plastome sequence of Tropaeolum pentaphyllum revealed molecular markers, hotspots of nucleotide polymorphism, RNA editing sites and phylogenetic aspects Tropaeolaceae Juss. ex DC. comprises approximately 95 species across North and South Americas. Tropaeolum pentaphyllum Lam. is an unconventional and endangered species with occurrence in some countries of South America. Although this species presents nutritional, medicinal and ornamental uses, genetic studies involving natural populations or promising genotypes are practically non-existent. Here, we report the nucleotide sequence of T. pentaphyllum plastome. It represents the first complete plastome sequence of the family Tropaeolaceae to be fully sequenced and analyzed in detail. The sequencing data revealed that the T. pentaphyllum plastome is highly similar to the plastomes of other Brassicales. Notwithstanding, our analyses detected some specific features concerning events of IR expansion and structural changes in some genes such as matK, rpoA, and rpoC2. We also detected 251 SSR loci, nine hotspots of nucleotide polymorphism, and two specific RNA editing sites in the plastome of T. pentaphyllum. Moreover, plastid phylogenomic inference indicated a closed relationship between the families Tropaeolaceae and Akaniaceae, which formed a sister group to Moringaceae-Caricaceae. Finally, our data bring new molecular markers and evolutionary features to be applied in the natural population, germplasm collection, and genotype selection aiming conservation, genetic diversity evaluation, and exploitation of this endangered species.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - José Daniel de Oliveira
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Juliana Marcia Rogalski
- Núcleo de Ciências Biológicas e Ambientais, Instituto Federal do Rio Grande do Sul, Distrito Engenheiro Luiz Englert, Sertão, RS, Brazil
| | - Eduardo Balsanelli
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Núcleo de Fixação Biológica de Nitrogênio, Departamento de Bioquímica e Biologia Molecular, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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15
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Machado LDO, Vieira LDN, Stefenon VM, Faoro H, Pedrosa FDO, Guerra MP, Nodari RO. Molecular relationships of Campomanesia xanthocarpa within Myrtaceae based on the complete plastome sequence and on the plastid ycf2 gene. Genet Mol Biol 2020; 43:e20180377. [PMID: 32555941 PMCID: PMC7288672 DOI: 10.1590/1678-4685-gmb-2018-0377] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 07/24/2019] [Indexed: 11/30/2022] Open
Abstract
Plastomes are very informative structures for comparative phylogenetic and evolutionary analyses. We sequenced and analyzed the complete plastome of Campomanesia xanthocarpa and compared its gene order, structure, and evolutionary characteristics within Myrtaceae. Analyzing 48 species of Myrtaceae, we identified six genes representing ‘hotspots’ of variability within the plastomes (ycf2, atpA, rpoC2, pcbE, ndhH and rps16), and performed phylogenetic analyses based on: (i) the ycf2 gene, (ii) all the six genes identified as ‘hotspots’ of variability, and (iii) the genes identified as ‘hotspots’ of variability, except the ycf2 gene. The structure, gene order, and gene content of the C. xanthocarpa plastome are similar to other Myrtaceae species. Phylogenetic analyses revealed the ycf2 gene as a promissing region for barcoding within this family, having also a robust phylogenetic signal. The synonymous and nonsynonymous substitution rates and the Ka/Ks ratio revealed low values for the ycf2 gene among C. xanthocarpa and the other 47 analyzed species of Myrtaceae, with moderate purifying selection acting on this gene. The average nucleotide identity (ANI) analysis of the whole plastomes produced phylogenetic trees supporting the monophyly of three Myrtaceae tribes. The findings of this study provide support for planning conservation, breeding, and biotechnological programs for this species.
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Affiliation(s)
- Lilian de Oliveira Machado
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
| | | | - Valdir Marcos Stefenon
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil.,Universidade Federal do Pampa, Campus São Gabriel, São Gabriel, RS, Brazil
| | - Helisson Faoro
- Fundação Oswaldo Cruz, Instituto Carlos Chagas, Curitiba, PR, Brazil
| | | | - Miguel Pedro Guerra
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Universidade Federal de Santa Catarina, Centro de Ciências Agrárias, Departamento de Fitotecnia, Florianópolis, SC, Brazil
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16
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Li H, Ma D, Li J, Wei M, Zheng H, Zhu X. Illumina sequencing of complete chloroplast genome of Avicennia marina, a pioneer mangrove species. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2131-2132. [PMID: 33366945 PMCID: PMC7510616 DOI: 10.1080/23802359.2020.1768927] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 05/09/2020] [Indexed: 10/25/2022]
Abstract
Mangrove tree Avicenna marina has great ecological significance in maintaining coastal ecosystem, but its unique potential for gene functions and genetic diversity underlying ecological adaptation remains investigation. In this study, the chloroplast genome of A. marina was first characterized by sequencing chloroplast DNA with Illumina technology. The A. marina genome was 147,909 bp in size with a typical quadripartite structure, which was deposited in GenBank under the accession number MT108381.
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Affiliation(s)
- Huan Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Dongna Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Mingyue Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Hailei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Xueyi Zhu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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17
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Rodrigues NF, Nogueira FCS, Domont GB, Margis R. Identification of soybean trans-factors associated with plastid RNA editing sites. Genet Mol Biol 2020; 43:e20190067. [PMID: 32459826 PMCID: PMC7231544 DOI: 10.1590/1678-4685-gmb-2019-0067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 08/09/2019] [Indexed: 12/05/2022] Open
Abstract
RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
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Affiliation(s)
- Nureyev F. Rodrigues
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
| | - Fábio C. S. Nogueira
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Laboratório de Apoio ao Desenvolvimento Tecnológico (LADETEC), Rio de Janeiro, RJ,
Brazil
| | - Gilberto B. Domont
- Universidade Federal do Rio de Janeiro (UFRJ), Instituto de Química,
Departamento de Bioquímica, Programa de Pós-Graduação em Bioquímica (PPGBq), Unidade
Proteômica, Rio de Janeiro, RJ, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul (UFRGS), Centro de Biotecnologia,
Programa de Pós-Graduação em Biologia Celular e Molecular (PPGBCM), Porto Alegre,
RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Departamento de
Biofísica, Porto Alegre, RS, Brazil
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18
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Rodrigues NF, Balbinott N, Paim I, Guzman F, Margis R. Comparative analysis of the complete chloroplast genomes from six Neotropical species of Myrteae (Myrtaceae). Genet Mol Biol 2020; 43:e20190302. [PMID: 32384134 PMCID: PMC7212760 DOI: 10.1590/1678-4685-gmb-2019-0302] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/29/2020] [Indexed: 01/15/2023] Open
Abstract
Myrteae is the largest and most diverse tribe within Myrtaceae and represents the majority of its diversity in the Neotropics. Members of Myrteae hold ecological importance in tropical biomes for the provision of food sources for many animal species. Thus, due to its several roles, a growing interest has been addressed to this group. In this study, we report the sequencing and de novo assembly of the complete chloroplast (cp) genomes of six Myrteae species: Eugenia brasiliensis, E. pyriformis, E. nitida, Myrcianthes pungens, Plinia edulis and Psidium cattleianum. We characterized genome structure, gene content, and identified SSRs to detect variation within Neotropical Myrteae. The six newly sequenced plastomes exhibit a typical quadripartite structure, gene content and organization highly conserved among Myrtaceae species. Some differences in genome length, protein-coding genes and non-coding regions were found. Besides, IR boundaries present structural changes among species. Increased sequence diversity was observed in some intergenic regions, suggesting their suitability for investigating intraand interspecific genetic diversity in populational studies. These data also contribute to the improvement of taxa sampling in further phylogenetic investigations to understand Myrtaceae evolution.
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Affiliation(s)
- Nureyev F Rodrigues
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Natalia Balbinott
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Igor Paim
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil
| | - Frank Guzman
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil
| | - Rogerio Margis
- Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Laboratório de Genomas e Populações de Plantas, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul , Centro de Biotecnologia, PPGBCM, Porto Alegre, RS, Brazil.,Universidade Federal do Rio Grande do Sul, Departamento de Biofísica, Porto Alegre, RS, Brazil
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19
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Smidt EDC, Páez MZ, Vieira LDN, Viruel J, de Baura VA, Balsanelli E, de Souza EM, Chase MW. Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae). PLoS One 2020; 15:e0227991. [PMID: 31990943 PMCID: PMC6986716 DOI: 10.1371/journal.pone.0227991] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/03/2020] [Indexed: 11/26/2022] Open
Abstract
This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.
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Affiliation(s)
| | - Michelle Zavala Páez
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | | | - Juan Viruel
- Royal Botanic Gardens, Kew, Richmond, Surrey, England, United Kingdom
| | - Valter Antônio de Baura
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica, Universidade Federal do Paraná, Núcleo de Fixação Biológica de Nitrogênio, Curitiba, Paraná, Brazil
| | - Mark W. Chase
- Royal Botanic Gardens, Kew, Richmond, Surrey, England, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
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20
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Zhang Y, Huang R, Wu L, Wang Y, Jin T, Liang Q. The complete chloroplast genome of Epimedium brevicornu Maxim (Berberidaceae), a traditional Chinese medicine herb. MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:588-590. [PMID: 33366659 PMCID: PMC7748679 DOI: 10.1080/23802359.2019.1710593] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Epimedium brevicornu Maxim. is a traditional Chinese medicine herb with good effects on many diseases. In the present paper, the complete chloroplast genome of E. brevicornu was sequenced. The complete chloroplast genome of E. brevicornu was 159572 bp in length with 38.83% GC content, including four distinct regions: large single-copy region (86535 bp), small single-copy region (17641 bp), and a pair of inverted repeat regions (27698 bp). The chloroplast genome encoded 112 unique genes, which included 78 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Phylogenetic analysis with the previously reported chloroplast genomes of Epimedium showed that E. brevicornu with small flowers at first clustered with large-flowered E. acuminatum into a strongly supported branch, but not with Epimedium species having similar floral characters.
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Affiliation(s)
- Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Ruoqi Huang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li Wu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
| | - Ying Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, People's Republic of China
| | - Tae Jin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, People's Republic of China
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21
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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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22
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Omelchenko DO, Krinitsina AA, Belenikin MS, Konorov EA, Kuptsov SV, Logacheva MD, Speranskaya AS. Complete plastome sequencing of Allium paradoxum reveals unusual rearrangements and the loss of the ndh genes as compared to Allium ursinum and other onions. Gene 2019; 726:144154. [PMID: 31589962 DOI: 10.1016/j.gene.2019.144154] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 07/12/2019] [Accepted: 10/02/2019] [Indexed: 01/17/2023]
Abstract
In this work the complete chloroplast DNAs of Allium paradoxum and Allium ursinum, two edible species of Allium subg. Amerallium (the first lineage), were sequenced, assembled, annotated, and compared with complete Allium plastomes of the second and third evolutionary lines from GenBank database. The A. ursinum plastome contains 90 predicted genes (81 unique) including 5 pseudogenes, while A. paradoxum has 88 predicted genes (79 unique) including 19 pseudogenes. The comparative analysis has revealed that the A. paradoxum plastome differs markedly from those of other species. Due to many deletions, the A. paradoxum plastome is the shortest of known for Allium species, being only 145,819 bp long. The most prominent distinctions are (1) a 4825 bp long local inversion that spans from the ndhE to the rpl32 gene in the small single copy region and (2) pseudogenization, or the loss of all NADH-genes. In contrast, the plastome of A. ursinum - a species from the first evolutionary line (as well as A. paradoxum) - resembles the Allium species of the second and third evolutionary lines, showing no large rearrangements or discrepancies in gene content. It is unclear yet whether only A. paradoxum was affected by some evolutionary events or its close relatives from both sect. Briseis and other sections of Amerallium were altered as well. We speculate the sunlight-intolerant, shade-loving nature of A. paradoxum and the impairment of the ndh genes in its plastome could be interrelated phenomena.
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Affiliation(s)
- Denis O Omelchenko
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia; Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow Region 143026, Russia.
| | - Anastasia A Krinitsina
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia; All-Russia Research Institute of Agricultural Biotechnology, Timiryasevskaya St. 42, Moscow 127550, Russia.
| | - Maxim S Belenikin
- Moscow Institute of Physics and Technology, Institutskiy Ln. 9, Dolgoprudny Moscow Region 141701, Russia
| | - Evgenii A Konorov
- Vavilov Institute of General Genetics RAS, Gubkina St. 3, Moscow 119991, Russia; V.M. Gorbatov Federal Research Center for Food Systems RAS, Talalikhina 26, Moscow 109316, Russia
| | - Sergey V Kuptsov
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia
| | - Maria D Logacheva
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia; Institute for Information Transmission Problems, Bolshoy Karetny per. 19, build.1, Moscow 127051, Russia; Skolkovo Institute of Science and Technology, Nobel St. 3, Moscow Region 143026, Russia
| | - Anna S Speranskaya
- Lomonosov Moscow State University, Leninskie Gory, GSP-1, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya St. 3a, Moscow 111123, Russia.
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23
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de Santana Lopes A, Gomes Pacheco T, Nascimento da Silva O, Magalhães Cruz L, Balsanelli E, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The plastomes of Astrocaryum aculeatum G. Mey. and A. murumuru Mart. show a flip-flop recombination between two short inverted repeats. PLANTA 2019; 250:1229-1246. [PMID: 31222493 DOI: 10.1007/s00425-019-03217-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 06/18/2019] [Indexed: 06/09/2023]
Abstract
The plastomes of Astrocaryum murumuru and A. aculeatum revealed a lineage-specific structural feature originated by flip-flop recombination, non-synonymous substitutions in conserved genes and several molecular markers. Astrocaryum murumuru Mart. and A. aculeatum G.Mey. are two palm species of Amazon forest that are economically important as source of food, oil and raw material for several applications. Genetic studies aiming to establish strategies for conservation and domestication of both species are still in the beginning given that the exploitation is mostly by extractive activity. The identification and characterization of molecular markers are essential to assess the genetic diversity of natural populations of both species. Therefore, we sequenced and characterized in detail the plastome of both species. We compared both species and identified 32 polymorphic SSR loci, 150 SNPs, 46 indels and eight hotspots of nucleotide diversity. Additionally, we reported a specific RNA editing site found in the ccsA gene, which is exclusive to A. murumuru. Moreover, the structural analysis in the plastomes of both species revealed a 4.6-kb inversion encompassing a set of genes involved in chlororespiration and plastid translation. This 4.6-kb inversion is a lineage-specific structural feature of the genus Astrocaryum originated by flip-flop recombination between two short inverted repeats. Furthermore, our phylogenetic analysis using whole plastomes of 39 Arecaceae species placed the Astrocaryum species sister to Acrocomia within the tribe Cocoseae. Finally, our data indicated substantial changes in the plastome structure and sequence of both species of the genus Astrocaryum, bringing new molecular markers, several structural and evolving features, which can be applied in several areas such as genetic, evolution, breeding, phylogeny and conservation strategies for both species.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leonardo Magalhães Cruz
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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24
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Complete chloroplast genome sequences of four Allium species: comparative and phylogenetic analyses. Sci Rep 2019; 9:12250. [PMID: 31439882 PMCID: PMC6706373 DOI: 10.1038/s41598-019-48708-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 08/09/2019] [Indexed: 11/26/2022] Open
Abstract
The genus Allium is one of the largest monocotyledonous genera, containing over 850 species, and most of these species are found in temperate climates of the Northern Hemisphere. Furthermore, as a large number of new Allium species continue to be identified, phylogenetic classification based on morphological characteristics and a few genetic markers will gradually exhibit extremely low discriminatory power. In this study, we present the use of complete chloroplast genome sequences in genome-scale phylogenetic studies of Allium. We sequenced and assembled four Allium chloroplast genomes and retrieved five published chloroplast genomes from GenBank. All nine chloroplast genomes were used for genomic comparison and phylogenetic inference. The chloroplast genomes, ranging from 152,387 bp to 154,482 bp in length, exhibited conservation of genomic structure, and gene organization and order. Subsequently, we observed the expansion of IRs from the basal monocot Acorus americanus to Allium, identified 814 simple sequence repeats, 131 tandem repeats, 154 dispersed repeats and 109 palindromic repeats, and found six highly variable regions. The phylogenetic relationships of the Allium species inferred from the chloroplast genomes obtained high support, indicating that chloroplast genome data will be useful for further resolution of the phylogeny of the genus Allium.
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25
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Matielo CBD, Lemos RPM, Sarzi DS, Machado LDO, Beise DC, Dobbler PCT, Castro RM, Fett MS, Roesch LFW, Camargo FADO, Stefenon VM. Whole Plastome Sequences of Two Drug-Type Cannabis: Insights Into the Use of Plastid in Forensic Analyses. J Forensic Sci 2019; 65:259-265. [PMID: 31411746 DOI: 10.1111/1556-4029.14155] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/15/2019] [Accepted: 07/17/2019] [Indexed: 11/29/2022]
Abstract
DNA is one of the fastest growing tools in forensic sciences, increasing reliability in forensic reports and judgments. The use of DNA has increased in different areas of the forensic sciences, such as investigation of plant species, where plastid DNA has been used to elucidate and generate evidence in cases of traceability of genetically modified and controlled plants. Even with several advances and the practice of using DNA in forensic investigations, there are just few studies related to the identification of genetic tools for the characterization of drug and nondrug-types of Cannabis. Herein, the whole plastomes of two drug-type Cannabis are presented and have their structures compared with other Cannabis plastomes deposited in the GenBank, focusing in the forensic use of plastome sequences. The plastomes of Cannabis sativa "Brazuka" and of the hybrid Cannabis AK Royal Automatic presented general structure that does not differs from the reported for other C. sativa cultivars. A phylogenomic analyses grouped C. sativa "Brazuka" with the nondrug C. sativa cultivars, while the hybrid Cannabis AK Royal Automatic placed isolated, basal to this group. This suggests that the analysis of plastomes is useful toward genetic identification of hybrids in relation to C. sativa.
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Affiliation(s)
- Cristiane Barbosa D'Oliveira Matielo
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Rafael Plá Matielo Lemos
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Deise Schröder Sarzi
- Instituto de Bioquímica Médica Leopoldo de Meis - CCS, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, 21941-902, RJ, Brasil
| | - Lilian de Oliveira Machado
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Universidade Federal de Santa Catarina - UFSC, Florianópolis, 88040-900, Santa Catarina, Brasil
| | - Dalvan Carlos Beise
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Priscila Caroline Thiago Dobbler
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Renata Machado Castro
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Mauro Sander Fett
- Setor Técnico-Científico, Superintendência Regional do Departamento de Polícia Federal no Rio Grande do Sul, Porto Alegre, 90160-093, Rio Grande do Sul, Brasil
| | - Luiz Fernando Würdig Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
| | - Flávio Anastácio de Oliveira Camargo
- Departamento de Ciências do Solo, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, 91540-000, Rio Grande do Sul, Brasil
| | - Valdir Marcos Stefenon
- Núcleo de Ecologia Molecular e Micropropagação de Plantas, Universidade Federal do Pampa - UNIPAMPA, São Gabriel, 97307-020, Rio Grande do Sul, Brasil
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26
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Gomes Pacheco T, de Santana Lopes A, Monteiro Viana GD, Nascimento da Silva O, Morais da Silva G, do Nascimento Vieira L, Guerra MP, Nodari RO, Maltempi de Souza E, de Oliveira Pedrosa F, Otoni WC, Rogalski M. Genetic, evolutionary and phylogenetic aspects of the plastome of annatto (Bixa orellana L.), the Amazonian commercial species of natural dyes. PLANTA 2019; 249:563-582. [PMID: 30310983 DOI: 10.1007/s00425-018-3023-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
The plastome of B. orellana reveals specific evolutionary features, unique RNA editing sites, molecular markers and the position of Bixaceae within Malvales. Annatto (Bixa orellana L.) is a native species of tropical Americas with center of origin in Brazilian Amazonia. Its seeds accumulate the apocarotenoids, bixin and norbixin, which are only found in high content in this species. The seeds of B. orellana are commercially valued by the food industry because its dyes replace synthetic ones from the market due to potential carcinogenic risks. The increasing consumption of B. orellana seeds for dye extraction makes necessary the increase of productivity, which is possible accessing the genetic basis and searching for elite genotypes. The identification and characterization of molecular markers are essential to analyse the genetic diversity of natural populations and to establish suitable strategies for conservation, domestication, germplasm characterization and genetic breeding. Therefore, we sequenced and characterized in detail the plastome of B. orellana. The plastome of B. orellana is a circular DNA molecule of 159,708 bp with a typical quadripartite structure and 112 unique genes. Additionally, a total of 312 SSR loci were identified in the plastome of B. orellana. Moreover, we predicted in 23 genes a total of 57 RNA-editing sites of which 11 are unique for B. orellana. Furthermore, our plastid phylogenomic analyses, using the plastome sequences available in the plastid database belonging to species of order Malvales, indicate a closed relationship between Bixaceae and Malvaceae, which formed a sister group to Thymelaeaceae. Finally, our study provided useful data to be employed in several genetic and biotechnological approaches in B. orellana and related species of the family Bixaceae.
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Affiliation(s)
- Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gélia Dinah Monteiro Viana
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Odyone Nascimento da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Gleyson Morais da Silva
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia Vegetal, BIOAGRO, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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de Santana Lopes A, Gomes Pacheco T, do Nascimento Vieira L, Guerra MP, Nodari RO, Maltempi de Souza E, de Oliveira Pedrosa F, Rogalski M. The Crambe abyssinica plastome: Brassicaceae phylogenomic analysis, evolution of RNA editing sites, hotspot and microsatellite characterization of the tribe Brassiceae. Gene 2018; 671:36-49. [DOI: 10.1016/j.gene.2018.05.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 12/18/2022]
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Lin M, Qi X, Chen J, Sun L, Zhong Y, Fang J, Hu C. The complete chloroplast genome sequence of Actinidia arguta using the PacBio RS II platform. PLoS One 2018; 13:e0197393. [PMID: 29795601 PMCID: PMC5968424 DOI: 10.1371/journal.pone.0197393] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 05/01/2018] [Indexed: 01/01/2023] Open
Abstract
Actinidia arguta is the most basal species in a phylogenetically and economically important genus in the family Actinidiaceae. To better understand the molecular basis of the Actinidia arguta chloroplast (cp), we sequenced the complete cp genome from A. arguta using Illumina and PacBio RS II sequencing technologies. The cp genome from A. arguta was 157,611 bp in length and composed of a pair of 24,232 bp inverted repeats (IRs) separated by a 20,463 bp small single copy region (SSC) and an 88,684 bp large single copy region (LSC). Overall, the cp genome contained 113 unique genes. The cp genomes from A. arguta and three other Actinidia species from GenBank were subjected to a comparative analysis. Indel mutation events and high frequencies of base substitution were identified, and the accD and ycf2 genes showed a high degree of variation within Actinidia. Forty-seven simple sequence repeats (SSRs) and 155 repetitive structures were identified, further demonstrating the rapid evolution in Actinidia. The cp genome analysis and the identification of variable loci provide vital information for understanding the evolution and function of the chloroplast and for characterizing Actinidia population genetics.
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Affiliation(s)
- Miaomiao Lin
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Xiujuan Qi
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Jinyong Chen
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Leiming Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Yunpeng Zhong
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
| | - Jinbao Fang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agriculture Sciences, Zhengzhou, China
- * E-mail: (JF); (CH)
| | - Chungen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Hua Zhong Agricultural University, Wuhan, China
- * E-mail: (JF); (CH)
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de Santana Lopes A, Gomes Pacheco T, Nimz T, do Nascimento Vieira L, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F, Rogalski M. The complete plastome of macaw palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] and extensive molecular analyses of the evolution of plastid genes in Arecaceae. PLANTA 2018; 247:1011-1030. [PMID: 29340796 DOI: 10.1007/s00425-018-2841-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 01/10/2018] [Indexed: 05/08/2023]
Abstract
The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections. Therefore, we sequenced and characterized in detail the plastome of macaw palm. A total of 221 SSR loci were identified in the plastome of macaw palm. Additionally, eight polymorphism hotspots were characterized at level of subfamily and tribe. Moreover, several events of gain and loss of RNA editing sites were found within the subfamily Arecoideae. Aiming to uncover evolutionary events in Arecaceae, we also analyzed extensively the evolution of plastid genes. The analyses show that highly divergent genes seem to evolve in a species-specific manner, suggesting that gene degeneration events may be occurring within Arecaceae at the level of genus or species. Unexpectedly, we found that more than half of plastid protein-coding genes are under positive selection, including genes for photosynthesis, gene expression machinery and other essential plastid functions. Furthermore, we performed a phylogenomic analysis using whole plastomes of 40 taxa, representing all subfamilies of Arecaceae, which placed the macaw palm within the tribe Cocoseae. Finally, the data showed here are important for genetic studies in macaw palm and provide new insights into the evolution of plastid genes and environmental adaptation in Arecaceae.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Tabea Nimz
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel P Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens O Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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de Santana Lopes A, Pacheco TG, Santos KGD, Vieira LDN, Guerra MP, Nodari RO, de Souza EM, de Oliveira Pedrosa F, Rogalski M. The Linum usitatissimum L. plastome reveals atypical structural evolution, new editing sites, and the phylogenetic position of Linaceae within Malpighiales. PLANT CELL REPORTS 2018; 37:307-328. [PMID: 29086003 DOI: 10.1007/s00299-017-2231-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/18/2017] [Indexed: 05/12/2023]
Abstract
The plastome of Linum usitatissimum was completely sequenced allowing analyses of evolution of genome structure, RNA editing sites, molecular markers, and indicating the position of Linaceae within Malpighiales. Flax (Linum usitatissimum L.) is an economically important crop used as food, feed, and industrial feedstock. It belongs to the Linaceae family, which is noted by high morphological and ecological diversity. Here, we reported the complete sequence of flax plastome, the first species within Linaceae family to have the plastome sequenced, assembled and characterized in detail. The plastome of flax is a circular DNA molecule of 156,721 bp with a typical quadripartite structure including two IRs of 31,990 bp separating the LSC of 81,767 bp and the SSC of 10,974 bp. It shows two expansion events from IRB to LSC and from IRB to SSC, and a contraction event in the IRA-LSC junction, which changed significantly the size and the gene content of LSC, SSC and IRs. We identified 109 unique genes and 2 pseudogenes (rpl23 and ndhF). The plastome lost the conserved introns of clpP gene and the complete sequence of rps16 gene. The clpP, ycf1, and ycf2 genes show high nucleotide and aminoacid divergence, but they still possibly retain the functionality. Moreover, we also identified 176 SSRs, 20 tandem repeats, and 39 dispersed repeats. We predicted in 18 genes a total of 53 RNA editing sites of which 32 were not found before in other species. The phylogenetic inference based on 63 plastid protein-coding genes of 38 taxa supports three major clades within Malpighiales order. One of these clades has flax (Linaceae) sister to Chrysobalanaceae family, differing from earlier studies that included Linaceae into the euphorbioid clade.
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Affiliation(s)
- Amanda de Santana Lopes
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Túlio Gomes Pacheco
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Karla Gasparini Dos Santos
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-Graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, SC, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, PR, Brazil
| | - Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, MG, Brazil.
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Garcia A, Lopez F, Garcia L, Giraldo O, Bucheli V, Dumontier M. Biotea: semantics for Pubmed Central. PeerJ 2018; 6:e4201. [PMID: 29312824 PMCID: PMC5755483 DOI: 10.7717/peerj.4201] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/07/2017] [Indexed: 01/26/2023] Open
Abstract
A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies. In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology. We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language. We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.
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Affiliation(s)
- Alexander Garcia
- Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
| | - Federico Lopez
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Colombia
| | - Leyla Garcia
- Temporal Knowledge Bases Group, Department of Computer Languages and Systems, Universitat Jaume I, Castelló de la Plana, Spain
| | - Olga Giraldo
- Ontology Engineering Group, Universidad Politécnica de Madrid, Madrid, Spain
| | - Victor Bucheli
- Escuela de Ingeniería de Sistemas y Computación, Universidad del Valle, Cali, Colombia
| | - Michel Dumontier
- Maastricht University, Institute of Data Science, Maastricht, The Netherlands
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Cheng T, Weng Y, Yang L, Lu L, Hao Z, Shi J, Chen J. The chloroplast genome of Cerasus campanulata (Maxim.) A.N. Vassiljeva. Mitochondrial DNA B Resour 2018; 3:222-224. [PMID: 33474124 PMCID: PMC7799461 DOI: 10.1080/23802359.2018.1437799] [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: 11/18/2022] Open
Abstract
The complete chloroplast genome of Cerasus campanulata was obtained by using 454 pyrosequencing technology. Cerasus campanulata chloroplast genome is 157,906 base pairs containing 115 unique genes, including 79 protein-coding genes, 39 tRNAs and eight rRNAs. Phylogenetic analysis of the protein-coding genes indicates that C. campanulata is clearly a member of the Rosaceae order.
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Affiliation(s)
- Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China
| | - Yuhao Weng
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Liming Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Lu Lu
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jisen Shi
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
| | - Jinhui Chen
- Co-Innovation Center for the Sustainable Forestry in Southern China, Nanjing, China
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry University, Nanjing, China
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Logacheva MD, Krinitsina AA, Belenikin MS, Khafizov K, Konorov EA, Kuptsov SV, Speranskaya AS. Comparative analysis of inverted repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions. BMC PLANT BIOLOGY 2017; 17:255. [PMID: 29297348 PMCID: PMC5751766 DOI: 10.1186/s12870-017-1195-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
BACKGROUND Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns. We also sequenced the plastome of Adianthum hispidulum (Pteridaceae). Unexpectedly, we found high variability in the IR region, including duplication of rrn16 in D. blanfordii, complete loss of trnI-GAU in D. filix-mas, its pseudogenization due to the loss of an exon in D. blanfordii. Analysis of previously reported plastomes of Polypodiales demonstrated that Woodwardia unigemmata and Lepisorus clathratus have unusual insertions in the IR region. The sequence of these inserted regions has high similarity to several LSC fragments of ferns outside of Polypodiales and to spacer between tRNA-CGA and tRNA-TTT genes of mitochondrial genome of Asplenium nidus. We suggest that this reflects the ancient DNA transfer from mitochondrial to plastid genome occurred in a common ancestor of ferns. We determined the marked conservation of gene content and relative evolution rate of genes and intergenic spacers in the IRs of Polypodiales. Faster evolution of the four intergenic regions had been demonstrated (trnA- orf42, rrn16-rps12, rps7-psbA and ycf2-trnN). CONCLUSIONS IRs of Polypodiales plastomes are dynamic, driven by such events as gene loss, duplication and putative lateral transfer from mitochondria.
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Affiliation(s)
| | | | - Maxim S Belenikin
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Moscow Region, Russia
| | - Kamil Khafizov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141700, Moscow Region, Russia
- Federal Budget Institution of Science Central Research Institute of Epidemiology of The Federal Service on Customers, 111123, Moscow, Russia
| | - Evgenii A Konorov
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia
| | | | - Anna S Speranskaya
- M.V. Lomonosov Moscow State University, 119991, Moscow, Russia.
- Federal Budget Institution of Science Central Research Institute of Epidemiology of The Federal Service on Customers, 111123, Moscow, Russia.
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Krinitsina AA, Belenikin MS, Churikova OA, Kuptsov3 SV, Antipin MI, Logacheva MD, Speranskaya AS. The systematic position of Dryopteris blanfordii subsp. nigrosquamosa (Ching) Fraser-Jenkins within the genus Dryopteris Adans. PHYTOKEYS 2017; 90:89-112. [PMID: 29391852 PMCID: PMC5784233 DOI: 10.3897/phytokeys.90.14745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
Dryopteris blanfordii (C.Hope) C.Chr. is a member of the Dryopteridaceae, growing in high altitude Picea or Abies forests (2900-3500 m) in China and India. Phylogenetic relationships between D. blanfordii subsp. nigrosquamosa and closely related species of Dryopteris were investigated using a combined analysis of multiple molecular data sets (the protein-coding region of rbcL and matK genes and intergenic spacers psbA-trnH, trnP-petG, rps4-trnS, trnL-trnF and rbcL-accD). An assumption about the position of D. blanfordii subsp. nigrosquamosa within Dryopteris was made by using the Maximum Likelihood and Bayesian Inference approach and chloroplast marker sequences of Dryopteris species from GenBank. The results demonstrated that Asian taxa D. blanfordii subsp. nigrosquamosa and D. laeta as well as two American species D. arguta and D. marginalis belong to the same clade, all four of them being part of Dryopteris section Dryopteris.
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Affiliation(s)
- Anastasiya A. Krinitsina
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim S. Belenikin
- Department of Molecular and Biological Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia, 141700
| | - Olga A. Churikova
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Sergey V. Kuptsov3
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
| | - Maxim I. Antipin
- Botanical Garden, Lomonosov Moscow State University, Leninskie gory, Moscow, Russia, 119899
| | - Maria D. Logacheva
- Department of Evolutional Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskie gory, 1, 40, Moscow, Russia, 119992
| | - Anna S. Speranskaya
- Department of High Plants, Biological Faculty, Lomonosov Moscow State University, Leninskie gory, 1, 12, Moscow, Russia, 119234
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Cheng H, Li J, Zhang H, Cai B, Gao Z, Qiao Y, Mi L. The complete chloroplast genome sequence of strawberry ( Fragaria × ananassa Duch.) and comparison with related species of Rosaceae. PeerJ 2017; 5:e3919. [PMID: 29038765 PMCID: PMC5641433 DOI: 10.7717/peerj.3919] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/22/2017] [Indexed: 11/20/2022] Open
Abstract
Compared with other members of the family Rosaceae, the chloroplast genomes of Fragaria species exhibit low variation, and this situation has limited phylogenetic analyses; thus, complete chloroplast genome sequencing of Fragaria species is needed. In this study, we sequenced the complete chloroplast genome of F. × ananassa 'Benihoppe' using the Illumina HiSeq 2500-PE150 platform and then performed a combination of de novo assembly and reference-guided mapping of contigs to generate complete chloroplast genome sequences. The chloroplast genome exhibits a typical quadripartite structure with a pair of inverted repeats (IRs, 25,936 bp) separated by large (LSC, 85,531 bp) and small (SSC, 18,146 bp) single-copy (SC) regions. The length of the F. × ananassa 'Benihoppe' chloroplast genome is 155,549 bp, representing the smallest Fragaria chloroplast genome observed to date. The genome encodes 112 unique genes, comprising 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Comparative analysis of the overall nucleotide sequence identity among ten complete chloroplast genomes confirmed that for both coding and non-coding regions in Rosaceae, SC regions exhibit higher sequence variation than IRs. The Ka/Ks ratio of most genes was less than 1, suggesting that most genes are under purifying selection. Moreover, the mVISTA results also showed a high degree of conservation in genome structure, gene order and gene content in Fragaria, particularly among three octoploid strawberries which were F. × ananassa 'Benihoppe', F. chiloensis (GP33) and F. virginiana (O477). However, when the sequences of the coding and non-coding regions of F. × ananassa 'Benihoppe' were compared in detail with those of F. chiloensis (GP33) and F. virginiana (O477), a number of SNPs and InDels were revealed by MEGA 7. Six non-coding regions (trnK-matK, trnS-trnG, atpF-atpH, trnC-petN, trnT-psbD and trnP-psaJ) with a percentage of variable sites greater than 1% and no less than five parsimony-informative sites were identified and may be useful for phylogenetic analysis of the genus Fragaria.
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Affiliation(s)
- Hui Cheng
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jinfeng Li
- Laboratory of Fruit Tree, Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong, China
| | - Hong Zhang
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Binhua Cai
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhihong Gao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yushan Qiao
- Laboratory of Fruit Tree Biotechnology, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lin Mi
- Laboratory of Fruit Tree, Zhenjiang Institute of Agricultural Sciences in Hilly Area of Jiangsu Province, Jurong, China
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Nagy E, Hegedűs G, Taller J, Kutasy B, Virág E. Illumina sequencing of the chloroplast genome of common ragweed ( Ambrosia artemisiifolia L.). Data Brief 2017; 15:606-611. [PMID: 29085876 PMCID: PMC5655400 DOI: 10.1016/j.dib.2017.10.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/21/2017] [Accepted: 10/04/2017] [Indexed: 12/31/2022] Open
Abstract
Common ragweed (Ambrosia artemisiifolia L.) is the most widespread weed and the most dangerous pollen allergenic plant in large areas of the temperate zone. Since herbicides like PSI and PSII inhibitors have their target genes in the chloroplast genome, understanding the chloroplast genome may indirectly support the exploration of herbicide resistance and development of novel control methods. The aim of the present study was to sequence and reconstruct for the chloroplast genome of A. artemisiifolia and establish a molecular dataset. We used an Illumina MiSeq protocol to sequence the chloroplast genome of isolated intact organelles of ragweed plants grown in our experimental garden. The assembled chloroplast genome was found to be 152,215 bp (GC: 37.6%) in a quadripartite structure, where 80 protein coding genes, 30 tRNA and 4 rRNA genes were annotated in total. We also report the complete sequence of 114 genes encoded in A. artemisiifolia chloroplast genome supported by both MIRA and Velvet de novo assemblers and ordered to Helianthus annuus L. using the Geneious software.
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Affiliation(s)
- Erzsébet Nagy
- University of Pannonia, Georgikon Faculty, Department of Plant Science and Biotechnology, Keszthely, Hungary
| | - Géza Hegedűs
- University of Pannonia, Georgikon Faculty, Department of Economic Methodology, Keszthely, Hungary
| | - János Taller
- University of Pannonia, Georgikon Faculty, Department of Plant Science and Biotechnology, Keszthely, Hungary
| | - Barbara Kutasy
- University of Pannonia, Georgikon Faculty, Department of Plant Science and Biotechnology, Keszthely, Hungary
| | - Eszter Virág
- University of Pannonia, Georgikon Faculty, Department of Plant Science and Biotechnology, Keszthely, Hungary
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Sakaguchi S, Ueno S, Tsumura Y, Setoguchi H, Ito M, Hattori C, Nozoe S, Takahashi D, Nakamasu R, Sakagami T, Lannuzel G, Fogliani B, Wulff AS, L’Huillier L, Isagi Y. Application of a simplified method of chloroplast enrichment to small amounts of tissue for chloroplast genome sequencing. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps.1700002. [PMID: 28529832 PMCID: PMC5435405 DOI: 10.3732/apps.1700002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/09/2017] [Indexed: 05/30/2023]
Abstract
PREMISE OF THE STUDY High-throughput sequencing of genomic DNA can recover complete chloroplast genome sequences, but the sequence data are usually dominated by sequences from nuclear/mitochondrial genomes. To overcome this deficiency, a simple enrichment method for chloroplast DNA from small amounts of plant tissue was tested for eight plant species including a gymnosperm and various angiosperms. METHODS Chloroplasts were enriched using a high-salt isolation buffer without any step gradient procedures, and enriched chloroplast DNA was sequenced by multiplexed high-throughput sequencing. RESULTS Using this simple method, significant enrichment of chloroplast DNA-derived reads was attained, allowing deep sequencing of chloroplast genomes. As an example, the chloroplast genome of the conifer Callitris sulcata was assembled, from which polymorphic microsatellite loci were isolated successfully. DISCUSSION This chloroplast enrichment method from small amounts of plant tissue will be particularly useful for studies that use sequencers with relatively small throughput and that cannot use large amounts of tissue (e.g., for endangered species).
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Saneyoshi Ueno
- Tree Genetics Laboratory, Department of Forest Genetics, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Yoshihiko Tsumura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 3058572, Japan
| | - Hiroaki Setoguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
| | - Chie Hattori
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shogo Nozoe
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Daiki Takahashi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Riku Nakamasu
- Faculty of Integrated Human Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Taishi Sakagami
- Faculty of Integrated Human Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Guillaume Lannuzel
- Agronomic Institute of New Caledonia (IAC), Diversités biologique et fonctionnelle des écosystèmes terrestres, BP 73, Port Laguerre, Païta 98890, New Caledonia
| | - Bruno Fogliani
- Agronomic Institute of New Caledonia (IAC), Diversités biologique et fonctionnelle des écosystèmes terrestres, BP 73, Port Laguerre, Païta 98890, New Caledonia
| | - Adrien S. Wulff
- Agronomic Institute of New Caledonia (IAC), Diversités biologique et fonctionnelle des écosystèmes terrestres, BP 73, Port Laguerre, Païta 98890, New Caledonia
- SoREco-NC, 57 Route de l’Anse Vata, 98800 Nouméa, New Caledonia
| | - Laurent L’Huillier
- Agronomic Institute of New Caledonia (IAC), Diversités biologique et fonctionnelle des écosystèmes terrestres, BP 73, Port Laguerre, Païta 98890, New Caledonia
| | - Yuji Isagi
- Division of Forest and Biomaterials Science, Graduate School of Agriculture, Kyoto University, Kyoto 6068502, Japan
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Phylogenomic relationship of feijoa (Acca sellowiana (O.Berg) Burret) with other Myrtaceae based on complete chloroplast genome sequences. Genetica 2017; 145:163-174. [DOI: 10.1007/s10709-017-9954-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/19/2017] [Indexed: 10/20/2022]
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Ferradini N, Lancioni H, Torricelli R, Russi L, Dalla Ragione I, Cardinali I, Marconi G, Gramaccia M, Concezzi L, Achilli A, Veronesi F, Albertini E. Characterization and Phylogenetic Analysis of Ancient Italian Landraces of Pear. FRONTIERS IN PLANT SCIENCE 2017; 8:751. [PMID: 28539931 PMCID: PMC5423897 DOI: 10.3389/fpls.2017.00751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 04/21/2017] [Indexed: 05/19/2023]
Abstract
Pear is one of the oldest fruit tree crops and the third most important temperate fruit species. Its domestication took place independently in the Far East (China) and in the Caucasus region. While the origin of Eastern Asian cultivars is clear, that of European cultivars is still in doubt. Italy has a wealth of local varieties and genetic resources safeguarded by several public and private collections to face the erosion caused by the introduction of improved varieties in specialized orchards. The objectives of the present study were: (i) to characterize the existing germplasm through nuclear (SSR) and (ii) to clarify the genetic divergence between local and cultivated populations through chloroplast DNA (cpDNA) markers in order to provide insights into phylogenetic relationships of Pyrus spp. For this reason, 95 entries from five different germplasm collections, including nine European, Mediterranean and Eastern Asian species, were analyzed, and the intergenic accD-psaI sequences were compared to the worldwide distributed dataset encompassing a total of 298 sequences from 26 different Pyrus species. The nine nuclear SSRs were able to identify a total of 179 alleles, with a loci polymorphism P = 0.89. Most of the variation (97%) was found within groups. Five accessions from different sources were confirmed to be the same. Eight out of 20 accessions of unknown origin were identified, and six synonyms were detected. Locus NH030a was found to be monomorphic in all the cultivated accessions and in reference species interfertile with P. communis, leading to hypothesize selection pressures for adaptation to cultivation. The cpDNA sequences of the 95 accessions were represented by 14 haplotypes, six of which (derived from P. communis, P. cossonii and P. ussuriensis) are recorded here for the first time and may suggest the ancient origin of some local varieties. The network analysis of the 298 cpDNA sequences allowed two different haplogroups, Eastern and Western Eurasia, to be defined, supporting recent views of a clear division between Occidental and Oriental species. By combining the results from nuclear and uniparental markers, it was possible to better define many unknown accessions.
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Affiliation(s)
- Nicoletta Ferradini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Hovirag Lancioni
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di PerugiaPerugia, Italy
| | - Renzo Torricelli
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Luigi Russi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Isabella Dalla Ragione
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Irene Cardinali
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di PerugiaPerugia, Italy
| | - Gianpiero Marconi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Mauro Gramaccia
- 3A Parco Tecnologico Agroalimentare Dell'Umbria – TodiPerugia, Italy
| | - Luciano Concezzi
- 3A Parco Tecnologico Agroalimentare Dell'Umbria – TodiPerugia, Italy
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di PaviaPavia, Italy
| | - Fabio Veronesi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
| | - Emidio Albertini
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di PerugiaPerugia, Italy
- *Correspondence: Emidio Albertini
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40
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Characterization of the complete chloroplast genome of Pinus uliginosa (Neumann) from the Pinus mugo complex. CONSERV GENET RESOUR 2016. [DOI: 10.1007/s12686-016-0652-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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41
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Coombe L, Warren RL, Jackman SD, Yang C, Vandervalk BP, Moore RA, Pleasance S, Coope RJ, Bohlmann J, Holt RA, Jones SJM, Birol I. Assembly of the Complete Sitka Spruce Chloroplast Genome Using 10X Genomics' GemCode Sequencing Data. PLoS One 2016; 11:e0163059. [PMID: 27632164 PMCID: PMC5025161 DOI: 10.1371/journal.pone.0163059] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 09/01/2016] [Indexed: 11/19/2022] Open
Abstract
The linked read sequencing library preparation platform by 10X Genomics produces barcoded sequencing libraries, which are subsequently sequenced using the Illumina short read sequencing technology. In this new approach, long fragments of DNA are partitioned into separate micro-reactions, where the same index sequence is incorporated into each of the sequencing fragment inserts derived from a given long fragment. In this study, we exploited this property by using reads from index sequences associated with a large number of reads, to assemble the chloroplast genome of the Sitka spruce tree (Picea sitchensis). Here we report on the first Sitka spruce chloroplast genome assembled exclusively from P. sitchensis genomic libraries prepared using the 10X Genomics protocol. We show that the resulting 124,049 base pair long genome shares high sequence similarity with the related white spruce and Norway spruce chloroplast genomes, but diverges substantially from a previously published P. sitchensis- P. thunbergii chimeric genome. The use of reads from high-frequency indices enabled separation of the nuclear genome reads from that of the chloroplast, which resulted in the simplification of the de Bruijn graphs used at the various stages of assembly.
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Affiliation(s)
- Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - René L. Warren
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- * E-mail: (RW); (IB)
| | - Shaun D. Jackman
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Chen Yang
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Benjamin P. Vandervalk
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Richard A. Moore
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Robin J. Coope
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Robert A. Holt
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Steven J. M. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Inanc Birol
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
- * E-mail: (RW); (IB)
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Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus. Sci Rep 2016; 6:21669. [PMID: 26899134 PMCID: PMC4761949 DOI: 10.1038/srep21669] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 01/27/2016] [Indexed: 11/08/2022] Open
Abstract
Astragalus membranaceus is an important medicinal plant in Asia. Several of its varieties have been used interchangeably as raw materials for commercial production. High resolution genetic markers are in urgent need to distinguish these varieties. Here, we sequenced and analyzed the chloroplast genome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao using the next generation DNA sequencing technology. The genome was assembled using Abyss and then subjected to gene prediction using CPGAVAS and repeat analysis using MISA, Tandem Repeats Finder, and REPuter. Finally, the genome was subjected phylogenetic and comparative genomic analyses. The complete genome is 123,582 bp long, containing only one copy of the inverted repeat. Gene prediction revealed 110 genes encoding 76 proteins, 30 tRNAs, and four rRNAs. Five intra-specific hypermutation loci were identified, three of which are heteroplasmic. Furthermore, three gene losses and two large inversions were identified. Comparative genomic analyses demonstrated the dynamic nature of the Papilionoideae chloroplast genomes, which showed occurrence of numerous hypermutation loci, frequent gene losses, and fragment inversions. Results obtained herein elucidate the complex evolutionary history of chloroplast genomes and have laid the foundation for the identification of genetic markers to distinguish A. membranaceus varieties.
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Jackman SD, Warren RL, Gibb EA, Vandervalk BP, Mohamadi H, Chu J, Raymond A, Pleasance S, Coope R, Wildung MR, Ritland CE, Bousquet J, Jones SJM, Bohlmann J, Birol I. Organellar Genomes of White Spruce (Picea glauca): Assembly and Annotation. Genome Biol Evol 2015; 8:29-41. [PMID: 26645680 PMCID: PMC4758241 DOI: 10.1093/gbe/evv244] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The genome sequences of the plastid and mitochondrion of white spruce (Picea glauca) were assembled from whole-genome shotgun sequencing data using ABySS. The sequencing data contained reads from both the nuclear and organellar genomes, and reads of the organellar genomes were abundant in the data as each cell harbors hundreds of mitochondria and plastids. Hence, assembly of the 123-kb plastid and 5.9-Mb mitochondrial genomes were accomplished by analyzing data sets primarily representing low coverage of the nuclear genome. The assembled organellar genomes were annotated for their coding genes, ribosomal RNA, and transfer RNA. Transcript abundances of the mitochondrial genes were quantified in three developmental tissues and five mature tissues using data from RNA-seq experiments. C-to-U RNA editing was observed in the majority of mitochondrial genes, and in four genes, editing events were noted to modify ACG codons to create cryptic AUG start codons. The informatics methodology presented in this study should prove useful to assemble organellar genomes of other plant species using whole-genome shotgun sequencing data.
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Affiliation(s)
- Shaun D Jackman
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ewan A Gibb
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Benjamin P Vandervalk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Justin Chu
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Anthony Raymond
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Stephen Pleasance
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Robin Coope
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Mark R Wildung
- School of Molecular Biosciences, Washington State University
| | - Carol E Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Jean Bousquet
- Department of Forest and Environmental Genomics, Université Laval, Québec, QC, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Inanç Birol
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada School of Computing Science, Simon Fraser University, Burnaby, BC, Canada Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
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Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences. Curr Genet 2015; 62:443-53. [PMID: 26643654 DOI: 10.1007/s00294-015-0549-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 11/22/2015] [Accepted: 11/23/2015] [Indexed: 10/22/2022]
Abstract
The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.
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Hoang NV, Furtado A, McQualter RB, Henry RJ. Next generation sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.neps.2015.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Rogalski M, do Nascimento Vieira L, Fraga HP, Guerra MP. Plastid genomics in horticultural species: importance and applications for plant population genetics, evolution, and biotechnology. FRONTIERS IN PLANT SCIENCE 2015; 6:586. [PMID: 26284102 PMCID: PMC4520007 DOI: 10.3389/fpls.2015.00586] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/15/2015] [Indexed: 05/20/2023]
Abstract
During the evolution of the eukaryotic cell, plastids, and mitochondria arose from an endosymbiotic process, which determined the presence of three genetic compartments into the incipient plant cell. After that, these three genetic materials from host and symbiont suffered several rearrangements, bringing on a complex interaction between nuclear and organellar gene products. Nowadays, plastids harbor a small genome with ∼130 genes in a 100-220 kb sequence in higher plants. Plastid genes are mostly highly conserved between plant species, being useful for phylogenetic analysis in higher taxa. However, intergenic spacers have a relatively higher mutation rate and are important markers to phylogeographical and plant population genetics analyses. The predominant uniparental inheritance of plastids is like a highly desirable feature for phylogeny studies. Moreover, the gene content and genome rearrangements are efficient tools to capture and understand evolutionary events between different plant species. Currently, genetic engineering of the plastid genome (plastome) offers a number of attractive advantages as high-level of foreign protein expression, marker gene excision, gene expression in operon and transgene containment because of maternal inheritance of plastid genome in most crops. Therefore, plastid genome can be used for adding new characteristics related to synthesis of metabolic compounds, biopharmaceutical, and tolerance to biotic and abiotic stresses. Here, we describe the importance and applications of plastid genome as tools for genetic and evolutionary studies, and plastid transformation focusing on increasing the performance of horticultural species in the field.
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Affiliation(s)
- Marcelo Rogalski
- Laboratório de Fisiologia Molecular de Plantas, Departamento de Biologia Vegetal, Universidade Federal de ViçosaViçosa, Brazil
| | - Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Hugo P. Fraga
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
| | - Miguel P. Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa CatarinaFlorianópolis, Brazil
- *Correspondence: Miguel P. Guerra, Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Centro de Ciências Agrárias, Universidade Federal de Santa Catarina, Rod. Admar Gonzaga, 1346 Florianópolis, SC 88034-000, Brazil,
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Yigit E, Hernandez DI, Trujillo JT, Dimalanta E, Bailey CD. Genome and metagenome sequencing: Using the human methyl-binding domain to partition genomic DNA derived from plant tissues. APPLICATIONS IN PLANT SCIENCES 2014; 2:apps1400064. [PMID: 25383266 PMCID: PMC4222543 DOI: 10.3732/apps.1400064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/28/2014] [Indexed: 06/04/2023]
Abstract
PREMISE OF THE STUDY Variation in the distribution of methylated CpG (methyl-CpG) in genomic DNA (gDNA) across the tree of life is biologically interesting and useful in genomic studies. We illustrate the use of human methyl-CpG-binding domain (MBD2) to fractionate angiosperm DNA into eukaryotic nuclear (methyl-CpG-rich) vs. organellar and prokaryotic (methyl-CpG-poor) elements for genomic and metagenomic sequencing projects. • METHODS MBD2 has been used to enrich prokaryotic DNA in animal systems. Using gDNA from five model angiosperm species, we apply a similar approach to identify whether MBD2 can fractionate plant gDNA into methyl-CpG-depleted vs. enriched methyl-CpG elements. For each sample, three gDNA libraries were sequenced: (1) untreated gDNA, (2) a methyl-CpG-depleted fraction, and (3) a methyl-CpG-enriched fraction. • RESULTS Relative to untreated gDNA, the methyl-depleted libraries showed a 3.2-11.2-fold and 3.4-11.3-fold increase in chloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA), respectively. Methyl-enriched fractions showed a 1.8-31.3-fold and 1.3-29.0-fold decrease in cpDNA and mtDNA, respectively. • DISCUSSION The application of MBD2 enabled fractionation of plant gDNA. The effectiveness was particularly striking for monocot gDNA (Poaceae). When sufficiently effective on a sample, this approach can increase the cost efficiency of sequencing plant genomes as well as prokaryotes living in or on plant tissues.
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Affiliation(s)
- Erbay Yigit
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938 USA
| | - David I. Hernandez
- Department of Biology, New Mexico State University, P.O. Box 30001 Msc 3AF, Las Cruces, New Mexico 88003 USA
| | - Joshua T. Trujillo
- Department of Biology, New Mexico State University, P.O. Box 30001 Msc 3AF, Las Cruces, New Mexico 88003 USA
| | - Eileen Dimalanta
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938 USA
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, P.O. Box 30001 Msc 3AF, Las Cruces, New Mexico 88003 USA
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Vieira LDN, Faoro H, Rogalski M, Fraga HPDF, Cardoso RLA, de Souza EM, de Oliveira Pedrosa F, Nodari RO, Guerra MP. The complete chloroplast genome sequence of Podocarpus lambertii: genome structure, evolutionary aspects, gene content and SSR detection. PLoS One 2014; 9:e90618. [PMID: 24594889 PMCID: PMC3942463 DOI: 10.1371/journal.pone.0090618] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/01/2014] [Indexed: 11/18/2022] Open
Abstract
Background Podocarpus lambertii (Podocarpaceae) is a native conifer from the Brazilian Atlantic Forest Biome, which is considered one of the 25 biodiversity hotspots in the world. The advancement of next-generation sequencing technologies has enabled the rapid acquisition of whole chloroplast (cp) genome sequences at low cost. Several studies have proven the potential of cp genomes as tools to understand enigmatic and basal phylogenetic relationships at different taxonomic levels, as well as further probe the structural and functional evolution of plants. In this work, we present the complete cp genome sequence of P. lambertii. Methodology/Principal Findings The P. lambertii cp genome is 133,734 bp in length, and similar to other sequenced cupressophytes, it lacks one of the large inverted repeat regions (IR). It contains 118 unique genes and one duplicated tRNA (trnN-GUU), which occurs as an inverted repeat sequence. The rps16 gene was not found, which was previously reported for the plastid genome of another Podocarpaceae (Nageia nagi) and Araucariaceae (Agathis dammara). Structurally, P. lambertii shows 4 inversions of a large DNA fragment ∼20,000 bp compared to the Podocarpus totara cp genome. These unexpected characteristics may be attributed to geographical distance and different adaptive needs. The P. lambertii cp genome presents a total of 28 tandem repeats and 156 SSRs, with homo- and dipolymers being the most common and tri-, tetra-, penta-, and hexapolymers occurring with less frequency. Conclusion The complete cp genome sequence of P. lambertii revealed significant structural changes, even in species from the same genus. These results reinforce the apparently loss of rps16 gene in Podocarpaceae cp genome. In addition, several SSRs in the P. lambertii cp genome are likely intraspecific polymorphism sites, which may allow highly sensitive phylogeographic and population structure studies, as well as phylogenetic studies of species of this genus.
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Affiliation(s)
- Leila do Nascimento Vieira
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Helisson Faoro
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Marcelo Rogalski
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Hugo Pacheco de Freitas Fraga
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Rodrigo Luis Alves Cardoso
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Emanuel Maltempi de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Fábio de Oliveira Pedrosa
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Rubens Onofre Nodari
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Miguel Pedro Guerra
- Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Florianópolis, Santa Catarina, Brazil
- * E-mail:
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