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Keeling PJ. Horizontal gene transfer in eukaryotes: aligning theory with data. Nat Rev Genet 2024; 25:416-430. [PMID: 38263430 DOI: 10.1038/s41576-023-00688-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2023] [Indexed: 01/25/2024]
Abstract
Horizontal gene transfer (HGT), or lateral gene transfer, is the non-sexual movement of genetic information between genomes. It has played a pronounced part in bacterial and archaeal evolution, but its role in eukaryotes is less clear. Behaviours unique to eukaryotic cells - phagocytosis and endosymbiosis - have been proposed to increase the frequency of HGT, but nuclear genomes encode fewer HGTs than bacteria and archaea. Here, I review the existing theory in the context of the growing body of data on HGT in eukaryotes, which suggests that any increased chance of acquiring new genes through phagocytosis and endosymbiosis is offset by a reduced need for these genes in eukaryotes, because selection in most eukaryotes operates on variation not readily generated by HGT.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, BC, Canada.
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2
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Marczuk-Rojas JP, Salmerón A, Alcayde A, Isanbaev V, Carretero-Paulet L. Plastid DNA is a major source of nuclear genome complexity and of RNA genes in the orphan crop moringa. BMC PLANT BIOLOGY 2024; 24:437. [PMID: 38773387 PMCID: PMC11110229 DOI: 10.1186/s12870-024-05158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/16/2024] [Indexed: 05/23/2024]
Abstract
BACKGROUND Unlike Transposable Elements (TEs) and gene/genome duplication, the role of the so-called nuclear plastid DNA sequences (NUPTs) in shaping the evolution of genome architecture and function remains poorly studied. We investigate here the functional and evolutionary fate of NUPTs in the orphan crop Moringa oleifera (moringa), featured by the highest fraction of plastid DNA found so far in any plant genome, focusing on (i) any potential biases in their distribution in relation to specific nuclear genomic features, (ii) their contribution to the emergence of new genes and gene regions, and (iii) their impact on the expression of target nuclear genes. RESULTS In agreement with their potential mutagenic effect, NUPTs are underrepresented among structural genes, although their overall transcription levels and broadness were only lower when involved exonic regions; the occurrence of plastid DNA generally did not result in a broader expression, except among those affected in introns by older NUPTs. In contrast, we found a strong enrichment of NUPTs among specific superfamilies of retrotransposons and several classes of RNA genes, including those participating in the protein biosynthetic machinery (i.e., rRNA and tRNA genes) and a specific class of regulatory RNAs. A significant fraction of NUPT RNA genes was found to be functionally expressed, thus potentially contributing to the nuclear pool. CONCLUSIONS Our results complete our view of the molecular factors driving the evolution of nuclear genome architecture and function, and support plastid DNA in moringa as a major source of (i) genome complexity and (ii) the nuclear pool of RNA genes.
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Affiliation(s)
- Juan Pablo Marczuk-Rojas
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Antonio Salmerón
- Department of Mathematics and Center for the Development and Transfer of Mathematical Research to Industry (CDTIME), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Alfredo Alcayde
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Viktor Isanbaev
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
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3
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Marczuk-Rojas JP, Álamo-Sierra AM, Salmerón A, Alcayde A, Isanbaev V, Carretero-Paulet L. Spatial and temporal characterization of the rich fraction of plastid DNA present in the nuclear genome of Moringa oleifera reveals unanticipated complexity in NUPTs´ formation. BMC Genomics 2024; 25:60. [PMID: 38225585 PMCID: PMC10789010 DOI: 10.1186/s12864-024-09979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/06/2024] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Beyond the massive amounts of DNA and genes transferred from the protoorganelle genome to the nucleus during the endosymbiotic event that gave rise to the plastids, stretches of plastid DNA of varying size are still being copied and relocated to the nuclear genome in a process that is ongoing and does not result in the concomitant shrinking of the plastid genome. As a result, plant nuclear genomes feature small, but variable, fraction of their genomes of plastid origin, the so-called nuclear plastid DNA sequences (NUPTs). However, the mechanisms underlying the origin and fixation of NUPTs are not yet fully elucidated and research on the topic has been mostly focused on a limited number of species and of plastid DNA. RESULTS Here, we leveraged a chromosome-scale version of the genome of the orphan crop Moringa oleifera, which features the largest fraction of plastid DNA in any plant nuclear genome known so far, to gain insights into the mechanisms of origin of NUPTs. For this purpose, we examined the chromosomal distribution and arrangement of NUPTs, we explicitly modeled and tested the correlation between their age and size distribution, we characterized their sites of origin at the chloroplast genome and their sites of insertion at the nuclear one, as well as we investigated their arrangement in clusters. We found a bimodal distribution of NUPT relative ages, which implies NUPTs in moringa were formed through two separate events. Furthermore, NUPTs from every event showed markedly distinctive features, suggesting they originated through distinct mechanisms. CONCLUSIONS Our results reveal an unanticipated complexity of the mechanisms at the origin of NUPTs and of the evolutionary forces behind their fixation and highlight moringa species as an exceptional model to assess the impact of plastid DNA in the evolution of the architecture and function of plant nuclear genomes.
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Affiliation(s)
- Juan Pablo Marczuk-Rojas
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Angélica María Álamo-Sierra
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain
| | - Antonio Salmerón
- Department of Mathematics, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Alfredo Alcayde
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Viktor Isanbaev
- Department of Engineering, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain
| | - Lorenzo Carretero-Paulet
- Department of Biology and Geology, University of Almería, Ctra. Sacramento s/n, 04120, Almería, Spain.
- "Pabellón de Historia Natural-Centro de Investigación de Colecciones Científicas de la Universidad de Almería" (PHN-CECOUAL), University of Almería, Ctra. Sacramento s/n, Almería, 04120, Spain.
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Wu Y, Zheng Y, Xu W, Zhang Z, Li L, Wang Y, Cui J, Wang QM. Chimeric deletion mutation of rpoC2 underlies the leaf-patterning of Clivia miniata var. variegata. PLANT CELL REPORTS 2023; 42:1419-1431. [PMID: 37326841 DOI: 10.1007/s00299-023-03039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
KEY MESSAGE The deletion mutated rpoC2 leads to yellow stripes of Clivia miniata var. variegata by down regulating the transcription of 28 chloroplast genes and disturbing chloroplast biogenesis and thylakoid membrane development. Clivia miniata var. variegata (Cmvv) is a common mutant of Clivia miniata but its genetic basis is unclear. Here, we found that a 425 bp deletion mutation of chloroplast rpoC2 underlies the yellow stripes (YSs) of Cmvv. Both RNA polymerase PEP and NEP coexist in seed-plant chloroplasts and the β″ subunit of PEP is encoded by rpoC2. The rpoC2 mutation changed the discontinuous cleft domain required to form the PEP central cleft for DNA binding from 1103 to 59 aa. RNA-Seq revealed that 28 chloroplast genes (cpDEGs) were all down-regulated in YSs, of which, four involved in chloroplast protein translation and 21 of photosynthesis system (PS)I, PSII, cytochrome b6/f complex and ATP synthase are crucial for chloroplast biogenesis/development. The accuracy and reliability of RNA-Seq was verified by qRT-PCR. Moreover, the chlorophyll (Chl) a/b content, ratio of Chla/Chlb and photosynthetic rate (Pn) of YS decreased significantly. Meanwhile, chloroplasts of the YS mesophyll cells were smaller, irregular in shape, contain almost no thylakoid membrane, and even proplastid was found in YS. These findings indicate that the rpoC2 mutation down-regulated expression of the 28 cpDEGs, which disturb chloroplast biogenesis and its thylakoid membrane development. Thus, there are not enough PSI and II components to bind Chl, so that the corresponding areas of the leaf are yellow and show a low Pn. In this study, the molecular mechanism of three phenotypes of F1 (Cmvv ♀ × C. miniata ♂) was revealed, which lays a foundation for the breeding of variegated plants.
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Affiliation(s)
- Yiming Wu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yi Zheng
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Weiman Xu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yucheng Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Jianguo Cui
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China.
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Chen Y, Guo Y, Xie X, Wang Z, Miao L, Yang Z, Jiao Y, Xie C, Liu J, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Guo W. Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. PLANT PHYSIOLOGY 2023; 193:578-594. [PMID: 37249052 PMCID: PMC10469385 DOI: 10.1093/plphys/kiad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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6
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González-Sánchez M, García-Martínez V, Bravo S, Kobayashi H, Martínez de Toda I, González-Bermúdez B, Plaza GR, De la Fuente M. Mitochondrial DNA insertions into nuclear DNA affecting chromosome segregation: Insights for a novel mechanism of immunosenescence in mice. Mech Ageing Dev 2022; 207:111722. [PMID: 35961414 DOI: 10.1016/j.mad.2022.111722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 08/06/2022] [Accepted: 08/07/2022] [Indexed: 10/15/2022]
Abstract
Mitochondrial DNA sequences were found inserted in the nuclear genome of mouse peritoneal T lymphocytes that increased progressively with aging. These insertions were preferentially located at the pericentromeric heterochromatin. In the same individuals, binucleated T-cells with micronuclei showed a significantly increased frequency associated with age. Most of them were positive for centromere sequences, reflecting the loss of chromatids or whole chromosomes. The proliferative capacity of T lymphocytes decreased with age as well as the glutathione reductase activity, whereas the oxidized glutathione and malondialdehyde concentrations exhibited a significant increase. These results may point to a common process that provides insights for a new approach to understanding immunosenescence. We propose a novel mechanism in which mitochondrial fragments, originated by the increased oxidative stress status during aging, accumulate inside the nuclear genome of T lymphocytes in a time-dependent way. The primary entrance of mitochondrial fragments at the pericentromeric regions may compromise chromosome segregation, causing genetic loss that leads to micronuclei formation, rendering aneuploid cells with reduced proliferation capacity, one of the hallmark of immunosenescence. Future experiments deciphering the mechanistic basis of this phenomenon are needed.
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Affiliation(s)
- Mónica González-Sánchez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - Víctor García-Martínez
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Sara Bravo
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Hikaru Kobayashi
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Irene Martínez de Toda
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Blanca González-Bermúdez
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain; Department of Materials Science, ETSI de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
| | - Gustavo R Plaza
- Center for Biomedical Technology, Universidad Politécnica de Madrid, E-28223 Pozuelo de Alarcón, Spain; Department of Materials Science, ETSI de Caminos, Canales y Puertos, Universidad Politécnica de Madrid, E-28040 Madrid, Spain
| | - Mónica De la Fuente
- Department of Genetics, Physiology and Microbiology, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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7
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Kejnovsky E, Jedlicka P. Nucleic acids movement and its relation to genome dynamics of repetitive DNA: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components?: Is cellular and intercellular movement of DNA and RNA molecules related to the evolutionary dynamic genome components? Bioessays 2022; 44:e2100242. [PMID: 35112737 DOI: 10.1002/bies.202100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 11/07/2022]
Abstract
There is growing evidence of evolutionary genome plasticity. The evolution of repetitive DNA elements, the major components of most eukaryotic genomes, involves the amplification of various classes of mobile genetic elements, the expansion of satellite DNA, the transfer of fragments or entire organellar genomes and may have connections with viruses. In addition to various repetitive DNA elements, a plethora of large and small RNAs migrate within and between cells during individual development as well as during evolution and contribute to changes of genome structure and function. Such migration of DNA and RNA molecules often results in horizontal gene transfer, thus shaping the whole genomic network of interconnected species. Here, we propose that a high evolutionary dynamism of repetitive genome components is often related to the migration/movement of DNA or RNA molecules. We speculate that the cytoplasm is probably an ideal compartment for such evolutionary experiments.
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Affiliation(s)
- Eduard Kejnovsky
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
| | - Pavel Jedlicka
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic
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8
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Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
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Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
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9
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Kudo H, Matsuo M, Satoh S, Hata T, Hachisu R, Nakamura M, Yamamoto YY, Kimura H, Matsui M, Obokata J. Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:29-39. [PMID: 34252235 DOI: 10.1111/tpj.15420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/08/2021] [Indexed: 06/13/2023]
Abstract
In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different mechanisms using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) without an apparent promoter sequence was expressed from intergenic regions: one mechanism is 'cryptic promoter capturing', in which the LUC ORF captured pre-existing promoter-like chromatin marked by H3K4me3 and H2A.Z, and the other is 'promoter de novo origination', in which the promoter chromatin was newly formed near the 5' end of the inserted LUC ORF. The latter finding raises a question as to how the inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter-LUC constructs, we found that the functional core promoter region, where transcription start sites (TSSs) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the coding sequence alters the local distribution of TSSs in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.
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Affiliation(s)
- Hisayuki Kudo
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Mitsuhiro Matsuo
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Takayuki Hata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Rei Hachisu
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Masayuki Nakamura
- Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan
| | - Yoshiharu Y Yamamoto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagito, Gihu-shi, Gifu, 501-1193, Japan
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, 226-8501, Japan
| | - Minami Matsui
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Junichi Obokata
- Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan
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10
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Shrestha B, Gilbert LE, Ruhlman TA, Jansen RK. Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora. Genome Biol Evol 2021; 12:1313-1329. [PMID: 32539116 PMCID: PMC7488351 DOI: 10.1093/gbe/evaa123] [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] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.
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Affiliation(s)
- Bikash Shrestha
- Department of Integrative Biology, University of Texas, Austin
| | - Lawrence E Gilbert
- Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin.,Faculty of Science, Department of Biological Sciences, Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah, Saudi Arabia
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12
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Abstract
The plastid genome (plastome ) has proved a valuable source of data for evaluating evolutionary relationships among angiosperms. Through basic and applied approaches, plastid transformation technology offers the potential to understand and improve plant productivity, providing food, fiber, energy, and medicines to meet the needs of a burgeoning global population. The growing genomic resources available to both phylogenetic and biotechnological investigations is allowing novel insights and expanding the scope of plastome research to encompass new species. In this chapter, we present an overview of some of the seminal and contemporary research that has contributed to our current understanding of plastome evolution and attempt to highlight the relationship between evolutionary mechanisms and the tools of plastid genetic engineering.
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Affiliation(s)
- Tracey A Ruhlman
- Integrative Biology, University of Texas at Austin, Austin, TX, USA.
| | - Robert K Jansen
- Integrative Biology, University of Texas at Austin, Austin, TX, USA
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13
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Ma X, Fan J, Wu Y, Zhao S, Zheng X, Sun C, Tan L. Whole-genome de novo assemblies reveal extensive structural variations and dynamic organelle-to-nucleus DNA transfers in African and Asian rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:596-612. [PMID: 32748498 PMCID: PMC7693357 DOI: 10.1111/tpj.14946] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 05/05/2023]
Abstract
Asian cultivated rice (Oryza sativa) and African cultivated rice (Oryza glaberrima) originated from the wild rice species Oryza rufipogon and Oryza barthii, respectively. The genomes of both cultivated species have undergone profound changes during domestication. Whole-genome de novo assemblies of O. barthii, O. glaberrima, O. rufipogon and Oryza nivara, produced using PacBio single-molecule real-time (SMRT) and next-generation sequencing (NGS) technologies, showed that Gypsy-like retrotransposons are the major contributors to genome size variation in African and Asian rice. Through the detection of genome-wide structural variations (SVs), we observed that besides 28 shared SV hot spots, another 67 hot spots existed in either the Asian or African rice genomes. Based on gene annotation information of the SVs, we established that organelle-to-nucleus DNA transfers resulted in numerous SVs that participated in the nuclear genome divergence of rice species and subspecies. We detected 52 giant nuclear integrants of organelle DNA (NORGs, defined as >10 kb) in six Oryza AA genomes. In addition, we developed an effective method to genotype giant NORGs, based on genome assembly, and first showed the dynamic change in the distribution of giant NORGs in rice natural population. Interestingly, 16 highly differentiated giant NORGs tended to accumulate in natural populations of Asian rice from higher latitude regions, grown at lower temperatures and light intensities. Our study provides new insight into the genome divergence of African and Asian rice, and establishes that organelle-to-nucleus DNA transfers, as potentially powerful contributors to environmental adaptation during rice evolution, play a major role in producing SVs in rice genomes.
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Affiliation(s)
- Xin Ma
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
| | - Jinjian Fan
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
| | - Yongzhen Wu
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Shuangshuang Zhao
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Xu Zheng
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
| | - Chuanqing Sun
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of Plant Physiology and BiochemistryChina Agricultural UniversityBeijing100193China
| | - Lubin Tan
- MOE Key Laboratory of Crop Heterosis and UtilizationNational Center for Evaluation of Agricultural Wild Plants (Rice)Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing100193China
- State Key Laboratory of AgrobiotechnologyChina Agricultural UniversityBeijing100193China
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14
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Evolutionary analysis of the Moringa oleifera genome reveals a recent burst of plastid to nucleus gene duplications. Sci Rep 2020; 10:17646. [PMID: 33077763 PMCID: PMC7573628 DOI: 10.1038/s41598-020-73937-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/21/2020] [Indexed: 12/22/2022] Open
Abstract
It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in Moringa as compared with ten other flowering plant species. Despite the reduced number of genes in the compact Moringa genome, 101 gene families, grouping 957 genes, were found as significantly expanded. Expanded families were highly enriched for chloroplastidic and photosynthetic functions. Indeed, almost half of the genes belonging to Moringa expanded families grouped with their Arabidopsis thaliana plastid encoded orthologs. Microsynteny analysis together with modeling the distribution of synonymous substitutions rates, supported most plastid duplicated genes originated recently through a burst of simultaneous insertions of large regions of plastid DNA into the nuclear genome. These, together with abundant short insertions of plastid DNA, contributed to the occurrence of massive amounts of plastid DNA in the Moringa nuclear genome, representing 4.71%, the largest reported so far. Our study provides key genetic resources for future breeding programs and highlights the potential of plastid DNA to impact the structure and function of nuclear genes and genomes.
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15
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Puertas MJ, González-Sánchez M. Insertions of mitochondrial DNA into the nucleus—effects and role in cell evolution. Genome 2020; 63:365-374. [DOI: 10.1139/gen-2019-0151] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We review the insertion of mitochondrial DNA (mtDNA) fragments into nuclear DNA (NUMTS) as a general and ongoing process that has occurred many times during genome evolution. Fragments of mtDNA are generated during the lifetime of organisms in both somatic and germinal cells, by the production of reactive oxygen species in the mitochondria. The fragments are inserted into the nucleus during the double-strand breaks repair via the non-homologous end-joining machinery, followed by genomic instability, giving rise to the high variability observed in NUMT patterns among species, populations, or genotypes. Some de novo produced mtDNA insertions show harmful effects, being involved in human diseases, carcinogenesis, and ageing. NUMT generation is a non-stop process overpassing the Mendelian transmission. This parasitic property ensures their survival even against their harmful effects. The accumulation of mtDNA fragments mainly at pericentromeric and subtelomeric regions is important to understand the transmission and integration of NUMTs into the genomes. The possible effect of female meiotic drive for mtDNA insertions at centromeres remains to be studied. In spite of the harmful feature of NUMTs, they are important in cell evolution, representing a major source of genomic variation.
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Affiliation(s)
- María J. Puertas
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
| | - Mónica González-Sánchez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense, José Antonio Novais 2, 28040 Madrid, Spain
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16
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Zhang GJ, Dong R, Lan LN, Li SF, Gao WJ, Niu HX. Nuclear Integrants of Organellar DNA Contribute to Genome Structure and Evolution in Plants. Int J Mol Sci 2020; 21:ijms21030707. [PMID: 31973163 PMCID: PMC7037861 DOI: 10.3390/ijms21030707] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 11/16/2022] Open
Abstract
The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed.
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Affiliation(s)
- Guo-Jun Zhang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Li-Na Lan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
| | - Hong-Xing Niu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; (G.-J.Z.); (R.D.); (L.-N.L.); (S.-F.L.)
- Correspondence: (W.-J.G.); (H.-X.N.)
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17
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Barja G. Towards a unified mechanistic theory of aging. Exp Gerontol 2019; 124:110627. [DOI: 10.1016/j.exger.2019.05.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/08/2019] [Accepted: 05/30/2019] [Indexed: 12/18/2022]
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18
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Li SF, Li JR, Wang J, Dong R, Jia KL, Zhu HW, Li N, Yuan JH, Deng CL, Gao WJ. Cytogenetic and genomic organization analyses of chloroplast DNA invasions in the nuclear genome of Asparagus officinalis L. provides signatures of evolutionary complexity and informativity in sex chromosome evolution. BMC PLANT BIOLOGY 2019; 19:361. [PMID: 31419941 PMCID: PMC6698032 DOI: 10.1186/s12870-019-1975-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 08/13/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND The transfer of chloroplast DNA into nuclear genome is a common process in plants. These transfers form nuclear integrants of plastid DNAs (NUPTs), which are thought to be driving forces in genome evolution, including sex chromosome evolution. In this study, NUPTs in the genome of a dioecious plant Asparagus officinalis L. were systematically analyzed, in order to investigate the characteristics of NUPTs in the nuclear genome and the relationship between NUPTs and sex chromosome evolution in this species. RESULTS A total of 3155 NUPT insertions were detected, and they represented approximated 0.06% of the nuclear genome. About 45% of the NUPTs were organized in clusters. These clusters were derived from various evolutionary events. The Y chromosome contained the highest number and largest proportion of NUPTs, suggesting more accumulation of NUPTs on sex chromosomes. NUPTs were distributed widely in all of the chromosomes, and some regions preferred these insertions. The highest density of NUPTs was found in a 47 kb region in the Y chromosome; more than 75% of this region was occupied by NUPTs. Further cytogenetic and sequence alignment analysis revealed that this region was likely the centromeric region of the sex chromosomes. On the other hand, the male-specific region of the Y chromosome (MSY) and the adjacent regions did not have NUPT insertions. CONCLUSIONS These results indicated that NUPTs were involved in shaping the genome of A. officinalis through complicated process. NUPTs may play important roles in the centromere shaping of the sex chromosomes of A. officinalis, but were not implicated in MSY formation.
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Affiliation(s)
- Shu-Fen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jia-Rong Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ran Dong
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ke-Li Jia
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
- SanQuan Medical College, Xinxiang Medical University, Xinxiang, 453003 China
| | - Hong-Wei Zhu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Jin-Hong Yuan
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Chuan-Liang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
| | - Wu-Jun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007 China
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Gao LZ, Liu YL, Zhang D, Li W, Gao J, Liu Y, Li K, Shi C, Zhao Y, Zhao YJ, Jiao JY, Mao SY, Gao CW, Eichler EE. Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats. Commun Biol 2019; 2:278. [PMID: 31372517 PMCID: PMC6659635 DOI: 10.1038/s42003-019-0531-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/18/2019] [Indexed: 01/05/2023] Open
Abstract
The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.
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Affiliation(s)
- Li-Zhi Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Ju Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Yuan Liu
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Kui Li
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Chao Shi
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Yuan Zhao
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Faculty of Plant Protection, Yunnan Agricultural University, 650204 Kunming, China
| | - You-Jie Zhao
- Southwest China Forestry University, 650224 Kunming, China
| | - Jun-Ying Jiao
- Southwest China Forestry University, 650224 Kunming, China
| | - Shu-Yan Mao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Cheng-Wen Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Evan E. Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA
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20
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Muniandy K, Tan MH, Song BK, Ayub Q, Rahman S. Comparative sequence and methylation analysis of chloroplast and amyloplast genomes from rice. PLANT MOLECULAR BIOLOGY 2019; 100:33-46. [PMID: 30788769 DOI: 10.1007/s11103-019-00841-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 02/11/2019] [Indexed: 05/15/2023]
Abstract
Grain amyloplast and leaf chloroplast DNA sequences are identical in rice plants but are differentially methylated. The leaf chloroplast DNA becomes more methylated as the rice plant ages. Rice is an important crop worldwide. Chloroplasts and amyloplasts are critical organelles but the amyloplast genome is poorly studied. We have characterised the sequence and methylation of grain amyloplast DNA and leaf chloroplast DNA in rice. We have also analysed the changes in methylation patterns in the chloroplast DNA as the rice plant ages. Total genomic DNA from grain, old leaf and young leaf tissues were extracted from the Oryza sativa ssp. indica cv. MR219 and sequenced using Illumina Miseq. Sequence variant analysis revealed that the amyloplast and chloroplast DNA of MR219 were identical to each other. However, comparison of CpG and CHG methylation between the identical amyloplast and chloroplast DNA sequences indicated that the chloroplast DNA from rice leaves collected at early ripening stage was more methylated than the amyloplast DNA from the grains of the same plant. The chloroplast DNA became more methylated as the plant ages so that chloroplast DNA from young leaves was less methylated overall than amyloplast DNA. These differential methylation patterns were primarily observed in organelle-encoded genes related to photosynthesis followed by those involved in transcription and translation.
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Affiliation(s)
- Kanagesswari Muniandy
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
| | - Mun Hua Tan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3220, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, 3220, Australia
| | - Beng Kah Song
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Qasim Ayub
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Sadequr Rahman
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia Genomics Facility, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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21
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Genome defense against integrated organellar DNA fragments from plastids into plant nuclear genomes through DNA methylation. Sci Rep 2019; 9:2060. [PMID: 30765781 PMCID: PMC6376042 DOI: 10.1038/s41598-019-38607-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 12/31/2018] [Indexed: 01/09/2023] Open
Abstract
Nuclear genomes are always faced with the modification of themselves by insertions and integrations of foreign DNAs and intrinsic parasites such as transposable elements. There is also substantial number of integrations from symbiotic organellar genomes to their host nuclear genomes. Such integration might have acted as a beneficial mutation during the evolution of symbiosis, while most of them have more or less deleterious effects on the stability of current genomes. Here we report the pattern of DNA substitution and methylation on organellar DNA fragments integrated from plastid into plant nuclear genomes. The genome analyses of 17 plants show homology–dependent DNA substitution bias. A certain number of these sequences are DNA methylated in the nuclear genome. The intensity of DNA methylation also decays according to the increase of relative evolutionary times after being integrated into nuclear genomes. The methylome data of epigenetic mutants shows that the DNA methylation of organellar DNA fragments in nuclear genomes are mainly dependent on the methylation maintenance machinery, while other mechanisms may also affect on the DNA methylation level. The DNA methylation on organellar DNA fragments may contribute to maintaining the genome stability and evolutionary dynamics of symbiotic organellar and their host’s genomes.
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Comparative assessment shows the reliability of chloroplast genome assembly using RNA-seq. Sci Rep 2018; 8:17404. [PMID: 30479362 PMCID: PMC6258696 DOI: 10.1038/s41598-018-35654-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 11/09/2018] [Indexed: 11/08/2022] Open
Abstract
Chloroplast genomes (cp genomes) are widely used in comparative genomics, population genetics, and phylogenetic studies. Obtaining chloroplast genomes from RNA-Seq data seems feasible due to the almost full transcription of cpDNA. However, the reliability of chloroplast genomes assembled from RNA-Seq instead of genomic DNA libraries remains to be thoroughly verified. In this study, we assembled chloroplast genomes for three Erysimum (Brassicaceae) species from three RNA-Seq replicas and from one genomic library of each species, using a streamlined bioinformatics protocol. We compared these assembled genomes, confirming that assembled cp genomes from RNA-Seq data were highly similar to each other and to those from genomic libraries in terms of overall structure, size, and composition. Although post-transcriptional modifications, such as RNA-editing, may introduce variations in the RNA-seq data, the assembly of cp genomes from RNA-seq appeared to be reliable. Moreover, RNA-Seq assembly was less sensitive to sources of error such as the recovery of nuclear plastid DNAs (NUPTs). Although some precautions should be taken when producing reference genomes in non-model plants, we conclude that assembling cp genomes from RNA-Seq data is a fast, accurate, and reliable strategy.
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23
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Portugez S, Martin WF, Hazkani-Covo E. Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination. BMC Evol Biol 2018; 18:162. [PMID: 30390623 PMCID: PMC6215612 DOI: 10.1186/s12862-018-1279-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/18/2018] [Indexed: 02/06/2023] Open
Abstract
Background Mitochondrial and plastid DNA fragments are continuously transferred into eukaryotic nuclear genomes, giving rise to nuclear copies of mitochondrial DNA (numts) and nuclear copies of plastid DNA (nupts). Numts and nupts are classified as simple if they are composed of a single organelle fragment or as complex if they are composed of multiple fragments. Mosaic insertions are complex insertions composed of fragments of both mitochondrial and plastid DNA. Simple numts and nupts in eukaryotes have been extensively studied, their mechanism of insertion involves non-homologous end joining (NHEJ). Mosaic insertions have been less well-studied and their mechanisms of integration are unknown. Results Here we estimated the number of nuclear mosaic insertions (numins) in nine plant genomes. We show that numins compose up to 10% of the total nuclear insertions of organelle DNA in these plant genomes. The NHEJ hallmarks typical for numts and nupts were also identified in mosaic insertions. However, the number of identified insertions that integrated via NHEJ mechanism is underestimated, as NHEJ signatures are conserved only in recent insertions and mutationally eroded in older ones. A few complex insertions show signatures of long homology that cannot be attributed to NHEJ, a novel observation that implicates gene conversion or single strand annealing mechanisms in organelle nuclear insertions. Conclusions The common NHEJ signature that was identified here reveals that, in plant cells, mitochondria and plastid fragments in numins must meet during or prior to integration into the nuclear genome. Electronic supplementary material The online version of this article (10.1186/s12862-018-1279-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shir Portugez
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel.,School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
| | - Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel.
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Marques A, Klemme S, Houben A. Evolution of Plant B Chromosome Enriched Sequences. Genes (Basel) 2018; 9:genes9100515. [PMID: 30360448 PMCID: PMC6210368 DOI: 10.3390/genes9100515] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 10/13/2018] [Accepted: 10/18/2018] [Indexed: 01/10/2023] Open
Abstract
B chromosomes are supernumerary chromosomes found in addition to the normal standard chromosomes (A chromosomes). B chromosomes are well known to accumulate several distinct types of repeated DNA elements. Although the evolution of B chromosomes has been the subject of numerous studies, the mechanisms of accumulation and evolution of repetitive sequences are not fully understood. Recently, new genomic approaches have shed light on the origin and accumulation of different classes of repetitive sequences in the process of B chromosome formation and evolution. Here we discuss the impact of repetitive sequences accumulation on the evolution of plant B chromosomes.
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Affiliation(s)
- André Marques
- Laboratory of Genetic Resources, Federal University of Alagoas, Av. Manoel Severino Barbosa, 57309-005 Arapiraca-AL, Brazil.
| | - Sonja Klemme
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, Branišovská 31, CZ-37005 České Budějovice, Czech Republic.
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany.
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de Vries J, Gould SB. The monoplastidic bottleneck in algae and plant evolution. J Cell Sci 2018; 131:jcs.203414. [PMID: 28893840 DOI: 10.1242/jcs.203414] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plastids in plants and algae evolved from the endosymbiotic integration of a cyanobacterium by a heterotrophic eukaryote. New plastids can only emerge through fission; thus, the synchronization of bacterial division with the cell cycle of the eukaryotic host was vital to the origin of phototrophic eukaryotes. Most of the sampled algae house a single plastid per cell and basal-branching relatives of polyplastidic lineages are all monoplastidic, as are some non-vascular plants during certain stages of their life cycle. In this Review, we discuss recent advances in our understanding of the molecular components necessary for plastid division, including those of the peptidoglycan wall (of which remnants were recently identified in moss), in a wide range of phototrophic eukaryotes. Our comparison of the phenotype of 131 species harbouring plastids of either primary or secondary origin uncovers that one prerequisite for an algae or plant to house multiple plastids per nucleus appears to be the loss of the bacterial genes minD and minE from the plastid genome. The presence of a single plastid whose division is coupled to host cytokinesis was a prerequisite of plastid emergence. An escape from such a monoplastidic bottleneck succeeded rarely and appears to be coupled to the evolution of additional layers of control over plastid division and a complex morphology. The existence of a quality control checkpoint of plastid transmission remains to be demonstrated and is tied to understanding the monoplastidic bottleneck.
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Affiliation(s)
- Jan de Vries
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada, B3H 4R2
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University, 40225 Düsseldorf, Germany
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Takamatsu T, Baslam M, Inomata T, Oikawa K, Itoh K, Ohnishi T, Kinoshita T, Mitsui T. Optimized Method of Extracting Rice Chloroplast DNA for High-Quality Plastome Resequencing and de Novo Assembly. FRONTIERS IN PLANT SCIENCE 2018; 9:266. [PMID: 29541088 PMCID: PMC5835797 DOI: 10.3389/fpls.2018.00266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Chloroplasts, which perform photosynthesis, are one of the most important organelles in green plants and algae. Chloroplasts maintain an independent genome that includes important genes encoding their photosynthetic machinery and various housekeeping functions. Owing to its non-recombinant nature, low mutation rates, and uniparental inheritance, the chloroplast genome (plastome) can give insights into plant evolution and ecology and in the development of biotechnological and breeding applications. However, efficient methods to obtain high-quality chloroplast DNA (cpDNA) are currently not available, impeding powerful sequencing and further functional genomics research. To investigate effects on rice chloroplast genome quality, we compared cpDNA extraction by three extraction protocols: liquid nitrogen coupled with sucrose density gradient centrifugation, high-salt buffer, and Percoll gradient centrifugation. The liquid nitrogen-sucrose gradient method gave a high yield of high-quality cpDNA with reliable purity. The cpDNA isolated by this technique was evaluated, resequenced, and assembled de novo to build a robust framework for genomic and genetic studies. Comparison of this high-purity cpDNA with total DNAs revealed the read coverage of the sequenced regions; next-generation sequencing data showed that the high-quality cpDNA eliminated noise derived from contamination by nuclear and mitochondrial DNA, which frequently occurs in total DNA. The assembly process produced highly accurate, long contigs. We summarize the extent to which this improved method of isolating cpDNA from rice can provide practical progress in overcoming challenges related to chloroplast genomes and in further exploring the development of new sequencing technologies.
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Affiliation(s)
- Takeshi Takamatsu
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Takuya Inomata
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Kazusato Oikawa
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Kimiko Itoh
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
| | - Takayuki Ohnishi
- Center for Education and Research of Community Collaboration, Utsunomiya University, Utsunomiya, Japan
| | - Tetsu Kinoshita
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Toshiaki Mitsui
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata, Japan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata, Japan
- *Correspondence: Toshiaki Mitsui,
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Wang D, Gu J, David R, Wang Z, Yang S, Searle IR, Zhu JK, Timmis JN. Experimental reconstruction of double-stranded break repair-mediated plastid DNA insertion into the tobacco nucleus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:227-234. [PMID: 29155472 DOI: 10.1111/tpj.13769] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 10/26/2017] [Accepted: 10/30/2017] [Indexed: 06/07/2023]
Abstract
The mitochondria and plastids of eukaryotic cells evolved from endosymbiotic prokaryotes. DNA from the endosymbionts has bombarded nuclei since the ancestral prokaryotes were engulfed by a precursor of the nucleated eukaryotic host. An experimental confirmation regarding the molecular mechanisms responsible for organelle DNA incorporation into nuclei has not been performed until the present analysis. Here we introduced double-stranded DNA breaks into the nuclear genome of tobacco through inducible expression of I-SceI, and showed experimentally that tobacco chloroplast DNAs insert into nuclear genomes through double-stranded DNA break repair. Microhomology-mediated linking of disparate segments of chloroplast DNA occurs frequently during healing of induced nuclear double-stranded breaks (DSB) but the resulting nuclear integrants are often immediately unstable. Non-Mendelian inheritance of a selectable marker (neo), used to identify plastid DNA transfer, was observed in the progeny of about 50% of lines emerging from the screen. The instability of these de novo nuclear insertions of plastid DNA (nupts) was shown to be associated with deletion not only of the nupt itself but also of flanking nuclear DNA within one generation of transfer. This deletion of pre-existing nuclear DNA suggests that the genetic impact of organellar DNA transfer to the nucleus is potentially far greater than previously thought.
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Affiliation(s)
- Dong Wang
- Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Jiangxi, 330031, China
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinbao Gu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Rakesh David
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Zhen Wang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Songtao Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Iain R Searle
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Jeremy N Timmis
- Department of Genetics and Evolution, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
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Hazkani-Covo E, Martin WF. Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health. Genome Biol Evol 2017; 9:1190-1203. [PMID: 28444372 PMCID: PMC5570036 DOI: 10.1093/gbe/evx078] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 12/28/2022] Open
Abstract
Fragments of organelle genomes are often found as insertions in nuclear DNA. These fragments of mitochondrial DNA (numts) and plastid DNA (nupts) are ubiquitous components of eukaryotic genomes. They are, however, often edited out during the genome assembly process, leading to systematic underestimation of their frequency. Numts and nupts, once inserted, can become further fragmented through subsequent insertion of mobile elements or other recombinational events that disrupt the continuity of the inserted sequence relative to the genuine organelle DNA copy. Because numts and nupts are typically identified through sequence comparison tools such as BLAST, disruption of insertions into smaller fragments can lead to systematic overestimation of numt and nupt frequencies. Accurate identification of numts and nupts is important, however, both for better understanding of their role during evolution, and for monitoring their increasingly evident role in human disease. Human populations are polymorphic for 141 numt loci, five numts are causal to genetic disease, and cancer genomic studies are revealing an abundance of numts associated with tumor progression. Here, we report investigation of salient parameters involved in obtaining accurate estimates of numt and nupt numbers in genome sequence data. Numts and nupts from 44 sequenced eukaryotic genomes reveal lineage-specific differences in the number, relative age and frequency of insertional events as well as lineage-specific dynamics of their postinsertional fragmentation. Our findings outline the main technical parameters influencing accurate identification and frequency estimation of numts in genomic studies pertinent to both evolution and human health.
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Affiliation(s)
- Einat Hazkani-Covo
- Department of Natural and Life Sciences, The Open University of Israel, Ra'anana, Israel
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine University, Düsseldorf, Germany
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Raman G, Park V, Kwak M, Lee B, Park S. Characterization of the complete chloroplast genome of Arabis stellari and comparisons with related species. PLoS One 2017; 12:e0183197. [PMID: 28809950 PMCID: PMC5557495 DOI: 10.1371/journal.pone.0183197] [Citation(s) in RCA: 21] [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: 05/30/2017] [Accepted: 07/31/2017] [Indexed: 01/25/2023] Open
Abstract
Arabis stellari var. japonica is an ornamental plant of the Brassicaceae family, and is widely distributed in South Korea. However, no information is available about its molecular biology and no genomic study has been performed on A. stellari. In this paper, the authors report the complete chloroplast genome sequence of A. stellari. The plastome of A. stellari was 153,683 bp in length with 36.4% GC and included a pair of inverted repeats (IRs) of 26,423 bp that separated a large single-copy (LSC) region of 82,807 bp and a small single-copy (SSC) region of 18,030 bp. It was also found to contain 113 unique genes, of which 79 were protein-coding genes, 30 were transfer RNAs, and four were ribosomal RNAs. The gene content and organization of the A. stellari chloroplast genome were similar to those of other Brassicaceae genomes except for the absence of the rps16 protein-coding gene. A total of 991 SSRs were identified in the genome. The chloroplast genome of A. stellari was compared with closely related species of the Brassicaceae family. Comparative analysis showed a minor divergence occurred in the protein-coding matK, ycf1, ccsA, accD and rpl22 genes and that the KA/KS nucleotide substitution ratio of the ndhA genes of A. stellari and A. hirsuta was 1.35135. The genes infA and rps16 were absent in the Arabis genus and phylogenetic evolutionary studies revealed that these genes evolved independently. However, phylogenetic analysis showed that the positions of Brassicaceae species are highly conserved. The present study provides A. stellari genomic information that may be found useful in conservation and molecular phylogenetic studies on Brassicaceae.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Veronica Park
- Mcneil high school, Austin, Texas, United States of America
| | - Myounghai Kwak
- Plant Resources Division, National Institute of Biological Resources of Korea, Incheon, Republic of Korea
| | - Byoungyoon Lee
- Plant Resources Division, National Institute of Biological Resources of Korea, Incheon, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- * E-mail:
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Hong CP, Park J, Lee Y, Lee M, Park SG, Uhm Y, Lee J, Kim CK. accD nuclear transfer of Platycodon grandiflorum and the plastid of early Campanulaceae. BMC Genomics 2017; 18:607. [PMID: 28800729 PMCID: PMC5553655 DOI: 10.1186/s12864-017-4014-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/03/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Campanulaceae species are known to have highly rearranged plastid genomes lacking the acetyl-CoA carboxylase (ACC) subunit D gene (accD), and instead have a nuclear (nr)-accD. Plastid genome information has been thought to depend on studies concerning Trachelium caeruleum and genome announcements for Adenophora remotiflora, Campanula takesimana, and Hanabusaya asiatica. RNA editing information for plastid genes is currently unavailable for Campanulaceae. To understand plastid genome evolution in Campanulaceae, we have sequenced and characterized the chloroplast (cp) genome and nr-accD of Platycodon grandiflorum, a basal member of Campanulaceae. RESULTS We sequenced the 171,818 bp cp genome containing a 79,061 bp large single-copy (LSC) region, a 42,433 bp inverted repeat (IR) and a 7840 bp small single-copy (SSC) region, which represents the cp genome with the largest IR among species of Campanulaceae. The genome contains 110 genes and 18 introns, comprising 77 protein-coding genes, four RNA genes, 29 tRNA genes, 17 group II introns, and one group I intron. RNA editing of genes was detected in 18 sites of 14 protein-coding genes. Platycodon has an IR containing a 3' rps12 operon, which occurs in the middle of the LSC region in four other species of Campanulaceae (T. caeruleum, A. remotiflora, C. takesimana, and H. asiatica), but lacks accD, clpP, infA, and rpl23, as has been found in these four species. Platycodon nr-accD contains about 3.2 kb intron between nr-accD.e1 and nr-accD.e2 at the same insertion point as in other Campanulaceae. The phylogenies of the plastid genomes and accD show that Platycodon is basal in the Campanulaceae clade, indicating that IR disruption in Campanulaceae occurred after the loss of accD, clpP, infA, and rpl23 in the cp genome, which occurred during plastid evolution in Campanulaceae. CONCLUSIONS The plastid genome of P. grandiflorum lacks the rearrangement of the IR found in T. caeruleum, A. remotiflora, C. takesimana, and H. asiatica. The absence of accD, clpP, infA, and rpl23 in the plastid genome is a synapomorphic characteristic of Campanulaceae. The chloroplast genome phylogeny supports the hypothesis that chloroplast genomic arrangement occurred after accD nuclear transfer and loss of the four genes in the plastid of early Campanulaceae as a lineage of asterids.
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Affiliation(s)
- Chang Pyo Hong
- Bioinformatics Team, Theragen Etex Bio Institute, Suwon, 443-270, South Korea
| | - Jihye Park
- Green Plant Institute, B-301, Heungdeok IT Valley, Giheung-gu, Yongin, 446-908, South Korea
| | - Yi Lee
- Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, 362-763, South Korea
| | - Minjee Lee
- Green Plant Institute, B-301, Heungdeok IT Valley, Giheung-gu, Yongin, 446-908, South Korea
| | - Sin Gi Park
- Bioinformatics Team, Theragen Etex Bio Institute, Suwon, 443-270, South Korea
| | - Yurry Uhm
- Herbal Crop Research Division, National Institute of Horticultural and Herbal Science (NIHH), RDA, Eumseong, 369-873, South Korea
| | - Jungho Lee
- Green Plant Institute, B-301, Heungdeok IT Valley, Giheung-gu, Yongin, 446-908, South Korea.
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Science (NAS), RDA, Jeonju, 560-500, South Korea.
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Nguyen VB, Park HS, Lee SC, Lee J, Park JY, Yang TJ. Authentication Markers for Five Major Panax Species Developed via Comparative Analysis of Complete Chloroplast Genome Sequences. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:6298-6306. [PMID: 28530408 DOI: 10.1021/acs.jafc.7b00925] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Ginseng represents a set of high-value medicinal plants of different species: Panax ginseng (Asian ginseng), Panax quinquefolius (American ginseng), Panax notoginseng (Chinese ginseng), Panax japonicus (Bamboo ginseng), and Panax vietnamensis (Vietnamese ginseng). Each species is pharmacologically and economically important, with differences in efficacy and price. Accordingly, an authentication system is needed to combat economically motivated adulteration of Panax products. We conducted comparative analysis of the chloroplast genome sequences of these five species, identifying 34-124 InDels and 141-560 SNPs. Fourteen InDel markers were developed to authenticate the Panax species. Among these, eight were species-unique markers that successfully differentiated one species from the others. We generated at least one species-unique marker for each of the five species, and any of the species can be authenticated by selection among these markers. The markers are reliable, easily detectable, and valuable for applications in the ginseng industry as well as in related research.
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Affiliation(s)
- Van Binh Nguyen
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University , Seoul, 151-921, Republic of Korea
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University , Pyeongchang 232-916, Republic of Korea
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Huang Y, Wang J, Yang Y, Fan C, Chen J. Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae. FRONTIERS IN PLANT SCIENCE 2017; 8:1050. [PMID: 28676809 PMCID: PMC5476734 DOI: 10.3389/fpls.2017.01050] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 05/31/2017] [Indexed: 05/24/2023]
Abstract
Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species.
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Affiliation(s)
- Yuan Huang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of SciencesKunming, China
- School of Life Sciences, Yunnan Normal UniversityKunming, China
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, DetroitMI, United States
| | - Yongping Yang
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, DetroitMI, United States
| | - Jiahui Chen
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Chinese Academy of SciencesKunming, China
- Institute of Tibetan Plateau Research at Kunming, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
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Wang XC, Chen H, Yang D, Liu C. Diversity of mitochondrial plastid DNAs (MTPTs) in seed plants. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:635-642. [PMID: 28573928 DOI: 10.1080/24701394.2017.1334772] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Mitochondrial plastid DNAs (MTPTs) refer to plastid-derived DNA fragments in mitochondrial genomes. While the MTPTs have been described for numerous species, its overall patterns have not been examined in details. Here, we carried out a systematic analysis of MTPTs among 73 plant species, including 28 algae, 1 liverwort, 2 moss, 1 lycophyte, 1 gymnosperm, 1 magnoliid, 12 monocots, 26 eudicots and 1 relic angiosperm Amborella trichopoda. A total of 300 MTPT gene clusters were found in 39 seed plants, which represented 144 MTPT gene cluster types. The detected MTPT gene clusters were evaluated in seven aspects, and they were found to be enriched particularly in monocots and asterids of eudicots. Some MTPT gene clusters were found to be shared by closely related species. All chloroplast genes were found in MTPTs, suggesting that there is no functional relevancy for genes that were transferred. However, after calculation of the frequency of the 115 chloroplast genes, five hot spots and three cold spots were discovered in chloroplast genome. In summary, this study demonstrated the high degree of diversity in MTPTs. The discovered MTPTs would facilitate the accurate assembly of chloroplast and mitochondrial genomes as well as the understanding of organelle genome evolution.
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Affiliation(s)
- Xin-Cun Wang
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Haimei Chen
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Dan Yang
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
| | - Chang Liu
- a Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Institute of Medicinal Plant Development , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing , P.R. China
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Yoshida T, Furihata HY, Kawabe A. Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species. Genes Genet Syst 2017; 92:27-33. [PMID: 28228607 DOI: 10.1266/ggs.16-00039] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sequences homologous to organellar DNA that have been integrated into nuclear genomes are referred to as nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs). NUMTs in nine plant species were analyzed to reveal the integration patterns and possible factors involved. The cumulative lengths of NUMTs in two-thirds of species analyzed were greater than those of NUPTs observed in a previous study. The age distribution of NUMTs was similar to that of NUPTs, suggesting similar mechanisms for integration and degradation of both NUPTs and NUMTs. Nuclear genome size and the cumulative length of NUMTs showed a significant positive correlation for older but not younger NUMTs. The same correlation was also found between nuclear genome size and older NUPTs in 17 species. These results suggested that genome size is a key factor to determine the cumulative length of relatively older NUPTs/NUMTs. Although the factor(s) determining the cumulative length of younger NUPTs/NUMTs is unclear, these sequences may be more deleterious, which could explain the different manner of determining the cumulative length of younger NUPTs/NUMTs in nuclear genomes. In addition, a relationship between the cumulative length of integrated NUMTs and complexity of mitochondrial genomes (i.e., the number of repeats) was found. The results indicate that the structural complexity of both NUMTs and their original mitochondrial sequences affects integration and degradation processes.
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Affiliation(s)
| | | | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University
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35
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Zuo LH, Shang AQ, Zhang S, Yu XY, Ren YC, Yang MS, Wang JM. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing: Genome comparative and taxonomic position analysis. PLoS One 2017; 12:e0171264. [PMID: 28158318 PMCID: PMC5291543 DOI: 10.1371/journal.pone.0171264] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/17/2017] [Indexed: 12/05/2022] Open
Abstract
Elm (Ulmus) has a long history of use as a high-quality heavy hardwood famous for its resistance to drought, cold, and salt. It grows in temperate, warm temperate, and subtropical regions. This is the first report of Ulmaceae chloroplast genomes by de novo sequencing. The Ulmus chloroplast genomes exhibited a typical quadripartite structure with two single-copy regions (long single copy [LSC] and short single copy [SSC] sections) separated by a pair of inverted repeats (IRs). The lengths of the chloroplast genomes from five Ulmus ranged from 158,953 to 159,453 bp, with the largest observed in Ulmus davidiana and the smallest in Ulmus laciniata. The genomes contained 137–145 protein-coding genes, of which Ulmus davidiana var. japonica and U. davidiana had the most and U. pumila had the fewest. The five Ulmus species exhibited different evolutionary routes, as some genes had been lost. In total, 18 genes contained introns, 13 of which (trnL-TAA+, trnL-TAA−, rpoC1-, rpl2-, ndhA-, ycf1, rps12-, rps12+, trnA-TGC+, trnA-TGC-, trnV-TAC-, trnI-GAT+, and trnI-GAT) were shared among all five species. The intron of ycf1 was the longest (5,675bp) while that of trnF-AAA was the smallest (53bp). All Ulmus species except U. davidiana exhibited the same degree of amplification in the IR region. To determine the phylogenetic positions of the Ulmus species, we performed phylogenetic analyses using common protein-coding genes in chloroplast sequences of 42 other species published in NCBI. The cluster results showed the closest plants to Ulmaceae were Moraceae and Cannabaceae, followed by Rosaceae. Ulmaceae and Moraceae both belonged to Urticales, and the chloroplast genome clustering results were consistent with their traditional taxonomy. The results strongly supported the position of Ulmaceae as a member of the order Urticales. In addition, we found a potential error in the traditional taxonomies of U. davidiana and U. davidiana var. japonica, which should be confirmed with a further analysis of their nuclear genomes. This study is the first report on Ulmus chloroplast genomes, which has significance for understanding photosynthesis, evolution, and chloroplast transgenic engineering.
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Affiliation(s)
- Li-Hui Zuo
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
| | - Ai-Qin Shang
- Horticulture College, Agricultural University of Hebei, Baoding, PR China
| | - Shuang Zhang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
| | - Xiao-Yue Yu
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
| | - Ya-Chao Ren
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
| | - Min-Sheng Yang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
- * E-mail: (MSY); (JMW)
| | - Jin-Mao Wang
- Institute of Forest Biotechnology, Forestry College, Agricultural University of Hebei, Baoding, PR China
- Hebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, PR China
- * E-mail: (MSY); (JMW)
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Sousa A, Bellot S, Fuchs J, Houben A, Renner SS. Analysis of transposable elements and organellar DNA in male and female genomes of a species with a huge Y chromosome reveals distinct Y centromeres. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:387-396. [PMID: 27354172 DOI: 10.1111/tpj.13254] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/10/2016] [Accepted: 06/23/2016] [Indexed: 05/03/2023]
Abstract
Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.
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Affiliation(s)
- Aretuza Sousa
- Department of Biology, University of Munich (LMU), Munich, 80638, Germany
| | - Sidonie Bellot
- Plant Biodiversity Research, Technical University of Munich (TUM), Freising, 85354, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466, Germany
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Stadt Seeland, 06466, Germany
| | - Susanne S Renner
- Department of Biology, University of Munich (LMU), Munich, 80638, Germany
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37
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Abstract
Structurally and functionally diverged sex chromosomes have evolved in many animals as well as in some plants. Sex chromosomes represent a specific genomic region(s) with locally suppressed recombination. As a consequence, repetitive sequences involving transposable elements, tandem repeats (satellites and microsatellites), and organellar DNA accumulate on the Y (W) chromosomes. In this paper, we review the main types of repetitive elements, their gathering on the Y chromosome, and discuss new findings showing that not only accumulation of various repeats in non-recombining regions but also opposite processes form Y chromosome. The aim of this review is also to discuss the mechanisms of repetitive DNA spread involving (retro) transposition, DNA polymerase slippage or unequal crossing-over, as well as modes of repeat removal by ectopic recombination. The intensity of these processes differs in non-recombining region(s) of sex chromosomes when compared to the recombining parts of genome. We also speculate about the relationship between heterochromatinization and the formation of heteromorphic sex chromosomes.
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38
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Shi C, Wang S, Xia EH, Jiang JJ, Zeng FC, Gao LZ. Full transcription of the chloroplast genome in photosynthetic eukaryotes. Sci Rep 2016; 6:30135. [PMID: 27456469 PMCID: PMC4960489 DOI: 10.1038/srep30135] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/28/2016] [Indexed: 11/09/2022] Open
Abstract
Prokaryotes possess a simple genome transcription system that is different from that of eukaryotes. In chloroplasts (plastids), it is believed that the prokaryotic gene transcription features govern genome transcription. However, the polycistronic operon transcription model cannot account for all the chloroplast genome (plastome) transcription products at whole-genome level, especially regarding various RNA isoforms. By systematically analyzing transcriptomes of plastids of algae and higher plants, and cyanobacteria, we find that the entire plastome is transcribed in photosynthetic green plants, and that this pattern originated from prokaryotic cyanobacteria - ancestor of the chloroplast genomes that diverged about 1 billion years ago. We propose a multiple arrangement transcription model that multiple transcription initiations and terminations combine haphazardly to accomplish the genome transcription followed by subsequent RNA processing events, which explains the full chloroplast genome transcription phenomenon and numerous functional and/or aberrant pre-RNAs. Our findings indicate a complex prokaryotic genome regulation when processing primary transcripts.
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Affiliation(s)
- Chao Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Shuo Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,University of the Chinese Academy of Sciences, Beijing 100039, China
| | - Jian-Jun Jiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - Fan-Chun Zeng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming 650204, China.,Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650093, China
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Weng ML, Ruhlman TA, Jansen RK. Plastid-Nuclear Interaction and Accelerated Coevolution in Plastid Ribosomal Genes in Geraniaceae. Genome Biol Evol 2016; 8:1824-38. [PMID: 27190001 PMCID: PMC4943186 DOI: 10.1093/gbe/evw115] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plastids and mitochondria have many protein complexes that include subunits encoded by organelle and nuclear genomes. In animal cells, compensatory evolution between mitochondrial and nuclear-encoded subunits was identified and the high mitochondrial mutation rates were hypothesized to drive compensatory evolution in nuclear genomes. In plant cells, compensatory evolution between plastid and nucleus has rarely been investigated in a phylogenetic framework. To investigate plastid–nuclear coevolution, we focused on plastid ribosomal protein genes that are encoded by plastid and nuclear genomes from 27 Geraniales species. Substitution rates were compared for five sets of genes representing plastid- and nuclear-encoded ribosomal subunit proteins targeted to the cytosol or the plastid as well as nonribosomal protein controls. We found that nonsynonymous substitution rates (dN) and the ratios of nonsynonymous to synonymous substitution rates (ω) were accelerated in both plastid- (CpRP) and nuclear-encoded subunits (NuCpRP) of the plastid ribosome relative to control sequences. Our analyses revealed strong signals of cytonuclear coevolution between plastid- and nuclear-encoded subunits, in which nonsynonymous substitutions in CpRP and NuCpRP tend to occur along the same branches in the Geraniaceae phylogeny. This coevolution pattern cannot be explained by physical interaction between amino acid residues. The forces driving accelerated coevolution varied with cellular compartment of the sequence. Increased ω in CpRP was mainly due to intensified positive selection whereas increased ω in NuCpRP was caused by relaxed purifying selection. In addition, the many indels identified in plastid rRNA genes in Geraniaceae may have contributed to changes in plastid subunits.
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Affiliation(s)
- Mao-Lun Weng
- Department of Biology, University of Maryland, College Park Department of Integrative Biology, University of Texas, Austin
| | | | - Robert K Jansen
- Department of Integrative Biology, University of Texas, Austin Department of Biological Sciences, Biotechnology Research Group, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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40
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Kowar T, Zakrzewski F, Macas J, Kobližková A, Viehoever P, Weisshaar B, Schmidt T. Repeat Composition of CenH3-chromatin and H3K9me2-marked heterochromatin in Sugar Beet (Beta vulgaris). BMC PLANT BIOLOGY 2016; 16:120. [PMID: 27230558 PMCID: PMC4881148 DOI: 10.1186/s12870-016-0805-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 05/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world's annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the recently published genome sequence, due to the fact that regions with high repetitive DNA contents (e.g. satellite DNAs) are only partially included. Therefore, to fill these gaps and to gain information about the repeat composition of centromeres and heterochromatic regions, we performed chromatin immunoprecipitation followed by sequencing (ChIP-Seq) using antibodies against the centromere-specific histone H3 variant of sugar beet (CenH3) and the heterochromatic mark of dimethylated lysine 9 of histone H3 (H3K9me2). RESULTS ChIP-Seq analysis revealed that active centromeres containing CenH3 consist of the satellite pBV and the Ty3-gypsy retrotransposon Beetle7, while heterochromatin marked by H3K9me2 exhibits heterogeneity in repeat composition. H3K9me2 was mainly associated with the satellite family pEV, the Ty1-copia retrotransposon family Cotzilla and the DNA transposon superfamily of the En/Spm type. In members of the section Beta within the genus Beta, immunostaining using the CenH3 antibody was successful, indicating that orthologous CenH3 proteins are present in closely related species within this section. CONCLUSIONS The identification of repetitive genome portions by ChIP-Seq experiments complemented the sugar beet reference sequence by providing insights into the repeat composition of poorly characterized CenH3-chromatin and H3K9me2-heterochromatin. Therefore, our work provides the basis for future research and application concerning the sugar beet centromere and repeat-rich heterochromatic regions characterized by the presence of H3K9me2.
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Affiliation(s)
- Teresa Kowar
- Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany
| | - Falk Zakrzewski
- Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, Česke Budějovice, CZ-37005, Czech Republic
| | - Andrea Kobližková
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, Česke Budějovice, CZ-37005, Czech Republic
| | - Prisca Viehoever
- CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstr. 25, Bielefeld, D-33615, Germany
| | - Bernd Weisshaar
- CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstr. 25, Bielefeld, D-33615, Germany.
| | - Thomas Schmidt
- Department of Plant Cell and Molecular Biology, TU Dresden, Dresden, D-01062, Germany
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41
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Mohan V, Pandey A, Sreelakshmi Y, Sharma R. Neofunctionalization of Chromoplast Specific Lycopene Beta Cyclase Gene (CYC-B) in Tomato Clade. PLoS One 2016; 11:e0153333. [PMID: 27070417 PMCID: PMC4829152 DOI: 10.1371/journal.pone.0153333] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Accepted: 03/28/2016] [Indexed: 11/18/2022] Open
Abstract
The ancestor of tomato underwent whole genome triplication ca. 71 Myr ago followed by widespread gene loss. However, few of the triplicated genes are retained in modern day tomato including lycopene beta cyclase that mediates conversion of lycopene to β-carotene. The fruit specific β-carotene formation is mediated by a chromoplast-specific paralog of lycopene beta cyclase (CYC-B) gene. Presently limited information is available about how the variations in CYC-B gene contributed to its neofunctionalization. CYC-B gene in tomato clade contained several SNPs and In-Dels in the coding sequence (33 haplotypes) and promoter region (44 haplotypes). The CYC-B gene coding sequence in tomato appeared to undergo purifying selection. The transit peptide sequence of CYC-B protein was predicted to have a stronger plastid targeting signal than its chloroplast specific paralog indicating a possible neofunctionalization. In promoter of two Bog (Beta old gold) mutants, a NUPT (nuclear plastid) DNA fragment of 256 bp, likely derived from a S. chilense accession, was present. In transient expression assay, this promoter was more efficient than the "Beta type" promoter. CARGATCONSENSUS box sequences are required for the binding of the MADS-box regulatory protein RIPENING INHIBITOR (RIN). The loss of CARGATCONSENSUS box sequence from CYC-B promoter in tomato may be related to attenuation of its efficiency to promote higher accumulation of β-carotene than lycopene during fruit ripening.
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Affiliation(s)
- Vijee Mohan
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Arun Pandey
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
- * E-mail:
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42
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Lam VKY, Merckx VSFT, Graham SW. A few-gene plastid phylogenetic framework for mycoheterotrophic monocots. AMERICAN JOURNAL OF BOTANY 2016; 103:692-708. [PMID: 27056932 DOI: 10.3732/ajb.1500412] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 02/08/2016] [Indexed: 05/03/2023]
Abstract
PREMISE OF THE STUDY Few-gene studies with broad taxon sampling have provided major insights into phylogeny and underpin plant classification. However, they have typically excluded heterotrophic plants because of loss, pseudogenization, or rapid evolution of plastid genes. Here we performed a phylogenetic survey of three commonly retained plastid genes to assess their utility in placing mycoheterotrophs. METHODS We surveyed accD, clpP, and matK for 34 taxa from seven monocot families that include full mycoheterotrophs and a broad sampling of photosynthetic taxa. After screening for weak contaminants, we conducted phylogenetic analyses and characterized among-lineage rate variation. KEY RESULTS Likelihood analyses strongly supported local placements of fully mycoheterotrophic taxa for Corsiaceae, Iridaceae, Orchidaceae, and Petrosaviaceae, in positions consistent with other studies. Depression of likelihood bootstrap support values near mycoheterotrophic clades was alleviated when each mycoheterotrophic family was considered separately. Triuridaceae (Sciaphila) monophyly was recovered in a partitioned likelihood analysis, and the family then placed as sister to Cyclanthaceae-Pandanaceae. Burmanniaceae placed in Dioscoreales with weak to strong support depending on analysis details, and we inferred a plastid-based phylogeny for the family. Thismiaceae species may retain a plastid genome, based on accD retention. The inferred position of Thismiaceae is unstable, but was close to Taccaceae (Dioscoreales) in some analyses. CONCLUSIONS Long branches/elevated substitution rates, missing genes, and occasional contaminants are challenges for plastid-based phylogenetic inference with full mycoheterotrophs. However, most mycoheterotrophs can be readily integrated into the broad picture of plant phylogeny using several plastid genes and broad taxonomic sampling.
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Affiliation(s)
- Vivienne K Y Lam
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | | | - Sean W Graham
- Department of Botany, 6270 University Boulevard, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada UBC Botanical Garden & Centre for Plant Research, 6804 Marine Drive SW, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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Kim K, Lee SC, Lee J, Yu Y, Yang K, Choi BS, Koh HJ, Waminal NE, Choi HI, Kim NH, Jang W, Park HS, Lee J, Lee HO, Joh HJ, Lee HJ, Park JY, Perumal S, Jayakodi M, Lee YS, Kim B, Copetti D, Kim S, Kim S, Lim KB, Kim YD, Lee J, Cho KS, Park BS, Wing RA, Yang TJ. Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species. Sci Rep 2015; 5:15655. [PMID: 26506948 PMCID: PMC4623524 DOI: 10.1038/srep15655] [Citation(s) in RCA: 138] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/30/2015] [Indexed: 12/15/2022] Open
Abstract
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.
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Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Junki Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yeisoo Yu
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea.,Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Kiwoung Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Department of Horticulture, Sunchon National University, Suncheon, 540-950, Republic of Korea
| | - Beom-Soon Choi
- Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Hee-Jong Koh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nomar Espinosa Waminal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hong-Il Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Nam-Hoon Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Woojong Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun-Seung Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jonghoon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyun Oh Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.,Phyzen Genome Institute, 501-1, Gwanak Century Tower, Kwanak-gu, Seoul, 151-836, Republic of Korea
| | - Ho Jun Joh
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Hyeon Ju Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sampath Perumal
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Yun Sun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Backki Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Soonok Kim
- Biological and Genetic Resources Assessment Division, National Institute of Biological Resources, Incheon, 404-170, Republic of Korea
| | - Sunggil Kim
- Department of Plant Biotechnology, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Republic of Korea
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu, 702-701, Republic of Korea
| | - Young-Dong Kim
- Department of Life Science, Hallym University, Chuncheon, Kangwon-do, 200-702, Republic of Korea
| | - Jungho Lee
- Green Plant Institute, #2-202 Biovalley, 89 Seoho-ro, Kwonseon-gu, Suwon, Republic of Korea
| | - Kwang-Su Cho
- Highland Agriculture Research Institute, National Institute of Crop Science, Rural Development Administration, Pyeongchang-gun, Kangwon-do, 232-955, Republic of Korea
| | - Beom-Seok Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju, 560-500, Republic of Korea
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
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Garaycochea S, Speranza P, Alvarez-Valin F. A strategy to recover a high-quality, complete plastid sequence from low-coverage whole-genome sequencing. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1500022. [PMID: 26504677 PMCID: PMC4610308 DOI: 10.3732/apps.1500022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 08/28/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY We developed a bioinformatic strategy to recover and assemble a chloroplast genome using data derived from low-coverage 454 GS FLX/Roche whole-genome sequencing. METHODS A comparative genomics approach was applied to obtain the complete chloroplast genome from a weedy biotype of rice from Uruguay. We also applied appropriate filters to discriminate reads representing novel DNA transfer events between the chloroplast and nuclear genomes. RESULTS From a set of 295,159 reads (96 Mb data), we assembled the chloroplast genome into two contigs. This weedy rice was classified based on 23 polymorphic regions identified by comparison with reference chloroplast genomes. We detected recent and past events of genetic material transfer between the chloroplast and nuclear genomes and estimated their occurrence frequency. DISCUSSION We obtained a high-quality complete chloroplast genome sequence from low-coverage sequencing data. Intergenome DNA transfer appears to be more frequent than previously thought.
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Affiliation(s)
- Silvia Garaycochea
- Unidad de Biotecnología, Instituto Nacional de Investigación Agropecuaria (INIA), Rincón del Colorado, Canelones, Uruguay
| | - Pablo Speranza
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Fernando Alvarez-Valin
- Sección Biomatemática, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Cytogenetic and Sequence Analyses of Mitochondrial DNA Insertions in Nuclear Chromosomes of Maize. G3-GENES GENOMES GENETICS 2015; 5:2229-39. [PMID: 26333837 PMCID: PMC4632043 DOI: 10.1534/g3.115.020677] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The transfer of mitochondrial DNA (mtDNA) into nuclear genomes is a regularly occurring process that has been observed in many species. Few studies, however, have focused on the variation of nuclear-mtDNA sequences (NUMTs) within a species. This study examined mtDNA insertions within chromosomes of a diverse set of Zea mays ssp. mays (maize) inbred lines by the use of fluorescence in situ hybridization. A relatively large NUMT on the long arm of chromosome 9 (9L) was identified at approximately the same position in four inbred lines (B73, M825, HP301, and Oh7B). Further examination of the similarly positioned 9L NUMT in two lines, B73 and M825, indicated that the large size of these sites is due to the presence of a majority of the mitochondrial genome; however, only portions of this NUMT (~252 kb total) were found in the publically available B73 nuclear sequence for chromosome 9. Fiber-fluorescence in situ hybridization analysis estimated the size of the B73 9L NUMT to be ~1.8 Mb and revealed that the NUMT is methylated. Two regions of mtDNA (2.4 kb and 3.3 kb) within the 9L NUMT are not present in the B73 mitochondrial NB genome; however, these 2.4-kb and 3.3-kb segments are present in other Zea mitochondrial genomes, including that of Zea mays ssp. parviglumis, a progenitor of domesticated maize.
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Wolf PG, Sessa EB, Marchant DB, Li FW, Rothfels CJ, Sigel EM, Gitzendanner MA, Visger CJ, Banks JA, Soltis DE, Soltis PS, Pryer KM, Der JP. An Exploration into Fern Genome Space. Genome Biol Evol 2015; 7:2533-44. [PMID: 26311176 PMCID: PMC4607520 DOI: 10.1093/gbe/evv163] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Ferns are one of the few remaining major clades of land plants for which a complete genome sequence is lacking. Knowledge of genome space in ferns will enable broad-scale comparative analyses of land plant genes and genomes, provide insights into genome evolution across green plants, and shed light on genetic and genomic features that characterize ferns, such as their high chromosome numbers and large genome sizes. As part of an initial exploration into fern genome space, we used a whole genome shotgun sequencing approach to obtain low-density coverage (∼0.4X to 2X) for six fern species from the Polypodiales (Ceratopteris, Pteridium, Polypodium, Cystopteris), Cyatheales (Plagiogyria), and Gleicheniales (Dipteris). We explore these data to characterize the proportion of the nuclear genome represented by repetitive sequences (including DNA transposons, retrotransposons, ribosomal DNA, and simple repeats) and protein-coding genes, and to extract chloroplast and mitochondrial genome sequences. Such initial sweeps of fern genomes can provide information useful for selecting a promising candidate fern species for whole genome sequencing. We also describe variation of genomic traits across our sample and highlight some differences and similarities in repeat structure between ferns and seed plants.
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Affiliation(s)
- Paul G Wolf
- Ecology Center and Department of Biology, Utah State University
| | - Emily B Sessa
- Department of Biology, University of Florida Genetics Institute, University of Florida
| | - Daniel Blaine Marchant
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Carl J Rothfels
- University Herbarium and Department of Integrative Biology, University of California, Berkeley
| | - Erin M Sigel
- Department of Biology, Duke University Present address: Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia
| | - Matthew A Gitzendanner
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Clayton J Visger
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Jo Ann Banks
- Department of Botany and Plant Pathology, Purdue University
| | - Douglas E Soltis
- Department of Biology, University of Florida Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | - Pamela S Soltis
- Genetics Institute, University of Florida Florida Museum of Natural History, University of Florida
| | | | - Joshua P Der
- Department of Biological Science, California State University, Fullerton
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Suzuki K, Moriguchi K, Yamamoto S. Horizontal DNA transfer from bacteria to eukaryotes and a lesson from experimental transfers. Res Microbiol 2015; 166:753-63. [PMID: 26291765 DOI: 10.1016/j.resmic.2015.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 08/04/2015] [Accepted: 08/05/2015] [Indexed: 11/15/2022]
Abstract
Horizontal gene transfer (HGT) is widespread among bacteria and plays a key role in genome dynamics. HGT is much less common in eukaryotes, but is being reported with increasing frequency in eukaryotes. The mechanism as to how eukaryotes acquired genes from distantly related organisms remains obscure yet. This paper cites examples of bacteria-derived genes found in eukaryotic organisms, and then describes experimental DNA transports to eukaryotes by bacterial type 4 secretion systems in optimized conditions. The mechanisms of the latter are efficient, quite reproducible in vitro and predictable, and thereby would provide insight into natural HGT and to the development of new research tools.
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48
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Plastid DNA insertions in plant nuclear genomes: the sites, abundance and ages, and a predicted promoter analysis. Funct Integr Genomics 2014; 15:131-9. [DOI: 10.1007/s10142-014-0422-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 09/19/2014] [Accepted: 11/24/2014] [Indexed: 10/24/2022]
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49
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Vanburen R, Ming R. Dynamic transposable element accumulation in the nascent sex chromosomes of papaya. Mob Genet Elements 2014; 3:e23462. [PMID: 23734293 PMCID: PMC3661139 DOI: 10.4161/mge.23462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 01/02/2013] [Indexed: 02/03/2023] Open
Abstract
From their inception, Y chromosomes in plants and animals are subjected to the powerful effects of Müller's ratchet, a process spurred by suppression of recombination that results in a rapid accumulation of mutations and repetitive elements. These mutations eventually lead to gene loss and degeneration of the Y chromosome. Y chromosomes in mammals are ancient, whereas most sex chromosomes in plants and many in insects and fish evolved recently. Sex type in papaya is controlled by a pair of nascent sex chromosomes that evolved around 7 million years ago. The papaya X and Yh were recently sequenced, providing valuable insight into the early stages of sex chromosome evolution. Here we discuss the fruits of this work with a focus on the repeat accumulation, gene trafficking and promiscuous DNA sequences found in the slowly degenerating Yh chromosome of papaya.
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Affiliation(s)
- Robert Vanburen
- Department of Plant Biology; University of Illinois at Urbana-Champaign; Urbana, IL USA
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50
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Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 2014; 345:1181-4. [PMID: 25190796 DOI: 10.1126/science.1255274] [Citation(s) in RCA: 339] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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Affiliation(s)
- France Denoeud
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France
| | - Lorenzo Carretero-Paulet
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA
| | - Alexis Dereeper
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Gaëtan Droc
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Romain Guyot
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Marco Pietrella
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Chunfang Zheng
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Adriana Alberti
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - François Anthony
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Giuseppe Aprea
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Pascal Bento
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Maria Bernard
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Stéphanie Bocs
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Claudine Campa
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alberto Cenci
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France. Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Marie-Christine Combes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France
| | - Dominique Crouzillat
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | | | - Fabien De Bellis
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Stéphane Dussert
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Olivier Garsmeur
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Thomas Gayraud
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Valentin Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Katharina Jahn
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada. Center for Biotechnology, Universität Bielefeld, Universitätsstraße 27, D-33615 Bielefeld, Germany. AG Genominformatik, Technische Fakultät, Universität Bielefeld, 33594 Bielefeld, Germany
| | - Véronique Jamilloux
- Institut National de la Recherche Agronomique (INRA), Unité de Recherches en Génomique-Info (UR INRA 1164), Centre de Recherche de Versailles, 78026 Versailles Cedex, France
| | - Thierry Joët
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Tianying Lan
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA. Department of Biology, Chongqing University of Science and Technology, 4000042 Chongqing, China
| | - Julie Leclercq
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Maud Lepelley
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Thierry Leroy
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Lei-Ting Li
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Pablo Librado
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | | | - Adriana Muñoz
- Department of Mathematics, University of Maryland, Mathematics Building 084, University of Maryland, College Park, MD 20742, USA. School of Electrical Engineering and Computer Science, University of Ottawa, 800 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Benjamin Noel
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | | | - Valérie Poncet
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - David Pot
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Priyono
- Indonesian Coffee and Cocoa Institute, Jember, East Java, Indonesia
| | - Michel Rigoreau
- Nestlé Research and Development Centre, 101 Avenue Gustave Eiffel, Notre-Dame-d'Oé, BP 49716, 37097 Tours Cedex 2, France
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Diagonal 643, Barcelona 08028, Spain
| | - Christine Tranchant-Dubreuil
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Robert VanBuren
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Qiong Zhang
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alan C Andrade
- Laboratório de Genética Molecular, Núcleo de Biotecnologia (NTBio), Embrapa Recursos Genéticos e Biotecnologia, Final Av. W/5 Norte, Parque Estação Biológia, Brasília-DF 70770-917, Brazil
| | - Xavier Argout
- CIRAD, UMR Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales (AGAP), F-34398 Montpellier, France
| | - Benoît Bertrand
- CIRAD, UMR RPB (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Alexandre de Kochko
- IRD, UMR Diversité Adaptation et Développement des Plantes (CIRAD, IRD, UM2), BP 64501, 34394 Montpellier Cedex 5, France
| | - Giorgio Graziosi
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, 34127 Trieste, Italy. DNA Analytica Srl, Via Licio Giorgieri 5, 34127 Trieste, Italy
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia 4072, Australia
| | - Jayarama
- Central Coffee Research Institute, Coffee Board, Coffee Research Station (Post) - 577 117 Chikmagalur District, Karnataka State, India
| | - Ray Ming
- Department of Plant Biology, 148 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Chifumi Nagai
- Hawaii Agriculture Research Center, Post Office Box 100, Kunia, HI 96759-0100, USA
| | - Steve Rounsley
- BIO5 Institute, University of Arizona, 1657 Helen Street, Tucson, AZ 85721, USA
| | - David Sankoff
- Department of Mathematics and Statistics, University of Ottawa, 585 King Edward Avenue, Ottawa, Ontario K1N 6N5, Canada
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Roma, Italy
| | - Victor A Albert
- Department of Biological Sciences, 109 Cooke Hall, University at Buffalo (State University of New York), Buffalo, NY 14260, USA.
| | - Patrick Wincker
- Commissariat à l'Energie Atomique, Genoscope, Institut de Génomique, BP5706, 91057 Evry, France. CNRS, UMR 8030, CP5706, Evry, France. Université d'Evry, UMR 8030, CP5706, Evry, France.
| | - Philippe Lashermes
- Institut de Recherche pour le Développement (IRD), UMR Résistance des Plantes aux Bioagresseurs (RPB) [Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), IRD, UM2)], BP 64501, 34394 Montpellier Cedex 5, France.
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