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Park S, Park S. Intrageneric structural variation in organelle genomes from the genus Dystaenia (Apiaceae): genome rearrangement and mitochondrion-to-plastid DNA transfer. FRONTIERS IN PLANT SCIENCE 2023; 14:1283292. [PMID: 38116150 PMCID: PMC10728875 DOI: 10.3389/fpls.2023.1283292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Introduction During plant evolution, intracellular DNA transfer (IDT) occurs not only from organelles to the nucleus but also between organelles. To further comprehend these events, both organelle genomes and transcriptomes are needed. Methods In this study, we constructed organelle genomes and transcriptomes for two Dystaenia species and described their dynamic IDTs between their nuclear and mitochondrial genomes, or plastid and mitochondrial genomes (plastome and mitogenome). Results and Discussion We identified the putative functional transfers of the mitochondrial genes 5' rpl2, rps10, rps14, rps19, and sdh3 to the nucleus in both Dystaenia species and detected two transcripts for the rpl2 and sdh3 genes. Additional transcriptomes from the Apicaceae species also provided evidence for the transfers and duplications of these mitochondrial genes, showing lineage-specific patterns. Intrageneric variations of the IDT were found between the Dystaenia organelle genomes. Recurrent plastid-to-mitochondrion DNA transfer events were only identified in the D. takeshimana mitogenome, and a pair of mitochondrial DNAs of plastid origin (MIPTs) may generate minor alternative isoforms. We only found a mitochondrion-to-plastid DNA transfer event in the D. ibukiensis plastome. This event may be linked to inverted repeat boundary shifts in its plastome. We inferred that the insertion region involved an MIPT that had already acquired a plastid sequence in its mitogenome via IDT. We propose that the MIPT acts as a homologous region pairing between the donor and recipient sequences. Our results provide insight into the evolution of organelle genomes across the family Apiaceae.
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Affiliation(s)
- Seongjun Park
- Institute of Natural Science, Yeungnam University, Gyeongsan, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Republic of Korea
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Zhou S, Wei N, Jost M, Wanke S, Rees M, Liu Y, Zhou R. The Mitochondrial Genome of the Holoparasitic Plant Thonningia sanguinea Provides Insights into the Evolution of the Multichromosomal Structure. Genome Biol Evol 2023; 15:evad155. [PMID: 37603455 PMCID: PMC10476698 DOI: 10.1093/gbe/evad155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/23/2023] Open
Abstract
Multichromosomal mitochondrial genome (mitogenome) structures have repeatedly evolved in many lineages of angiosperms. However, the underlying mechanism remains unclear. The mitogenomes of three genera of Balanophoraceae, namely Lophophytum, Ombrophytum, and Rhopalocnemis, have already been sequenced and assembled, all showing a highly multichromosomal structure, albeit with different genome and chromosome sizes. It is expected that characterization of additional lineages of this family may expand the knowledge of mitogenome diversity and provide insights into the evolution of the plant mitogenome structure and size. Here, we assembled and characterized the mitogenome of Thonningia sanguinea, which, together with Balanophora, forms a clade sister to the clade comprising Lophophytum, Ombrophytum, and Rhopalocnemis. The mitogenome of T. sanguinea possesses a multichromosomal structure of 18 circular chromosomes of 8.7-19.2 kb, with a total size of 246,247 bp. There are very limited shared regions and poor chromosomal correspondence between T. sanguinea and other Balanophoraceae species, suggesting frequent rearrangements and rapid sequence turnover. Numerous medium- and small-sized repeats were identified in the T. sanguinea mitogenome; however, no repeat-mediated recombination was detected, which was verified by Illumina reads mapping and PCR experiments. Intraspecific mitogenome variations in T. sanguinea are mostly insertions and deletions, some of which can lead to degradation of perfect repeats in one or two accessions. Based on the mitogenome features of T. sanguinea, we propose a mechanism to explain the evolution of a multichromosomal mitogenome from a master circle, which involves mutation in organellar DNA replication, recombination and repair genes, decrease of recombination, and repeat degradation.
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Affiliation(s)
- Shuaixi Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Neng Wei
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Matthias Jost
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Stefan Wanke
- Institut für Botanik, Technische Universität Dresden, Dresden, Germany
| | - Mathew Rees
- School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden, Edinburgh, United Kingdom
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-Sen University, Guangzhou, Guangdong, China
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Lee Y, Cho CH, Noh C, Yang JH, Park SI, Lee YM, West JA, Bhattacharya D, Jo K, Yoon HS. Origin of minicircular mitochondrial genomes in red algae. Nat Commun 2023; 14:3363. [PMID: 37291154 PMCID: PMC10250338 DOI: 10.1038/s41467-023-39084-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
Eukaryotic organelle genomes are generally of conserved size and gene content within phylogenetic groups. However, significant variation in genome structure may occur. Here, we report that the Stylonematophyceae red algae contain multipartite circular mitochondrial genomes (i.e., minicircles) which encode one or two genes bounded by a specific cassette and a conserved constant region. These minicircles are visualized using fluorescence microscope and scanning electron microscope, proving the circularity. Mitochondrial gene sets are reduced in these highly divergent mitogenomes. Newly generated chromosome-level nuclear genome assembly of Rhodosorus marinus reveals that most mitochondrial ribosomal subunit genes are transferred to the nuclear genome. Hetero-concatemers that resulted from recombination between minicircles and unique gene inventory that is responsible for mitochondrial genome stability may explain how the transition from typical mitochondrial genome to minicircles occurs. Our results offer inspiration on minicircular organelle genome formation and highlight an extreme case of mitochondrial gene inventory reduction.
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Affiliation(s)
- Yongsung Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chung Hyun Cho
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Chanyoung Noh
- Department of Chemistry, Sogang University, Seoul, 04107, Korea
| | - Ji Hyun Yang
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Seung In Park
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Yu Min Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - John A West
- School of Biosciences 2, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, 08901, USA
| | - Kyubong Jo
- Department of Chemistry, Sogang University, Seoul, 04107, Korea.
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
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Møller IM, Rasmusson AG, Van Aken O. Plant mitochondria - past, present and future. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:912-959. [PMID: 34528296 DOI: 10.1111/tpj.15495] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 06/13/2023]
Abstract
The study of plant mitochondria started in earnest around 1950 with the first isolations of mitochondria from animal and plant tissues. The first 35 years were spent establishing the basic properties of plant mitochondria and plant respiration using biochemical and physiological approaches. A number of unique properties (compared to mammalian mitochondria) were observed: (i) the ability to oxidize malate, glycine and cytosolic NAD(P)H at high rates; (ii) the partial insensitivity to rotenone, which turned out to be due to the presence of a second NADH dehydrogenase on the inner surface of the inner mitochondrial membrane in addition to the classical Complex I NADH dehydrogenase; and (iii) the partial insensitivity to cyanide, which turned out to be due to an alternative oxidase, which is also located on the inner surface of the inner mitochondrial membrane, in addition to the classical Complex IV, cytochrome oxidase. With the appearance of molecular biology methods around 1985, followed by genomics, further unique properties were discovered: (iv) plant mitochondrial DNA (mtDNA) is 10-600 times larger than the mammalian mtDNA, yet it only contains approximately 50% more genes; (v) plant mtDNA has kept the standard genetic code, and it has a low divergence rate with respect to point mutations, but a high recombinatorial activity; (vi) mitochondrial mRNA maturation includes a uniquely complex set of activities for processing, splicing and editing (at hundreds of sites); (vii) recombination in mtDNA creates novel reading frames that can produce male sterility; and (viii) plant mitochondria have a large proteome with 2000-3000 different proteins containing many unique proteins such as 200-300 pentatricopeptide repeat proteins. We describe the present and fairly detailed picture of the structure and function of plant mitochondria and how the unique properties make their metabolism more flexible allowing them to be involved in many diverse processes in the plant cell, such as photosynthesis, photorespiration, CAM and C4 metabolism, heat production, temperature control, stress resistance mechanisms, programmed cell death and genomic evolution. However, it is still a challenge to understand how the regulation of metabolism and mtDNA expression works at the cellular level and how retrograde signaling from the mitochondria coordinates all those processes.
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Affiliation(s)
- Ian Max Møller
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, DK-4200, Slagelse, Denmark
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5
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Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence. Life (Basel) 2021; 11:life11070663. [PMID: 34357035 PMCID: PMC8303319 DOI: 10.3390/life11070663] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/11/2022] Open
Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
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Plant Mitochondria are a Riddle Wrapped in a Mystery Inside an Enigma. J Mol Evol 2021; 89:151-156. [PMID: 33486550 DOI: 10.1007/s00239-020-09980-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/03/2020] [Indexed: 12/23/2022]
Abstract
A fundamental paradox motivates the study of plant mitochondrial genomics: the mutation rate is very low (lower than in the nucleus) but the rearrangement rate is high. A landmark paper published in Journal of Molecular Evolution in 1988 established these facts and revealed the paradox. Jeffrey Palmer and Laura Herbon did a prodigious amount of work in the pre-genome sequencing era to identify both the high frequency of rearrangements between closely related species, and the low frequency of mutations, observations that have now been confirmed many times by sequencing. This paper was also the first to use molecular data on rearrangements as a phylogenetic trait to build a parsimonious tree. The work was a technical tour-de-force, its findings are still at the heart of plant mitochondrial genomics, and the underlying molecular mechanisms that produce this paradox are still not completely understood.
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7
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Thielen PM, Pendleton AL, Player RA, Bowden KV, Lawton TJ, Wisecaver JH. Reference Genome for the Highly Transformable Setaria viridis ME034V. G3 (BETHESDA, MD.) 2020; 10:3467-3478. [PMID: 32694197 PMCID: PMC7534418 DOI: 10.1534/g3.120.401345] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.
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Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Player
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Kenneth V Bowden
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Thomas J Lawton
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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8
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Mader M, Schroeder H, Schott T, Schöning-Stierand K, Leite Montalvão AP, Liesebach H, Liesebach M, Fussi B, Kersten B. Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1274. [PMID: 32992588 PMCID: PMC7650814 DOI: 10.3390/plants9101274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/16/2022]
Abstract
European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.
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Affiliation(s)
- Malte Mader
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Hilke Schroeder
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Thomas Schott
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Katrin Schöning-Stierand
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
- Center for Bioinformatics, Universität Hamburg, 20146 Hamburg, Germany
| | - Ana Paula Leite Montalvão
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Heike Liesebach
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Mirko Liesebach
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
| | - Barbara Fussi
- Bavarian Office for Forest Genetics, 83317 Teisendorf, Germany;
| | - Birgit Kersten
- Thünen Institute of Forest Genetics, D-22927 Grosshansdorf, Germany; (M.M.); (H.S.); (T.S.); (K.S.-S.); (A.P.L.M.); (H.L.); (M.L.)
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9
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Mower JP. Variation in protein gene and intron content among land plant mitogenomes. Mitochondrion 2020; 53:203-213. [PMID: 32535166 DOI: 10.1016/j.mito.2020.06.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/24/2020] [Accepted: 06/08/2020] [Indexed: 12/20/2022]
Abstract
The functional content of the mitochondrial genome (mitogenome) is highly diverse across eukaryotes. Among land plants, our understanding of the variation in mitochondrial gene and intron content is improving from concerted efforts to densely sample mitogenomes from diverse land plants. Here I review the current state of knowledge regarding the diversity in content of protein genes and introns in the mitogenomes of all major land plant lineages. Mitochondrial protein gene content is largely conserved among mosses and liverworts, but it varies substantially among and within other land plant lineages due to convergent losses of genes encoding ribosomal proteins and, to a lesser extent, genes for proteins involved in cytochrome c maturation and oxidative phosphorylation. Mitochondrial intron content is fairly stable within each major land plant lineage, but highly variable among lineages, resulting from occasional gains and many convergent losses over time. Trans-splicing has evolved dozens of times in various vascular plant lineages, particularly those with relatively higher rates of mitogenomic rearrangement. Across eukaryotes, mitochondrial protein gene and intron content has been shaped massive convergent evolution.
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Affiliation(s)
- Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE.
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10
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Gonçalves DJP, Simpson BB, Ortiz EM, Shimizu GH, Jansen RK. Incongruence between gene trees and species trees and phylogenetic signal variation in plastid genes. Mol Phylogenet Evol 2019; 138:219-232. [PMID: 31146023 DOI: 10.1016/j.ympev.2019.05.022] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 05/20/2019] [Accepted: 05/21/2019] [Indexed: 10/26/2022]
Abstract
The current classification of angiosperms is based primarily on concatenated plastid markers and maximum likelihood (ML) inference. This approach has been justified by the assumption that plastid DNA (ptDNA) is inherited as a single locus and that its individual genes produce congruent trees. However, structural and functional characteristics of ptDNA suggest that plastid genes may not evolve as a single locus and are experiencing different evolutionary forces. To examine this idea, we produced new complete plastid genome (plastome) sequences of 27 species and combined these data with publicly available sequences to produce a final dataset that includes 78 plastid genes for 89 species of rosids and five outgroups. We used four data matrices (i.e., gene, exon, codon-aligned, and amino acid) to infer species and gene trees using ML and multispecies coalescent (MSC) methods. Rosids include about one third of all angiosperms and their two major clades, fabids and malvids, were recovered in almost all analyses. However, we detected incongruence between species trees inferred with different matrices and methods and previously published plastid and nuclear phylogenies. We visualized and tested the significance of incongruence between gene trees and species trees. We then measured the distribution of phylogenetic signal across sites and genes supporting alternative placements of five controversial nodes at different taxonomic levels. Gene trees inferred with plastid data often disagree with species trees inferred using both ML (with unpartitioned or partitioned data) and MSC. Species trees inferred with both methods produced alternative topologies for a few taxa. Our results show that, in a phylogenetic context, plastid protein-coding genes may not be fully linked and behaving as a single locus. Furthermore, concatenated matrices may produce highly supported phylogenies that are discordant with individual gene trees. We also show that phylogenies inferred with MSC are accurate. We therefore emphasize the importance of considering variation in phylogenetic signal across plastid genes and the exploration of plastome data to increase accuracy of estimating relationships. We also support the use of MSC with plastome matrices in future phylogenomic investigations.
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Affiliation(s)
- Deise J P Gonçalves
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA.
| | - Beryl B Simpson
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA
| | - Edgardo M Ortiz
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Department of Ecology & Ecosystem Management, Plant Biodiversity Research, Technical University of Munich, Emil-Ramann Strasse 2, Freising D-85354, Germany
| | - Gustavo H Shimizu
- Department of Plant Biology, University of Campinas, 13083-970 Campinas, SP, Brazil
| | - Robert K Jansen
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway #C0930, Austin, TX 78713, USA; Genomics and Biotechnology Research Group, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
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11
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Sanitá Lima M, Smith DR. Pervasive Transcription of Mitochondrial, Plastid, and Nucleomorph Genomes across Diverse Plastid-Bearing Species. Genome Biol Evol 2018; 9:2650-2657. [PMID: 29048528 PMCID: PMC5737562 DOI: 10.1093/gbe/evx207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2017] [Indexed: 02/06/2023] Open
Abstract
Organelle genomes exhibit remarkable diversity in content, structure, and size, and in their modes of gene expression, which are governed by both organelle- and nuclear-encoded machinery. Next generation sequencing (NGS) has generated unprecedented amounts of genomic and transcriptomic data, which can be used to investigate organelle genome transcription. However, most of the available eukaryotic RNA-sequencing (RNA-seq) data are used to study nuclear transcription only, even though large numbers of organelle-derived reads can typically be mined from these experiments. Here, we use publicly available RNA-seq data to assess organelle genome transcription in 59 diverse plastid-bearing species. Our RNA mapping analyses unraveled pervasive (full or near-full) transcription of mitochondrial, plastid, and nucleomorph genomes. In all cases, 85% or more of the organelle genome was recovered from the RNA data, including noncoding (intergenic and intronic) regions. These results reinforce the idea that organelles transcribe all or nearly all of their genomic material and are dependent on post-transcriptional processing of polycistronic transcripts. We explore the possibility that transcribed intergenic regions are producing functional noncoding RNAs, and that organelle genome noncoding content might provide raw material for generating regulatory RNAs.
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Affiliation(s)
- Matheus Sanitá Lima
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - David Roy Smith
- Department of Biology, University of Western Ontario, London, Ontario, Canada
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12
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Del Cortona A, Leliaert F, Bogaert KA, Turmel M, Boedeker C, Janouškovec J, Lopez-Bautista JM, Verbruggen H, Vandepoele K, De Clerck O. The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes. Curr Biol 2017; 27:3771-3782.e6. [PMID: 29199074 DOI: 10.1016/j.cub.2017.11.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/30/2017] [Accepted: 11/01/2017] [Indexed: 12/28/2022]
Abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short- and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1- to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium; Botanic Garden Meise, Nieuwelaan 38, 1860 Meise, Belgium
| | - Kenny A Bogaert
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium
| | - Monique Turmel
- Institut de Biologie Intégrative et des Systèmes, Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Pavillon Charles-Eugène-Marchand 1030, Avenue de la Médecine, Québec City, QC G1V 0A6, Canada
| | - Christian Boedeker
- School of Biological Sciences, Victoria University of Wellington, New Kirk Building, Kelburn Parade, P.O. Box 600, Wellington 6012, New Zealand
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Juan M Lopez-Bautista
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35484-0345, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Professors Walk, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, 9052 Zwijnaarde, Belgium; Bioinformatics Institute Ghent, Ghent University, Technologiepark 927, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, Krijgslaan 281, 9000 Ghent, Belgium.
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13
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Chen Z, Nie H, Wang Y, Pei H, Li S, Zhang L, Hua J. Rapid evolutionary divergence of diploid and allotetraploid Gossypium mitochondrial genomes. BMC Genomics 2017; 18:876. [PMID: 29132310 PMCID: PMC5683544 DOI: 10.1186/s12864-017-4282-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/07/2017] [Indexed: 12/31/2022] Open
Abstract
Background Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups and an allotetraploid genomic group, AD. The mitochondrial genomes supply new information to understand both the evolution process and the mechanism of cytoplasmic male sterility. Based on previously released mitochondrial genomes of G. hirsutum (AD1), G. barbadense (AD2), G. raimondii (D5) and G. arboreum (A2), together with data of six other mitochondrial genomes, to elucidate the evolution and diversity of mitochondrial genomes within Gossypium. Results Six Gossypium mitochondrial genomes, including three diploid species from D and three allotetraploid species from AD genome groups (G. thurberi D1, G. davidsonii D3-d and G. trilobum D8; G. tomentosum AD3, G. mustelinum AD4 and G. darwinii AD5), were assembled as the single circular molecules of lengths about 644 kb in diploid species and 677 kb in allotetraploid species, respectively. The genomic structures of mitochondrial in D group species were identical but differed from the mitogenome of G. arboreum (A2), as well as from the mitogenomes of five species of the AD group. There mainly existed four or six large repeats in the mitogenomes of the A + AD or D group species, respectively. These variations in repeat sequences caused the major inversions and translocations within the mitochondrial genome. The mitochondrial genome complexity in Gossypium presented eight unique segments in D group species, three specific fragments in A + AD group species and a large segment (more than 11 kb) in diploid species. These insertions or deletions were most probably generated from crossovers between repetitive or homologous regions. Unlike the highly variable genome structure, evolutionary distance of mitochondrial genes was 1/6th the frequency of that in chloroplast genes of Gossypium. RNA editing events were conserved in cotton mitochondrial genes. We confirmed two near full length of the integration of the mitochondrial genome into chromosome 1 of G. raimondii and chromosome A03 of G. hirsutum, respectively, with insertion time less than 1.03 MYA. Conclusion Ten Gossypium mitochondrial sequences highlight the insights to the evolution of cotton mitogenomes. Electronic supplementary material The online version of this article (10.1186/s12864-017-4282-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiwen Chen
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yumei Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Haili Pei
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Shuangshuang Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Lida Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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14
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Vasileiou PVS, Mourouzis I, Pantos C. Principal Aspects Regarding the Maintenance of Mammalian Mitochondrial Genome Integrity. Int J Mol Sci 2017; 18:E1821. [PMID: 28829360 PMCID: PMC5578207 DOI: 10.3390/ijms18081821] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 12/11/2022] Open
Abstract
Mitochondria have emerged as key players regarding cellular homeostasis not only due to their contribution regarding energy production through oxidative phosphorylation, but also due to their involvement in signaling, ion regulation, and programmed cell death. Indeed, current knowledge supports the notion that mitochondrial dysfunction is a hallmark in the pathogenesis of various diseases. Mitochondrial biogenesis and function require the coordinated action of two genomes: nuclear and mitochondrial. Unfortunately, both intrinsic and environmental genotoxic insults constantly threaten the integrity of nuclear as well as mitochondrial DNA. Despite the extensive research that has been made regarding nuclear genome instability, the importance of mitochondrial genome integrity has only recently begun to be elucidated. The specific architecture and repair mechanisms of mitochondrial DNA, as well as the dynamic behavior that mitochondria exert regarding fusion, fission, and autophagy participate in mitochondrial genome stability, and therefore, cell homeostasis.
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Affiliation(s)
- Panagiotis V S Vasileiou
- Department of Basic Medical Sciences, Laboratory of Histology & Embryology, School of Medicine, National and Kapodistrian University of Athens, 75 MikrasAsias Avenue, Goudi, Athens 11527, Greece.
| | - Iordanis Mourouzis
- Department of Pharmacology, School of Medicine, National and Kapodistrian University of Athens, 75 MikrasAsias Avenue, Goudi, Athens 11527, Greece.
| | - Constantinos Pantos
- Department of Pharmacology, School of Medicine, National and Kapodistrian University of Athens, 75 MikrasAsias Avenue, Goudi, Athens 11527, Greece.
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15
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Chen Z, Nie H, Grover CE, Wang Y, Li P, Wang M, Pei H, Zhao Y, Li S, Wendel JF, Hua J. Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A-genome species as cytoplasmic donor of the allotetraploid species. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:484-493. [PMID: 28008701 DOI: 10.1111/plb.12536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 12/16/2016] [Indexed: 05/20/2023]
Abstract
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5 ) and G. arboreum (A2 ) are the putative contributors to the progenitor of G. hirsutum (AD1 ), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly. Gossypium raimondii (D5 ) and G. arboreum (A2 ) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D5 ) and 687,482 bp (A2 ), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D5 and A2 mitogenomes with mitogenomes of tetraploid Gossypium species (AD1 , G. hirsutum; AD2 , G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A2 ), G. hirsutum (AD1 ) and G. barbadense (AD2 ), while eight regions were specific to G. raimondii (D5 ). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense. The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution.
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Affiliation(s)
- Z Chen
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - H Nie
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - C E Grover
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Y Wang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - P Li
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - M Wang
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - H Pei
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Y Zhao
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - S Li
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - J F Wendel
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, USA
| | - J Hua
- Laboratory of Cotton Genetics, Genomics and Breeding, College of Agronomy and Biotechnology, Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
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16
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The linear plastid chromosomes of maize: terminal sequences, structures, and implications for DNA replication. Curr Genet 2015; 62:431-42. [PMID: 26650613 DOI: 10.1007/s00294-015-0548-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Revised: 11/15/2015] [Accepted: 11/22/2015] [Indexed: 01/13/2023]
Abstract
The structure of a chromosomal DNA molecule may influence the way in which it is replicated and inherited. For decades plastid DNA (ptDNA) was believed to be circular, with breakage invoked to explain linear forms found upon extraction from the cell. Recent evidence indicates that ptDNA in vivo consists of linear molecules with discrete termini, although these ends were not characterized. We report the sequences of two terminal regions, End1 and End2, for maize (Zea mays L.) ptDNA. We describe structural features of these terminal regions and similarities found in other plant ptDNAs. The terminal sequences are within inverted repeat regions (leading to four genomic isomers) and adjacent to origins of replication. Conceptually, stem-loop structures may be formed following melting of the double-stranded DNA ends. Exonuclease digestion indicates that the ends in maize are unobstructed, but tobacco (Nicotiana tabacum L.) ends may have a 5'-protein. If the terminal structure of ptDNA molecules influences the retention of ptDNA, the unprotected molecular ends in mature leaves of maize may be more susceptible to degradation in vivo than the protected ends in tobacco. The terminal sequences and cumulative GC skew profiles are nearly identical for maize, wheat (Triticum aestivum L.) and rice (Oryza sativa L.), with less similarity among other plants. The linear structure is now confirmed for maize ptDNA and inferred for other plants and suggests a virus-like recombination-dependent replication mechanism for ptDNA. Plastid transformation vectors containing the terminal sequences may increase the chances of success in generating transplastomic cereals.
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17
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Oldenburg DJ, Bendich AJ. DNA maintenance in plastids and mitochondria of plants. FRONTIERS IN PLANT SCIENCE 2015; 6:883. [PMID: 26579143 PMCID: PMC4624840 DOI: 10.3389/fpls.2015.00883] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/05/2015] [Indexed: 05/02/2023]
Abstract
The DNA molecules in plastids and mitochondria of plants have been studied for over 40 years. Here, we review the data on the circular or linear form, replication, repair, and persistence of the organellar DNA (orgDNA) in plants. The bacterial origin of orgDNA appears to have profoundly influenced ideas about the properties of chromosomal DNA molecules in these organelles to the point of dismissing data inconsistent with ideas from the 1970s. When found at all, circular genome-sized molecules comprise a few percent of orgDNA. In cells active in orgDNA replication, most orgDNA is found as linear and branched-linear forms larger than the size of the genome, likely a consequence of a virus-like DNA replication mechanism. In contrast to the stable chromosomal DNA molecules in bacteria and the plant nucleus, the molecular integrity of orgDNA declines during leaf development at a rate that varies among plant species. This decline is attributed to degradation of damaged-but-not-repaired molecules, with a proposed repair cost-saving benefit most evident in grasses. All orgDNA maintenance activities are proposed to occur on the nucleoid tethered to organellar membranes by developmentally-regulated proteins.
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18
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Raven JA. Implications of mutation of organelle genomes for organelle function and evolution. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5639-50. [PMID: 26077836 DOI: 10.1093/jxb/erv298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Organelle genomes undergo more variation, including that resulting from damage, than eukaryotic nuclear genomes, or bacterial genomes, under the same conditions. Recent advances in characterizing the changes to genomes of chloroplasts and mitochondria of Zea mays should, when applied more widely, help our understanding of how damage to organelle genomes relates to how organelle function is maintained through the life of individuals and in succeeding generations. Understanding of the degree of variation in the changes to organelle DNA and its repair among photosynthetic organisms might help to explain the variations in the rate of nucleotide substitution among organelle genomes. Further studies of organelle DNA variation, including that due to damage and its repair might also help us to understand why the extent of DNA turnover in the organelles is so much greater than that in their bacterial (cyanobacteria for chloroplasts, proteobacteria for mitochondria) relatives with similar rates of production of DNA-damaging reactive oxygen species. Finally, from the available data, even the longest-lived organelle-encoded proteins, and the RNAs needed for their synthesis, are unlikely to maintain organelle function for much more than a week after the complete loss of organelle DNA.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK †School of Plant Biology, University of Western Australia, M048, 35 Stirling Highway, Crawley, WA 6009, Australia
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19
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Abstract
The year 2014 saw more than a thousand new mitochondrial genome sequences deposited in GenBank—an almost 15% increase from the previous year. Hundreds of peer-reviewed articles accompanied these genomes, making mitochondrial DNAs (mtDNAs) the most sequenced and reported type of eukaryotic chromosome. These mtDNA data have advanced a wide range of scientific fields, from forensics to anthropology to medicine to molecular evolution. But for many biological lineages, mtDNAs are so well sampled that newly published genomes are arguably no longer contributing significantly to the progression of science, and in some cases they are tying up valuable resources, particularly journal editors and referees. Is it time to acknowledge that as a research community we have published enough mitochondrial genome papers? Here, I address this question, exploring the history, milestones and impacts of mitochondrial genomics, the benefits and drawbacks of continuing to publish mtDNAs at a high rate and what the future may hold for such an important and popular genetic marker. I highlight groups for which mtDNAs are still poorly sampled, thus meriting further investigation, and recommend that more energy be spent characterizing aspects of mitochondrial genomes apart from the DNA sequence, such as their chromosomal and transcriptional architectures. Ultimately, one should be mindful before writing a mitochondrial genome paper. Consider perhaps sending the sequence directly to GenBank instead, and be sure to annotate it correctly before submission.
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20
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Mitochondrial and plastid genome architecture: Reoccurring themes, but significant differences at the extremes. Proc Natl Acad Sci U S A 2015; 112:10177-84. [PMID: 25814499 DOI: 10.1073/pnas.1422049112] [Citation(s) in RCA: 236] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial and plastid genomes show a wide array of architectures, varying immensely in size, structure, and content. Some organelle DNAs have even developed elaborate eccentricities, such as scrambled coding regions, nonstandard genetic codes, and convoluted modes of posttranscriptional modification and editing. Here, we compare and contrast the breadth of genomic complexity between mitochondrial and plastid chromosomes. Both organelle genomes have independently evolved many of the same features and taken on similar genomic embellishments, often within the same species or lineage. This trend is most likely because the nuclear-encoded proteins mediating these processes eventually leak from one organelle into the other, leading to a high likelihood of processes appearing in both compartments in parallel. However, the complexity and intensity of genomic embellishments are consistently more pronounced for mitochondria than for plastids, even when they are found in both compartments. We explore the evolutionary forces responsible for these patterns and argue that organelle DNA repair processes, mutation rates, and population genetic landscapes are all important factors leading to the observed convergence and divergence in organelle genome architecture.
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21
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Regulation of mitochondrial genome inheritance by autophagy and ubiquitin-proteasome system: implications for health, fitness, and fertility. BIOMED RESEARCH INTERNATIONAL 2014; 2014:981867. [PMID: 25028670 PMCID: PMC4083708 DOI: 10.1155/2014/981867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/01/2014] [Accepted: 04/07/2014] [Indexed: 01/07/2023]
Abstract
Mitochondria, the energy-generating organelles, play a role in numerous cellular functions including adenosine triphosphate (ATP) production, cellular homeostasis, and apoptosis. Maternal inheritance of mitochondria and mitochondrial DNA (mtDNA) is universally observed in humans and most animals. In general, high levels of mitochondrial heteroplasmy might contribute to a detrimental effect on fitness and disease resistance. Therefore, a disposal of the sperm-derived mitochondria inside fertilized oocytes assures normal preimplantation embryo development. Here we summarize the current research and knowledge concerning the role of autophagic pathway and ubiquitin-proteasome-dependent proteolysis in sperm mitophagy in mammals, including humans. Current data indicate that sperm mitophagy inside the fertilized oocyte could occur along multiple degradation routes converging on autophagic clearance of paternal mitochondria. The influence of assisted reproductive therapies (ART) such as intracytoplasmic sperm injection (ICSI), mitochondrial replacement (MR), and assisted fertilization of oocytes from patients of advanced reproductive age on mitochondrial function, inheritance, and fitness and for the development and health of ART babies will be of particular interest to clinical audiences. Altogether, the study of sperm mitophagy after fertilization has implications in the timing of evolution and developmental and reproductive biology and in human health, fitness, and management of mitochondrial disease.
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22
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Bendich AJ. DNA abandonment and the mechanisms of uniparental inheritance of mitochondria and chloroplasts. Chromosome Res 2014; 21:287-96. [PMID: 23681660 DOI: 10.1007/s10577-013-9349-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
For most eukaryotic organisms, the nuclear genomes of both parents are transmitted to the progeny following biparental inheritance. For mitochondria and chloroplasts, however, uniparental inheritance (UPI) is frequently observed. The maternal mode of inheritance for mitochondria in animals can be nearly absolute, suggesting an adaptive advantage for UPI. In other organisms, however, the mode of inheritance for mitochondria and chloroplasts can vary greatly even among strains of a species. Here, I review the data on the transmission of organellar DNA (orgDNA) from parent to progeny and the structure, copy number, and stability of orgDNA molecules. I propose that UPI is an incidental by-product of DNA abandonment, a process that lowers the metabolic cost of orgDNA repair.
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Affiliation(s)
- Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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23
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Ramírez-Bahena MH, Vial L, Lassalle F, Diel B, Chapulliot D, Daubin V, Nesme X, Muller D. Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid. Mol Phylogenet Evol 2014; 73:202-7. [PMID: 24440816 DOI: 10.1016/j.ympev.2014.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Revised: 01/06/2014] [Accepted: 01/07/2014] [Indexed: 12/21/2022]
Abstract
Linear chromosomes are atypical in bacteria and likely a secondary trait derived from ancestral circular molecules. Within the Rhizobiaceae family, whose genome contains at least two chromosomes, a particularity of Agrobacterium fabrum (formerly A. tumefaciens) secondary chromosome (chromid) is to be linear and hairpin-ended thanks to the TelA protelomerase. Linear topology and telA distributions within this bacterial family was screened by pulse field gel electrophoresis and PCR. In A. rubi, A. larrymoorei, Rhizobium skierniewicense, A. viscosum, Agrobacterium sp. NCPPB 1650, and every genomospecies of the biovar 1/A. tumefaciens species complex (including R. pusense, A. radiobacter, A. fabrum, R. nepotum plus seven other unnamed genomospecies), linear chromid topologies were retrieved concomitantly with telA presence, whereas the remote species A. vitis, Allorhizobium undicola, Rhizobium rhizogenes and Ensifer meliloti harbored a circular chromid as well as no telA gene. Moreover, the telA phylogeny is congruent with that of recA used as a marker gene of the Agrobacterium phylogeny. Collectively, these findings strongly suggest that single acquisition of telA by an ancestor was the founding event of a large and diverse clade characterized by the presence of a linear chromid. This clade, characterized by unusual genome architecture, appears to be a relevant candidate to serve as a basis for a possible redefinition of the controversial Agrobacterium genus. In this respect, investigating telA in sequenced genomes allows to both ascertain the place of concerned strains into Agrobacterium spp. and their actual assignation to species/genomospecies in this genus.
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Affiliation(s)
- Martha H Ramírez-Bahena
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Ludovic Vial
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Florent Lassalle
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France; CNRS, UMR5558, Biométrie et Biologie Evolutive, 69622 Villeurbanne, France; Ecole Normale Supérieure de Lyon, 69342 Lyon, France
| | - Benjamin Diel
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France
| | - David Chapulliot
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France
| | - Vincent Daubin
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5558, Biométrie et Biologie Evolutive, 69622 Villeurbanne, France
| | - Xavier Nesme
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France; INRA, USC 1364, Ecologie Microbienne, 69622 Villeurbanne, France.
| | - Daniel Muller
- Université de Lyon, 69361 Lyon, France; Université Lyon 1, 69622 Villeurbanne, France; CNRS, UMR5557, Ecologie Microbienne, 69622 Villeurbanne, France
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Abstract
Recently, it was shown that gene conversion between the ends of linear mitochondrial chromosomes can cause telomere expansion and the duplication of subtelomeric loci. However, it is not yet known how widespread this phenomenon is and how significantly it has impacted organelle genome architecture. Using linear mitochondrial DNAs and mitochondrial plasmids from diverse eukaryotes, we argue that telomeric recombination has played a major role in fashioning linear organelle chromosomes. We find that mitochondrial telomeres frequently expand into subtelomeric regions, resulting in gene duplications, homogenizations, and/or fragmentations. We suggest that these features are a product of subtelomeric gene conversion, provide a hypothetical model for this process, and employ genetic diversity data to support the idea that the greater the effective population size the greater the potential for gene conversion between subtelomeric loci.
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Affiliation(s)
- David Roy Smith
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, Canada.
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25
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Lasserre JP, Plissonneau J, Velours C, Bonneu M, Litvak S, Laquel P, Castroviejo M. Biochemical, cellular and molecular identification of DNA polymerase α in yeast mitochondria. Biochimie 2013; 95:759-71. [DOI: 10.1016/j.biochi.2012.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Accepted: 11/07/2012] [Indexed: 11/15/2022]
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26
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Development-Dependent Changes in the Amount and Structural Organization of Plastid DNA. PLASTID DEVELOPMENT IN LEAVES DURING GROWTH AND SENESCENCE 2013. [DOI: 10.1007/978-94-007-5724-0_11] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gaillardin C, Neuvéglise C, Kerscher S, Nicaud JM. Mitochondrial genomes of yeasts of the Yarrowia clade. FEMS Yeast Res 2012; 12:317-31. [PMID: 22188421 DOI: 10.1111/j.1567-1364.2011.00782.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 11/25/2011] [Accepted: 12/07/2011] [Indexed: 12/13/2022] Open
Abstract
Candida alimentaria, Candida deformans, Candida galli, and Candida phangngensis have been recently reported to be the close relatives of Yarrowia lipolytica. To explore this clade of yeasts, we sequenced the mitochondrial genome (mtDNA) of these four species and compared it with the mtDNA of Y. lipolytica. The five mtDNAs exhibit a similar architecture and a high level of similarity of protein coding sequences. Genome sizes are variable, ranging from 28 017 bp in C. phangngensis to 48 508 bp in C. galli, mainly because of the variations in intron size and number. All introns are of group I, except for a group II intron inserted in the cob gene of a single species, C. galli. Putative endonuclease coding sequences were present in most group I introns, but also twice as free-standing ORFs in C. galli. Phylogenetic relationships of the five species were explored using protein alignments. No close relative of the Yarrowia clade could be identified, but protein and rRNA gene orders were partially conserved in the mtDNA of Candida salmanticensis.
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Seed Plant Mitochondrial Genomes: Complexity Evolving. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Smith DR, Burki F, Yamada T, Grimwood J, Grigoriev IV, Van Etten JL, Keeling PJ. The GC-rich mitochondrial and plastid genomes of the green alga Coccomyxa give insight into the evolution of organelle DNA nucleotide landscape. PLoS One 2011; 6:e23624. [PMID: 21887287 PMCID: PMC3162594 DOI: 10.1371/journal.pone.0023624] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 07/21/2011] [Indexed: 11/19/2022] Open
Abstract
Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this species. The Coccomyxa organelle genomes are also used for phylogenetic analyses, which highlight the complexities in trying to resolve the interrelationships among the core chlorophyte green algae, but ultimately favour a sister relationship between the Ulvophyceae and Chlorophyceae, with the Trebouxiophyceae branching at the base of the chlorophyte crown.
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Affiliation(s)
- David Roy Smith
- Department of Botany, Canadian Institute for Advanced Research, University of British Columbia, Vancouver, British Columbia, Canada.
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Wicke S, Schneeweiss GM, dePamphilis CW, Müller KF, Quandt D. The evolution of the plastid chromosome in land plants: gene content, gene order, gene function. PLANT MOLECULAR BIOLOGY 2011; 76:273-97. [PMID: 21424877 PMCID: PMC3104136 DOI: 10.1007/s11103-011-9762-4] [Citation(s) in RCA: 812] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Accepted: 02/19/2011] [Indexed: 05/18/2023]
Abstract
This review bridges functional and evolutionary aspects of plastid chromosome architecture in land plants and their putative ancestors. We provide an overview on the structure and composition of the plastid genome of land plants as well as the functions of its genes in an explicit phylogenetic and evolutionary context. We will discuss the architecture of land plant plastid chromosomes, including gene content and synteny across land plants. Moreover, we will explore the functions and roles of plastid encoded genes in metabolism and their evolutionary importance regarding gene retention and conservation. We suggest that the slow mode at which the plastome typically evolves is likely to be influenced by a combination of different molecular mechanisms. These include the organization of plastid genes in operons, the usually uniparental mode of plastid inheritance, the activity of highly effective repair mechanisms as well as the rarity of plastid fusion. Nevertheless, structurally rearranged plastomes can be found in several unrelated lineages (e.g. ferns, Pinaceae, multiple angiosperm families). Rearrangements and gene losses seem to correlate with an unusual mode of plastid transmission, abundance of repeats, or a heterotrophic lifestyle (parasites or myco-heterotrophs). While only a few functional gene gains and more frequent gene losses have been inferred for land plants, the plastid Ndh complex is one example of multiple independent gene losses and will be discussed in detail. Patterns of ndh-gene loss and functional analyses indicate that these losses are usually found in plant groups with a certain degree of heterotrophy, might rendering plastid encoded Ndh1 subunits dispensable.
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Affiliation(s)
- Susann Wicke
- Department of Biogeography and Botanical Garden, University of Vienna, Rennweg 14, 1030 Vienna, Austria.
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Parent JS, Lepage E, Brisson N. Divergent roles for the two PolI-like organelle DNA polymerases of Arabidopsis. PLANT PHYSIOLOGY 2011; 156:254-62. [PMID: 21427281 PMCID: PMC3091039 DOI: 10.1104/pp.111.173849] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 03/18/2011] [Indexed: 05/18/2023]
Abstract
DNA polymerases play a central role in the process of DNA replication. Yet, the proteins in charge of the replication of plant organelle DNA have not been unambiguously identified. There are however many indications that a family of proteins homologous to bacterial DNA polymerase I (PolI) is implicated in organelle DNA replication. Here, we have isolated mutant lines of the PolIA and PolIB genes of Arabidopsis (Arabidopsis thaliana) to test this hypothesis. We find that mutation of both genes is lethal, thus confirming an essential and redundant role for these two proteins. However, the mutation of a single gene is sufficient to cause a reduction in the levels of DNA in both mitochondria and plastids. We also demonstrate that polIb, but not polIa mutant lines, are hypersensitive to ciprofloxacin, a small molecule that specifically induces DNA double-strand breaks in plant organelles, suggesting a function for PolIB in DNA repair. In agreement with this result, a cross between polIb and a plastid Whirly mutant line yielded plants with high levels of DNA rearrangements and severe growth defects, indicating impairments in plastid DNA repair pathways. Taken together, this work provides further evidences for the involvement of the plant PolI-like genes in organelle DNA replication and suggests an additional role for PolIB in DNA repair.
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Affiliation(s)
| | | | - Normand Brisson
- Department of Biochemistry, Université de Montréal, Montreal, Quebec, Canada H3C 3J7
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Valach M, Farkas Z, Fricova D, Kovac J, Brejova B, Vinar T, Pfeiffer I, Kucsera J, Tomaska L, Lang BF, Nosek J. Evolution of linear chromosomes and multipartite genomes in yeast mitochondria. Nucleic Acids Res 2011; 39:4202-19. [PMID: 21266473 PMCID: PMC3105423 DOI: 10.1093/nar/gkq1345] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial genome diversity in closely related species provides an excellent platform for investigation of chromosome architecture and its evolution by means of comparative genomics. In this study, we determined the complete mitochondrial DNA sequences of eight Candida species and analyzed their molecular architectures. Our survey revealed a puzzling variability of genome architecture, including circular- and linear-mapping and multipartite linear forms. We propose that the arrangement of large inverted repeats identified in these genomes plays a crucial role in alterations of their molecular architectures. In specific arrangements, the inverted repeats appear to function as resolution elements, allowing genome conversion among different topologies, eventually leading to genome fragmentation into multiple linear DNA molecules. We suggest that molecular transactions generating linear mitochondrial DNA molecules with defined telomeric structures may parallel the evolutionary emergence of linear chromosomes and multipartite genomes in general and may provide clues for the origin of telomeres and pathways implicated in their maintenance.
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Affiliation(s)
- Matus Valach
- Department of Biochemistry, Comenius University, Mlynska dolina CH-1, 842 15 Bratislava, Slovak republic
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Abstract
In this issue of Molecular Cell, Gerhold et al. (2010) find no circular DNA during mitochondrial DNA (mtDNA) replication in the aerobic yeast Candida albicans, a result with important implications for mtDNA replication in Saccharomyces cerevisiae.
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Affiliation(s)
- Arnold J Bendich
- Department of Biology, University of Washington, Seattle, WA 98195, USA.
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Borza T, Redmond EK, Laflamme M, Lee RW. MITOCHONDRIAL DNA IN THE OOGAMOCHLAMYS CLADE (CHLOROPHYCEAE): HIGH GC CONTENT AND UNIQUE GENOME ARCHITECTURE FOR GREEN ALGAE(1). JOURNAL OF PHYCOLOGY 2009; 45:1323-34. [PMID: 27032590 DOI: 10.1111/j.1529-8817.2009.00753.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Most mitochondrial genomes in the green algal phylum Chlorophyta are AT-rich, circular-mapping DNA molecules. However, mitochondrial genomes from the Reinhardtii clade of the Chlorophyceae lineage are linear and sometimes fragmented into subgenomic forms. Moreover, Polytomella capuana, from the Reinhardtii clade, has an elevated GC content (57.2%). In the present study, we examined mitochondrial genome conformation and GC bias in the Oogamochlamys clade of the Chlorophyceae, which phylogenetic data suggest is closely related to the Reinhardtii clade. Total DNA from selected Oogamochlamys taxa, including four Lobochlamys culleus (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian strains, Lobochlamys segnis (H. Ettl) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, and Oogamochlamys gigantea (O. Dill) Pröschold, B. Marin, U. G. Schlöss. et Melkonian, was subjected to Southern blot analyses with cob and cox1 probes, and the results suggest that the mitochondrial genome of these taxa is represented by multiple-sized linear DNA fragments with overlapping homologies. On the basis of these data, we propose that linear mitochondrial DNA with a propensity to become fragmented arose in an ancestor common to the Reinhardtii and Oogamochlamys clades or even earlier in the evolutionary history of the Chlorophyceae. Analyses of partial cob and cox1 sequences from these Oogamochlamys taxa revealed an unusually high GC content (49.9%-65.1%) and provided evidence for the accumulation of cob and cox1 pseudogenes and truncated sequences in the mitochondrial genome of all L. culleus strains examined.
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Affiliation(s)
- Tudor Borza
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Erin K Redmond
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Mark Laflamme
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
| | - Robert W Lee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia B3H 4J1, Canada
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Weihe A, Apitz J, Pohlheim F, Salinas-Hartwig A, Börner T. Biparental inheritance of plastidial and mitochondrial DNA and hybrid variegation in Pelargonium. Mol Genet Genomics 2009; 282:587-93. [PMID: 19787375 PMCID: PMC2777209 DOI: 10.1007/s00438-009-0488-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2009] [Accepted: 09/14/2009] [Indexed: 11/29/2022]
Abstract
Plastidial (pt) and mitochondrial (mt) genes usually show maternal inheritance. Non-Mendelian, biparental inheritance of plastids was first described by Baur (Z Indukt Abstamm Vererbungslehre 1:330–351, 1909) for crosses between Pelargonium cultivars. We have analyzed the inheritance of pt and mtDNA by examining the progeny from reciprocal crosses of Pelargoniumzonale and P. inquinans using nucleotide sequence polymorphisms of selected pt and mt genes. Sequence analysis of the progeny revealed biparental inheritance of both pt and mtDNA. Hybrid plants exhibited variegation: our data demonstrate that the inquinans chloroplasts, but not the zonale chloroplasts bleach out, presumably due to incompatibility of the former with the hybrid nuclear genome. Different distribution of maternal and paternal sequences could be observed in different sectors of the same leaf, in different leaves of the same plant, and in different plants indicating random segregation and sorting-out of maternal and paternal plastids and mitochondria in the hybrids. The substantial transmission of both maternal and paternal mitochondria to the progeny turns Pelargonium into a particular interesting subject for studies on the inheritance, segregation and recombination of mt genes.
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Affiliation(s)
- Andreas Weihe
- Institut für Biologie, Humboldt-Universität zu Berlin, Chausseestr. 117, 10115, Berlin, Germany
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