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Qin N, Yang S, Wang Y, Cheng H, Gao Y, Cheng X, Li S. The de novo assembly and characterization of the complete mitochondrial genome of bottle gourd ( Lagenaria siceraria) reveals the presence of homologous conformations produced by repeat-mediated recombination. FRONTIERS IN PLANT SCIENCE 2024; 15:1416913. [PMID: 39188545 PMCID: PMC11345175 DOI: 10.3389/fpls.2024.1416913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/24/2024] [Indexed: 08/28/2024]
Abstract
Introduction Bottle gourd is an annual herbaceous plant that not only has high nutritional value and many medicinal applications but is also used as a rootstock for the grafting of cucurbit crops such as watermelon, cucumber and melon. Organellar genomes provide valuable resources for genetic breeding. Methods A hybrid strategy with Illumina and Oxford Nanopore Technology sequencing data was used to assemble bottle gourd mitochondrial and chloroplast genomes. Results The length of the bottle gourd mitochondrial genome was 357547 bp, and that of the chloroplast genome was 157121 bp. These genomes had 27 homologous fragments, accounting for 6.50% of the total length of the bottle gourd mitochondrial genome. In the mitochondrial genome, 101 simple sequence repeats (SSRs) and 10 tandem repeats were identified. Moreover, 1 pair of repeats was shown to mediate homologous recombination into 1 major conformation and 1 minor conformation. The existence of these conformations was verified via PCR amplification and Sanger sequencing. Evolutionary analysis revealed that the mitochondrial genome sequence of bottle gourd was highly conserved. Furthermore, collinearity analysis revealed many rearrangements between the homologous fragments of Cucurbita and its relatives. The Ka/Ks values for most genes were between 0.3~0.9, which means that most of the genes in the bottle gourd mitochondrial genome are under purifying selection. We also identified a total of 589 potential RNA editing sites on 38 mitochondrial protein-coding genes (PCGs) on the basis of long noncoding RNA (lncRNA)-seq data. The RNA editing sites of nad1-2, nad4L-2, atp6-718, atp9-223 and rps10-391 were successfully verified via PCR amplification and Sanger sequencing. Conclusion In conclusion, we assembled and annotated bottle gourd mitochondrial and chloroplast genomes to provide a theoretical basis for similar organelle genomic studies.
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Affiliation(s)
- Nannan Qin
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
- Department of Development Planning & Cooperation, Shanxi Agricultural University, Taiyuan, China
| | - Shanjie Yang
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Yunan Wang
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Hui Cheng
- Department of Scientific Research Management, Shanxi Agricultural University, Taiyuan, China
| | - Yang Gao
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Xiaojing Cheng
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
| | - Sen Li
- College of Horticulture, Shanxi Agricultural University, Jinzhong, China
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Gong Y, Xie X, Zhou G, Chen M, Chen Z, Li P, Huang H. Assembly and comparative analysis of the complete mitochondrial genome of Brassica rapa var. Purpuraria. BMC Genomics 2024; 25:546. [PMID: 38824587 PMCID: PMC11143693 DOI: 10.1186/s12864-024-10457-1] [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: 02/02/2024] [Accepted: 05/26/2024] [Indexed: 06/03/2024] Open
Abstract
BACKGROUND Purple flowering stalk (Brassica rapa var. purpuraria) is a widely cultivated plant with high nutritional and medicinal value and exhibiting strong adaptability during growing. Mitochondrial (mt) play important role in plant cells for energy production, developing with an independent genetic system. Therefore, it is meaningful to assemble and annotate the functions for the mt genome of plants independently. Though there have been several reports referring the mt genome of in Brassica species, the genome of mt in B. rapa var. purpuraria and its functional gene variations when compared to its closely related species has not yet been addressed. RESULTS The mt genome of B. rapa var. purpuraria was assembled through the Illumina and Nanopore sequencing platforms, which revealed a length of 219,775 bp with a typical circular structure. The base composition of the whole B. rapa var. purpuraria mt genome revealed A (27.45%), T (27.31%), C (22.91%), and G (22.32%). 59 functional genes, composing of 33 protein-coding genes (PCGs), 23 tRNA genes, and 3 rRNA genes, were annotated. The sequence repeats, codon usage, RNA editing, nucleotide diversity and gene transfer between the cp genome and mt genome were examined in the B. rapa var. purpuraria mt genome. Phylogenetic analysis show that B. rapa var. Purpuraria was closely related to B. rapa subsp. Oleifera and B. juncea. Ka/Ks analysis reflected that most of the PCGs in the B. rapa var. Purpuraria were negatively selected, illustrating that those mt genes were conserved during evolution. CONCLUSIONS The results of our findings provide valuable information on the B.rapa var. Purpuraria genome, which might facilitate molecular breeding, genetic variation and evolutionary researches for Brassica species in the future.
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Affiliation(s)
- Yihui Gong
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China.
| | - Xin Xie
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Guihua Zhou
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Meiyu Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Zhiyin Chen
- Development and Utilization and Quality and Safety Control of Characteristic Agricultural Resources in Central Hunan, College of Agriculture and Biotechnology , Hunan University of Humanities, Science and Technology, Loudi, 417000, China
| | - Peng Li
- Xiangtan Agricultural Science Research Institute, Xiangtan, 411100, China
| | - Hua Huang
- Institute of Fruit Tree Research, Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, 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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Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmF C genes. BMC Genomics 2021; 22:816. [PMID: 34772334 PMCID: PMC8588681 DOI: 10.1186/s12864-021-08105-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/19/2021] [Indexed: 01/30/2023] Open
Abstract
Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08105-z.
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Ramu VS, Dawane A, Lee S, Oh S, Lee H, Sun L, Senthil‐Kumar M, Mysore KS. Ribosomal protein QM/RPL10 positively regulates defence and protein translation mechanisms during nonhost disease resistance. MOLECULAR PLANT PATHOLOGY 2020; 21:1481-1494. [PMID: 32964634 PMCID: PMC7548997 DOI: 10.1111/mpp.12991] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/03/2020] [Accepted: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Ribosomes play an integral part in plant growth, development, and defence responses. We report here the role of ribosomal protein large (RPL) subunit QM/RPL10 in nonhost disease resistance. The RPL10-silenced Nicotiana benthamiana plants showed compromised disease resistance against nonhost pathogen Pseudomonas syringae pv. tomato T1. The RNA-sequencing analysis revealed that many genes involved in defence and protein translation mechanisms were differentially affected due to silencing of NbRPL10. Arabidopsis AtRPL10 RNAi and rpl10 mutant lines showed compromised nonhost disease resistance to P. syringae pv. tomato T1 and P. syringae pv. tabaci. Overexpression of AtRPL10A in Arabidopsis resulted in reduced susceptibility against host pathogen P. syringae pv. tomato DC3000. RPL10 interacts with the RNA recognition motif protein and ribosomal proteins RPL30, RPL23, and RPS30 in the yeast two-hybrid assay. Silencing or mutants of genes encoding these RPL10-interacting proteins in N. benthamiana or Arabidopsis, respectively, also showed compromised disease resistance to nonhost pathogens. These results suggest that QM/RPL10 positively regulates the defence and translation-associated genes during nonhost pathogen infection.
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Affiliation(s)
- Vemanna S. Ramu
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Labortory of Plant Functional GenomicsRegional Centre for BiotechnologyFaridabadIndia
| | - Akashata Dawane
- Labortory of Plant Functional GenomicsRegional Centre for BiotechnologyFaridabadIndia
| | - Seonghee Lee
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Present address:
Gulf Coast Research and Education CenterInstitute of Food and Agricultural ScienceUniversity of FloridaWimaumaFloridaUSA
| | - Sunhee Oh
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
| | | | - Liang Sun
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
| | - Muthappa Senthil‐Kumar
- Noble Research Institute, LLC.ArdmoreOklahomaUSA
- Present address:
National Institute of Plant Genome ResearchNew DelhiIndia
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Hall ND, Zhang H, Mower JP, McElroy JS, Goertzen LR. The Mitochondrial Genome of Eleusine indica and Characterization of Gene Content within Poaceae. Genome Biol Evol 2020; 12:3684-3697. [PMID: 31665327 PMCID: PMC7145533 DOI: 10.1093/gbe/evz229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2019] [Indexed: 12/12/2022] Open
Abstract
Plant mitochondrial (mt) genome assembly provides baseline data on size, structure, and gene content, but resolving the sequence of these large and complex organelle genomes remains challenging due to fragmentation, frequent recombination, and transfers of DNA from neighboring plastids. The mt genome for Eleusine indica (Poaceae: goosegrass) is comprehensibly analyzed here, providing key reference data for an economically significant invasive species that is also the maternal parent of the allotetraploid crop Finger millet (Eleusine coracana). The assembled E. indica genome contains 33 protein coding genes, 6 rRNA subunits, 24 tRNA, 8 large repetitive regions 15 kb of transposable elements across a total of 520,691 bp. Evidence of RNA editing and loss of rpl2, rpl5, rps14, rps11, sdh4, and sdh3 genes is evaluated in the context of an updated survey of mt genomic gene content across the grasses through an analysis of publicly available data. Hypothesized patterns of Poaceae mt gene loss are examined in a phylogenetic context to clarify timing, showing that rpl2 was transferred to the nucleus from the mitochondrion prior to the origin of the PACMAD clade.
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Affiliation(s)
- Nathan D Hall
- Department of Biological Sciences, Auburn University
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University
| | - Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln
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Logacheva MD, Schelkunov MI, Fesenko AN, Kasianov AS, Penin AA. Mitochondrial Genome of Fagopyrum esculentum and the Genetic Diversity of Extranuclear Genomes in Buckwheat. PLANTS (BASEL, SWITZERLAND) 2020; 9:E618. [PMID: 32408719 PMCID: PMC7285332 DOI: 10.3390/plants9050618] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 12/27/2022]
Abstract
Fagopyrum esculentum (common buckwheat) is an important agricultural non-cereal grain plant. Despite extensive genetic studies, the information on its mitochondrial genome is still lacking. Using long reads generated by single-molecule real-time technology coupled with circular consensus sequencing (CCS) protocol, we assembled the buckwheat mitochondrial genome and detected that its prevalent form consists of 10 circular chromosomes with a total length of 404 Kb. In order to confirm the presence of a multipartite structure, we developed a new targeted assembly tool capable of processing long reads. The mitogenome contains all genes typical for plant mitochondrial genomes and long inserts of plastid origin (~6.4% of the total mitogenome length). Using this new information, we characterized the genetic diversity of mitochondrial and plastid genomes in 11 buckwheat cultivars compared with the ancestral subspecies, F. esculentum ssp. ancestrale. We found it to be surprisingly low within cultivars: Only three to six variations in the mitogenome and one to two in the plastid genome. In contrast, the divergence with F. esculentum ssp. ancestrale is much higher: 220 positions differ in the mitochondrial genome and 159 in the plastid genome. The SNPs in the plastid genome are enriched in non-synonymous substitutions, in particular in the genes involved in photosynthesis: psbA, psbC, and psbH. This presumably reflects the selection for the increased photosynthesis efficiency as a part of the buckwheat breeding program.
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Affiliation(s)
- Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Mikhail I. Schelkunov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
- Skolkovo Institute of Science and Technology, 143026 Moscow, Russia
| | - Aleksey N. Fesenko
- Federal Scientific Center of Legumes and Groat Crops, 302502 Orel, Russia;
| | - Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, 127051 Moscow, Russia; (M.I.S.); (A.S.K.); (A.A.P.)
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Kan SL, Shen TT, Gong P, Ran JH, Wang XQ. The complete mitochondrial genome of Taxus cuspidata (Taxaceae): eight protein-coding genes have transferred to the nuclear genome. BMC Evol Biol 2020; 20:10. [PMID: 31959109 PMCID: PMC6971862 DOI: 10.1186/s12862-020-1582-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 01/13/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gymnosperms represent five of the six lineages of seed plants. However, most sequenced plant mitochondrial genomes (mitogenomes) have been generated for angiosperms, whereas mitogenomic sequences have been generated for only six gymnosperms. In particular, complete mitogenomes are available for all major seed plant lineages except Conifer II (non-Pinaceae conifers or Cupressophyta), an important lineage including six families, which impedes a comprehensive understanding of the mitogenomic diversity and evolution in gymnosperms. RESULTS Here, we report the complete mitogenome of Taxus cuspidata in Conifer II. In comparison with previously released gymnosperm mitogenomes, we found that the mitogenomes of Taxus and Welwitschia have lost many genes individually, whereas all genes were identified in the mitogenomes of Cycas, Ginkgo and Pinaceae. Multiple tRNA genes and introns also have been lost in some lineages of gymnosperms, similar to the pattern observed in angiosperms. In general, gene clusters could be less conserved in gymnosperms than in angiosperms. Moreover, fewer RNA editing sites were identified in the Taxus and Welwitschia mitogenomes than in other mitogenomes, which could be correlated with fewer introns and frequent gene losses in these two species. CONCLUSIONS We have sequenced the Taxus cuspidata mitogenome, and compared it with mitogenomes from the other four gymnosperm lineages. The results revealed the diversity in size, structure, gene and intron contents, foreign sequences, and mutation rates of gymnosperm mitogenomes, which are different from angiosperm mitogenomes.
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Affiliation(s)
- Sheng-Long Kan
- 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
| | - Ting-Ting Shen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Ping Gong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jin-Hua Ran
- 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.
| | - Xiao-Quan Wang
- 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
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Dynamic evolution of mitochondrial genomes in Trebouxiophyceae, including the first completely assembled mtDNA from a lichen-symbiont microalga (Trebouxia sp. TR9). Sci Rep 2019; 9:8209. [PMID: 31160653 PMCID: PMC6547736 DOI: 10.1038/s41598-019-44700-7] [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: 09/27/2018] [Accepted: 05/22/2019] [Indexed: 12/21/2022] Open
Abstract
Trebouxiophyceae (Chlorophyta) is a species-rich class of green algae with a remarkable morphological and ecological diversity. Currently, there are a few completely sequenced mitochondrial genomes (mtDNA) from diverse Trebouxiophyceae but none from lichen symbionts. Here, we report the mitochondrial genome sequence of Trebouxia sp. TR9 as the first complete mtDNA sequence available for a lichen-symbiont microalga. A comparative study of the mitochondrial genome of Trebouxia sp. TR9 with other chlorophytes showed important organizational changes, even between closely related taxa. The most remarkable change is the enlargement of the genome in certain Trebouxiophyceae, which is principally due to larger intergenic spacers and seems to be related to a high number of large tandem repeats. Another noticeable change is the presence of a relatively large number of group II introns interrupting a variety of tRNA genes in a single group of Trebouxiophyceae, which includes Trebouxiales and Prasiolales. In addition, a fairly well-resolved phylogeny of Trebouxiophyceae, along with other Chlorophyta lineages, was obtained based on a set of seven well-conserved mitochondrial genes.
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Ribosomal protein L10 in mitochondria serves as a regulator for ROS level in pancreatic cancer cells. Redox Biol 2018; 19:158-165. [PMID: 30172100 PMCID: PMC6122146 DOI: 10.1016/j.redox.2018.08.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/13/2018] [Accepted: 08/23/2018] [Indexed: 11/21/2022] Open
Abstract
Tumorigenesis is commonly known as a complicated process, in which reactive oxygen species (ROS) plays a critical role to involve in signal transduction, metabolism, cell proliferation and differentiation. Previously, ribosomal protein L10 (RPL10) was suggested to possess extra-ribosomal functions in pancreatic cancer cells in addition to being proposed as a tumor suppressor or transcription co-regulator. To better understand the relationship between RPL10 and tumorigenic potential in pancreatic cancer cells, chromatin immunoprecipitation sequencing reveals that RPL10 is unlikely to be a transcription factor without a specific binding motif for gene transcription. Additionally, transcriptome analysis indicates that RPL10 could regulate the expression of proteins related to ROS production. Moreover, RPL10 in mitochondria is closely associated with the regulation of ROS level by affecting Complex I activity and the subsequent events. Together, the present study suggests that the regulation of ROS level by mitochondrial RPL10 is one of the major extra-ribosomal functions in pancreatic cancer cells, which could be used as an indicator for the tumorigenesis of pancreatic cancer. RPL10 exists in mitochondria. RPL10 affects the expression of proteins related to oxidative stress and ROS generation. RPL10 regulates ROS level in pancreatic cancer cells.
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Schelkunov MI, Penin AA, Logacheva MD. RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants. BMC Genomics 2018; 19:602. [PMID: 30092758 PMCID: PMC6085651 DOI: 10.1186/s12864-018-4968-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 07/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND While photosynthesis is the most notable trait of plants, several lineages of plants (so-called full heterotrophs) have adapted to obtain organic compounds from other sources. The switch to heterotrophy leads to profound changes at the morphological, physiological and genomic levels. RESULTS Here, we characterize the transcriptomes of three species representing two lineages of mycoheterotrophic plants: orchids (Epipogium aphyllum and Epipogium roseum) and Ericaceae (Hypopitys monotropa). Comparative analysis is used to highlight the parallelism between distantly related fully heterotrophic plants. In both lineages, we observed genome-wide elimination of nuclear genes that encode proteins related to photosynthesis, while systems associated with protein import to plastids as well as plastid transcription and translation remain active. Genes encoding components of plastid ribosomes that have been lost from the plastid genomes have not been transferred to the nuclear genomes; instead, some of the encoded proteins have been substituted by homologs. The nuclear genes of both Epipogium species accumulated nucleotide substitutions twice as rapidly as their photosynthetic relatives; in contrast, no increase in the substitution rate was observed in H. monotropa. CONCLUSIONS Full heterotrophy leads to profound changes in nuclear gene content. The observed increase in the rate of nucleotide substitutions is lineage specific, rather than a universal phenomenon among non-photosynthetic plants.
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Affiliation(s)
- Mikhail I Schelkunov
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.
| | - Aleksey A Penin
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia.,A.N Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia. .,Skolkovo Institute of Science and Technology, Moscow, Russia. .,Extreme Biology Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia.
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12
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Goryunov DV, Logacheva MD, Ignatov MS, Milyutina IA, Fedorova AV, Troitsky AV. The Mitochondrial Genome of the Moss Brachythecium rivulare (Hypnales, Brachytheciaceae). BIOCHEMISTRY. BIOKHIMIIA 2017; 82:1373-1379. [PMID: 29223164 DOI: 10.1134/s0006297917110153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The mitochondrial genome of the pleurocarpous moss Brachythecium rivulare has been sequenced and annotated. The genome consists of 104,460 base pairs and has approximately the same gene set and organization as other bryophyte mitogenomes. Whole mitochondrial genome comparison between B. rivulare and Physcomitrella patens, Tetraphis pellucida, Anomodon rugelii, and Anomodon attenuatus was performed. The primary cause of bryophyte mitochondrial gene length variation was found to be numerous indels in the introns. Bryophyte mitochondrial gene conservation level was estimated, and it was in a good congruence with the overall phylogeny of bryophytes with the percentage of mitogenome similarity being proportional to the age estimated by phylochronologic analysis. Annotation discrepancies in the analyzed mitogenome sequences were identified. The simple sequence repeat (SSR) content was evaluated, and candidate sites of RNA editing were predicted in the B. rivulare mitochondrial genome.
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Affiliation(s)
- D V Goryunov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Park S, Ruhlman TA, Weng ML, Hajrah NH, Sabir JS, Jansen RK. Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium. Genome Biol Evol 2017; 9:1766-1780. [PMID: 28854633 PMCID: PMC5570028 DOI: 10.1093/gbe/evx124] [Citation(s) in RCA: 44] [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] [Accepted: 07/03/2017] [Indexed: 12/25/2022] Open
Abstract
Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid.
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Affiliation(s)
- Seongjun Park
- Department of Integrative Biology, University of Texas at Austin
| | | | - Mao-Lun Weng
- Department of Integrative Biology, University of Texas at Austin
- Department of Biology and Microbiology, South Dakota State University
| | - Nahid H. Hajrah
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jamal S.M. Sabir
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin
- Genomic and Biotechnology Research Group, Department of Biological Science, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
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14
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Petersen G, Cuenca A, Zervas A, Ross GT, Graham SW, Barrett CF, Davis JI, Seberg O. Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes. PLoS One 2017; 12:e0177606. [PMID: 28545148 PMCID: PMC5435185 DOI: 10.1371/journal.pone.0177606] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/28/2017] [Indexed: 11/18/2022] Open
Abstract
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.
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Affiliation(s)
- Gitte Petersen
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Argelia Cuenca
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Athanasios Zervas
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Gregory T. Ross
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean W. Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig F. Barrett
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Jerrold I. Davis
- L. H. Bailey Hortorium and Plant Biology Section, Cornell University, Ithaca, New York, United States of America
| | - Ole Seberg
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Pervaiz T, Sun X, Zhang Y, Tao R, Zhang J, Fang J. Association between Chloroplast and Mitochondrial DNA sequences in Chinese Prunus genotypes (Prunus persica, Prunus domestica, and Prunus avium). BMC PLANT BIOLOGY 2015; 15:4. [PMID: 0 PMCID: PMC4310034 DOI: 10.1186/s12870-014-0402-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/22/2014] [Indexed: 05/13/2023]
Abstract
BACKGROUND The nuclear DNA is conventionally used to assess the diversity and relatedness among different species, but variations at the DNA genome level has also been used to study the relationship among different organisms. In most species, mitochondrial and chloroplast genomes are inherited maternally; therefore it is anticipated that organelle DNA remains completely associated. Many research studies were conducted simultaneously on organelle genome. The objectives of this study was to analyze the genetic relationship between chloroplast and mitochondrial DNA in three Chinese Prunus genotypes viz., Prunus persica, Prunus domestica, and Prunus avium. RESULTS We investigated the genetic diversity of Prunus genotypes using simple sequence repeat (SSR) markers relevant to the chloroplast and mitochondria. Most of the genotypes were genetically similar as revealed by phylogenetic analysis. The Y2 Wu Xing (Cherry) and L2 Hong Xin Li (Plum) genotypes have a high similarity index (0.89), followed by Zi Ye Li (0.85), whereas; L1 Tai Yang Li (plum) has the lowest genetic similarity (0.35). In case of cpSSR, Hong Tao (Peach) and L1 Tai Yang Li (Plum) genotypes demonstrated similarity index of 0.85 and Huang Tao has the lowest similarity index of 0.50. The mtSSR nucleotide sequence analysis revealed that each genotype has similar amplicon length (509 bp) except M5Y1 i.e., 505 bp with CCB256 primer; while in case of NAD6 primer, all genotypes showed different sizes. The MEHO (Peach), MEY1 (Cherry), MEL2 (Plum) and MEL1 (Plum) have 586 bps; while MEY2 (Cherry), MEZI (Plum) and MEHU (Peach) have 585, 584 and 566 bp, respectively. The CCB256 primer showed highly conserved sequences and minute single polymorphic nucleotides with no deletion or mutation. The cpSSR (ARCP511) microsatellites showed the harmonious amplicon length. The CZI (Plum), CHO (Peach) and CL1 (Plum) showed 182 bp; whileCHU (Peach), CY2 (Cherry), CL2 (Plum) and CY1 (Cherry) showed 181 bp amplicon lengths. CONCLUSIONS These results demonstrated high conservation in chloroplast and mitochondrial genome among Prunus species during the evolutionary process. These findings are valuable to study the organelle DNA diversity in different species and genotypes of Prunus to provide in depth insight in to the mitochondrial and chloroplast genomes.
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Affiliation(s)
- Tariq Pervaiz
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China.
| | - Xin Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China.
| | - Yanyi Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China.
| | - Ran Tao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China.
| | - Junhuan Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Science, Beijing, 100093, P R China.
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, P R China.
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16
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Gupta A, Shah P, Haider A, Gupta K, Siddiqi MI, Ralph SA, Habib S. Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics. Open Biol 2015; 4:140045. [PMID: 24850912 PMCID: PMC4042851 DOI: 10.1098/rsob.140045] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Apicomplexan protists such as Plasmodium and Toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast and mitochondrion. A cross-species comparison with other apicomplexan, algal and diatom species revealed compositional differences in apicomplexan organelle ribosomes and identified considerable reduction and divergence with ribosomes of bacteria or characterized organelle ribosomes from other organisms. We assembled structural models of sections of Plasmodium falciparum organellar ribosomes and predicted interactions with translation inhibitory antibiotics. Differences in predicted drug–ribosome interactions with some of the modelled structures suggested specificity of inhibition between the apicoplast and mitochondrion. Our results indicate that Plasmodium and Toxoplasma organellar ribosomes have a unique composition, resulting from the loss of several large and small subunit proteins accompanied by significant sequence and size divergences in parasite orthologues of ribosomal proteins.
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Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Priyanka Shah
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Afreen Haider
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Kirti Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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17
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Jo YD, Choi Y, Kim DH, Kim BD, Kang BC. Extensive structural variations between mitochondrial genomes of CMS and normal peppers (Capsicum annuum L.) revealed by complete nucleotide sequencing. BMC Genomics 2014; 15:561. [PMID: 24996600 PMCID: PMC4108787 DOI: 10.1186/1471-2164-15-561] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/20/2014] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) is an inability to produce functional pollen that is caused by mutation of the mitochondrial genome. Comparative analyses of mitochondrial genomes of lines with and without CMS in several species have revealed structural differences between genomes, including extensive rearrangements caused by recombination. However, the mitochondrial genome structure and the DNA rearrangements that may be related to CMS have not been characterized in Capsicum spp. RESULTS We obtained the complete mitochondrial genome sequences of the pepper CMS line FS4401 (507,452 bp) and the fertile line Jeju (511,530 bp). Comparative analysis between mitochondrial genomes of peppers and tobacco that are included in Solanaceae revealed extensive DNA rearrangements and poor conservation in non-coding DNA. In comparison between pepper lines, FS4401 and Jeju mitochondrial DNAs contained the same complement of protein coding genes except for one additional copy of an atp6 gene (ψatp6-2) in FS4401. In terms of genome structure, we found eighteen syntenic blocks in the two mitochondrial genomes, which have been rearranged in each genome. By contrast, sequences between syntenic blocks, which were specific to each line, accounted for 30,380 and 17,847 bp in FS4401 and Jeju, respectively. The previously-reported CMS candidate genes, orf507 and ψatp6-2, were located on the edges of the largest sequence segments that were specific to FS4401. In this region, large number of small sequence segments which were absent or found on different locations in Jeju mitochondrial genome were combined together. The incorporation of repeats and overlapping of connected sequence segments by a few nucleotides implied that extensive rearrangements by homologous recombination might be involved in evolution of this region. Further analysis using mtDNA pairs from other plant species revealed common features of DNA regions around CMS-associated genes. CONCLUSIONS Although large portion of sequence context was shared by mitochondrial genomes of CMS and male-fertile pepper lines, extensive genome rearrangements were detected. CMS candidate genes located on the edges of highly-rearranged CMS-specific DNA regions and near to repeat sequences. These characteristics were detected among CMS-associated genes in other species, implying a common mechanism might be involved in the evolution of CMS-associated genes.
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Affiliation(s)
- Yeong Deuk Jo
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
- />Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup, 580-185 South Korea
| | - Yoomi Choi
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Dong-Hwan Kim
- />Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712 USA
| | - Byung-Dong Kim
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
| | - Byoung-Cheorl Kang
- />Department of Plant Science, Plant Genomics and Breeding Institute, and Institute of Green BioScience and Technology, Seoul National University, Seoul, 151-921 South Korea
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18
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Grewe F, Edger PP, Keren I, Sultan L, Pires JC, Ostersetzer-Biran O, Mower JP. Comparative analysis of 11 Brassicales mitochondrial genomes and the mitochondrial transcriptome of Brassica oleracea. Mitochondrion 2014; 19 Pt B:135-43. [PMID: 24907441 DOI: 10.1016/j.mito.2014.05.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
Abstract
To elucidate the evolution of mitochondrial genomic diversity within a single order of angiosperms, we sequenced seven Brassicales genomes and the transcriptome of Brassica oleracea. In the common ancestor of Brassicaceae, several genes of known function were lost and the ccmFN gene was split into two independent genes, which also coincides with a trend of genome reduction towards the smallest sequenced angiosperm genomes of Brassica. For most ORFs of unknown function, the lack of conservation throughout Brassicales and the generally low expression and absence of RNA editing in B. oleracea argue against functionality. However, two chimeric ORFs were expressed and edited in B. oleracea, suggesting a potential role in cytoplasmic male sterility in certain nuclear backgrounds. These results demonstrate how frequent shifts in size, structure, and content of plant mitochondrial genomes can occur over short evolutionary time scales.
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Affiliation(s)
- Felix Grewe
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Patrick P Edger
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Ido Keren
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Laure Sultan
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Oren Ostersetzer-Biran
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat-Ram, Jerusalem 91904, Israel
| | - Jeffrey P Mower
- Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA; Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
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19
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Grimes BT, Sisay AK, Carroll HD, Cahoon AB. Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions. BMC Genomics 2014; 15:31. [PMID: 24433288 PMCID: PMC3898247 DOI: 10.1186/1471-2164-15-31] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 01/13/2014] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The purpose of this study was to sequence and assemble the tobacco mitochondrial transcriptome and obtain a genomic-level view of steady-state RNA abundance. Plant mitochondrial genomes have a small number of protein coding genes with large and variably sized intergenic spaces. In the tobacco mitogenome these intergenic spaces contain numerous open reading frames (ORFs) with no clear function. RESULTS The assembled transcriptome revealed distinct monocistronic and polycistronic transcripts along with large intergenic spaces with little to no detectable RNA. Eighteen of the 117 ORFs were found to have steady-state RNA amounts above background in both deep-sequencing and qRT-PCR experiments and ten of those were found to be polysome associated. In addition, the assembled transcriptome enabled a full mitogenome screen of RNA C→U editing sites. Six hundred and thirty five potential edits were found with 557 occurring within protein-coding genes, five in tRNA genes, and 73 in non-coding regions. These sites were found in every protein-coding transcript in the tobacco mitogenome. CONCLUSION These results suggest that a small number of the ORFs within the tobacco mitogenome may produce functional proteins and that RNA editing occurs in coding and non-coding regions of mitochondrial transcripts.
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Affiliation(s)
- Benjamin T Grimes
- Department of Biology, Box 60, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Awa K Sisay
- Computational Science Program, Middle Tennessee State University, Box 48, Murfreesboro, TN 37132, USA
| | - Hyrum D Carroll
- Computational Science Program, Middle Tennessee State University, Box 48, Murfreesboro, TN 37132, USA
| | - A Bruce Cahoon
- Department of Biology, Box 60, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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20
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Sloan DB, Triant DA, Wu M, Taylor DR. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol 2013; 31:673-82. [PMID: 24336923 DOI: 10.1093/molbev/mst259] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Many mitochondrial and plastid protein complexes contain subunits that are encoded in different genomes. In animals, nuclear-encoded mitochondrial proteins often exhibit rapid sequence evolution, which has been hypothesized to result from selection for mutations that compensate for changes in interacting subunits encoded in mutation-prone animal mitochondrial DNA. To test this hypothesis, we analyzed nuclear genes encoding cytosolic and organelle ribosomal proteins in flowering plants. The model angiosperm genus Arabidopsis exhibits low organelle mutation rates, typical of most plants. Nevertheless, we found that (nuclear-encoded) subunits of organelle ribosomes in Arabidopsis have higher amino acid sequence polymorphism and divergence than their counterparts in cytosolic ribosomes, suggesting that organelle ribosomes experience relaxed functional constraint. However, the observed difference between organelle and cytosolic ribosomes was smaller than in animals and could be partially attributed to rapid evolution in N-terminal organelle-targeting peptides that are not involved in ribosome function. To test the role of organelle mutation more directly, we used transcriptomic data from an angiosperm genus (Silene) with highly variable rates of organelle genome evolution. We found that Silene species with unusually fast-evolving mitochondrial and plastid DNA exhibited increased amino acid sequence divergence in ribosomal proteins targeted to the organelles but not in those that function in cytosolic ribosomes. Overall, these findings support the hypothesis that rapid organelle genome evolution has selected for compensatory mutations in nuclear-encoded proteins. We conclude that coevolution between interacting subunits encoded in different genomic compartments within the eukaryotic cell is an important determinant of variation in rates of protein sequence evolution.
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21
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Davydov II, Wohlgemuth I, Artamonova II, Urlaub H, Tonevitsky AG, Rodnina MV. Evolution of the protein stoichiometry in the L12 stalk of bacterial and organellar ribosomes. Nat Commun 2013; 4:1387. [DOI: 10.1038/ncomms2373] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 12/12/2012] [Indexed: 01/08/2023] Open
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22
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Goremykin VV, Lockhart PJ, Viola R, Velasco R. The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:615-26. [PMID: 22469001 DOI: 10.1111/j.1365-313x.2012.05014.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Mitochondrial genomes of spermatophytes are the largest of all organellar genomes. Their large size has been attributed to various factors; however, the relative contribution of these factors to mitochondrial DNA (mtDNA) expansion remains undetermined. We estimated their relative contribution in Malus domestica (apple). The mitochondrial genome of apple has a size of 396 947 bp and a one to nine ratio of coding to non-coding DNA, close to the corresponding average values for angiosperms. We determined that 71.5% of the apple mtDNA sequence was highly similar to sequences of its nuclear DNA. Using nuclear gene exons, nuclear transposable elements and chloroplast DNA as markers of promiscuous DNA content in mtDNA, we estimated that approximately 20% of the apple mtDNA consisted of DNA sequences imported from other cell compartments, mostly from the nucleus. Similar marker-based estimates of promiscuous DNA content in the mitochondrial genomes of other species ranged between 21.2 and 25.3% of the total mtDNA length for grape, between 23.1 and 38.6% for rice, and between 47.1 and 78.4% for maize. All these estimates are conservative, because they underestimate the import of non-functional DNA. We propose that the import of promiscuous DNA is a core mechanism for mtDNA size expansion in seed plants. In apple, maize and grape this mechanism contributed far more to genome expansion than did homologous recombination. In rice the estimated contribution of both mechanisms was found to be similar.
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Affiliation(s)
- Vadim V Goremykin
- IASMA Research and Innovation Center, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige (TN), Italy.
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23
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A reevaluation of dual-targeting of proteins to mitochondria and chloroplasts. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1833:253-9. [PMID: 22683762 DOI: 10.1016/j.bbamcr.2012.05.029] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 05/26/2012] [Accepted: 05/28/2012] [Indexed: 01/08/2023]
Abstract
Over 100 proteins are found in both mitochondria and chloroplasts, via a variety of processes known generally as 'dual-targeting'. Dual-targeting has attracted interest from many different research groups because of its profound implications concerning the mechanisms of protein import into these organelles and the evolution of both the protein import machinery and the targeting sequences within the imported proteins. Beyond these aspects, dual-targeting is also interesting for its implications concerning shared functions between mitochondria and chloroplasts, and especially the control of the activities of these two very different energy organelles. We discuss each of these points in the light of the latest relevant research findings and make some suggestions for where research might be most illuminating in the near future. This article is part of a Special Issue entitled: Protein Import and Quality Control in Mitochondria and Plastids.
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24
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Fang Y, Wu H, Zhang T, Yang M, Yin Y, Pan L, Yu X, Zhang X, Hu S, Al-Mssallem IS, Yu J. A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome. PLoS One 2012; 7:e37164. [PMID: 22655034 PMCID: PMC3360038 DOI: 10.1371/journal.pone.0037164] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 04/16/2012] [Indexed: 11/21/2022] Open
Abstract
Based on next-generation sequencing data, we assembled the mitochondrial (mt) genome of date palm (Phoenix dactylifera L.) into a circular molecule of 715,001 bp in length. The mt genome of P. dactylifera encodes 38 proteins, 30 tRNAs, and 3 ribosomal RNAs, which constitute a gene content of 6.5% (46,770 bp) over the full length. The rest, 93.5% of the genome sequence, is comprised of cp (chloroplast)-derived (10.3% with respect to the whole genome length) and non-coding sequences. In the non-coding regions, there are 0.33% tandem and 2.3% long repeats. Our transcriptomic data from eight tissues (root, seed, bud, fruit, green leaf, yellow leaf, female flower, and male flower) showed higher gene expression levels in male flower, root, bud, and female flower, as compared to four other tissues. We identified 120 potential SNPs among three date palm cultivars (Khalas, Fahal, and Sukry), and successfully found seven SNPs in the coding sequences. A phylogenetic analysis, based on 22 conserved genes of 15 representative plant mitochondria, showed that P. dactylifera positions at the root of all sequenced monocot mt genomes. In addition, consistent with previous discoveries, there are three co-transcribed gene clusters–18S-5S rRNA, rps3-rpl16 and nad3-rps12–in P. dactylifera, which are highly conserved among all known mitochondrial genomes of angiosperms.
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Affiliation(s)
- Yongjun Fang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Hao Wu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Tongwu Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Meng Yang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Yuxin Yin
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Linlin Pan
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiaoguang Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
| | - Xiaowei Zhang
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
- * E-mail: (JY); (XZ); (SH); (ISAM)
| | - Songnian Hu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
- * E-mail: (JY); (XZ); (SH); (ISAM)
| | - Ibrahim S. Al-Mssallem
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
- Department of Biotechnology, College of Agriculture and Food Sciences, King Faisal University, Hofuf, Kingdom of Saudi Arabia
- * E-mail: (JY); (XZ); (SH); (ISAM)
| | - Jun Yu
- Joint Center for Genomics Research (JCGR), King Abdulaziz City for Science and Technology (KACST) and Chinese Academy of Sciences (CAS), Riyadh, Kingdom of Saudi Arabia
- James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS), Beijing, China
- * E-mail: (JY); (XZ); (SH); (ISAM)
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Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, Spooner D, Simon P. De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. BMC PLANT BIOLOGY 2012; 12:61. [PMID: 22548759 PMCID: PMC3413510 DOI: 10.1186/1471-2229-12-61] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/01/2012] [Indexed: 05/02/2023]
Abstract
BACKGROUND Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. RESULTS Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. CONCLUSIONS This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.
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Affiliation(s)
- Massimo Iorizzo
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
| | - Douglas Senalik
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | - Marek Szklarczyk
- Department of Genetics, Plant Breeding and Seed Science, University of Agriculture Krakow, Al. 29 Listopada 54, 31-425, Krakow, Poland
| | - Dariusz Grzebelus
- Department of Genetics, Plant Breeding and Seed Science, University of Agriculture Krakow, Al. 29 Listopada 54, 31-425, Krakow, Poland
| | - David Spooner
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
| | - Philipp Simon
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Drive, Madison, WI 53706, USA
- USDA-Agricultural Research Service, Vegetable Crops Research Unit, University of Wisconsin, 1575 Linden Drive, Madison, WI 53706, USA
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26
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Mower JP, Case AL, Floro ER, Willis JH. Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS. Genome Biol Evol 2012; 4:670-86. [PMID: 22534162 PMCID: PMC3381676 DOI: 10.1093/gbe/evs042] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Despite intense investigation for over 25 years, the in vivo structure of plant mitochondrial genomes remains uncertain. Mapping studies and genome sequencing generally produce large circular chromosomes, whereas electrophoretic and microscopic studies typically reveal linear and multibranched molecules. To more fully assess the structure of plant mitochondrial genomes, the complete sequence of the monkeyflower (Mimulus guttatus DC. line IM62) mitochondrial DNA was constructed from a large (35 kb) paired-end shotgun sequencing library to a high depth of coverage (∼30×). The complete genome maps as a 525,671 bp circular molecule and exhibits a fairly conventional set of features including 62 genes (encoding 35 proteins, 24 transfer RNAs, and 3 ribosomal RNAs), 22 introns, 3 large repeats (2.7, 9.6, and 29 kb), and 96 small repeats (40–293 bp). Most paired-end reads (71%) mapped to the consensus sequence at the expected distance and orientation across the entire genome, validating the accuracy of assembly. Another 10% of reads provided clear evidence of alternative genomic conformations due to apparent rearrangements across large repeats. Quantitative assessment of these repeat-spanning read pairs revealed that all large repeat arrangements are present at appreciable frequencies in vivo, although not always in equimolar amounts. The observed stoichiometric differences for some arrangements are inconsistent with a predominant master circular structure for the mitochondrial genome of M. guttatus IM62. Finally, because IM62 contains a cryptic cytoplasmic male sterility (CMS) system, an in silico search for potential CMS genes was undertaken. The three chimeric open reading frames (ORFs) identified in this study, in addition to the previously identified ORFs upstream of the nad6 gene, are the most likely CMS candidate genes in this line.
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Affiliation(s)
- Jeffrey P Mower
- Center for Plant Science Innovation and Department of Agronomy and Horticulture, University of Nebraska, NE, USA.
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27
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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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Lloyd AH, Rousseau-Gueutin M, Timmis JN, Sheppard AE, Ayliffe MA. Promiscuous Organellar DNA. ADVANCES IN PHOTOSYNTHESIS AND RESPIRATION 2012. [DOI: 10.1007/978-94-007-2920-9_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Chang S, Yang T, Du T, Huang Y, Chen J, Yan J, He J, Guan R. Mitochondrial genome sequencing helps show the evolutionary mechanism of mitochondrial genome formation in Brassica. BMC Genomics 2011; 12:497. [PMID: 21988783 PMCID: PMC3204307 DOI: 10.1186/1471-2164-12-497] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 10/11/2011] [Indexed: 11/24/2022] Open
Abstract
Background Angiosperm mitochondrial genomes are more complex than those of other organisms. Analyses of the mitochondrial genome sequences of at least 11 angiosperm species have showed several common properties; these cannot easily explain, however, how the diverse mitotypes evolved within each genus or species. We analyzed the evolutionary relationships of Brassica mitotypes by sequencing. Results We sequenced the mitotypes of cam (Brassica rapa), ole (B. oleracea), jun (B. juncea), and car (B. carinata) and analyzed them together with two previously sequenced mitotypes of B. napus (pol and nap). The sizes of whole single circular genomes of cam, jun, ole, and car are 219,747 bp, 219,766 bp, 360,271 bp, and 232,241 bp, respectively. The mitochondrial genome of ole is largest as a resulting of the duplication of a 141.8 kb segment. The jun mitotype is the result of an inherited cam mitotype, and pol is also derived from the cam mitotype with evolutionary modifications. Genes with known functions are conserved in all mitotypes, but clear variation in open reading frames (ORFs) with unknown functions among the six mitotypes was observed. Sequence relationship analysis showed that there has been genome compaction and inheritance in the course of Brassica mitotype evolution. Conclusions We have sequenced four Brassica mitotypes, compared six Brassica mitotypes and suggested a mechanism for mitochondrial genome formation in Brassica, including evolutionary events such as inheritance, duplication, rearrangement, genome compaction, and mutation.
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Affiliation(s)
- Shengxin Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, PR China
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Liu Y, Xue JY, Wang B, Li L, Qiu YL. The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution. PLoS One 2011; 6:e25836. [PMID: 21998706 PMCID: PMC3187804 DOI: 10.1371/journal.pone.0025836] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
Early land plant mitochondrial genomes captured important changes of mitochondrial genome evolution when plants colonized land. The chondromes of seed plants show several derived characteristics, e.g., large genome size variation, rapid intra-genomic rearrangement, abundant introns, and highly variable levels of RNA editing. On the other hand, the chondromes of charophytic algae are still largely ancestral in these aspects, resembling those of early eukaryotes. When the transition happened has been a long-standing question in studies of mitochondrial genome evolution. Here we report complete mitochondrial genome sequences from an early-diverging liverwort, Treubia lacunosa, and a late-evolving moss, Anomodon rugelii. The two genomes, 151,983 and 104,239 base pairs in size respectively, contain standard sets of protein coding genes for respiration and protein synthesis, as well as nearly full sets of rRNA and tRNA genes found in the chondromes of the liverworts Marchantia polymorpha and Pleurozia purpurea and the moss Physcomitrella patens. The gene orders of these two chondromes are identical to those of the other liverworts and moss. Their intron contents, with all cis-spliced group I or group II introns, are also similar to those in the previously sequenced liverwort and moss chondromes. These five chondromes plus the two from the hornworts Phaeoceros laevis and Megaceros aenigmaticus for the first time allowed comprehensive comparative analyses of structure and organization of mitochondrial genomes both within and across the three major lineages of bryophytes. These analyses led to the conclusion that the mitochondrial genome experienced dynamic evolution in genome size, gene content, intron acquisition, gene order, and RNA editing during the origins of land plants and their major clades. However, evolution of this organellar genome has remained rather conservative since the origin and initial radiation of early land plants, except within vascular plants.
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Affiliation(s)
- Yang Liu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jia-Yu Xue
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- School of Life Sciences, Nanjing University, Nanjing, Jiangsu, People’s Republic of China
| | - Bin Wang
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Libo Li
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Yin-Long Qiu
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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31
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Rivarola M, Foster JT, Chan AP, Williams AL, Rice DW, Liu X, Melake-Berhan A, Huot Creasy H, Puiu D, Rosovitz MJ, Khouri HM, Beckstrom-Sternberg SM, Allan GJ, Keim P, Ravel J, Rabinowicz PD. Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 2011; 6:e21743. [PMID: 21750729 PMCID: PMC3131294 DOI: 10.1371/journal.pone.0021743] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 06/10/2011] [Indexed: 11/26/2022] Open
Abstract
Castor bean is an important oil-producing plant in the Euphorbiaceae family. Its high-quality oil contains up to 90% of the unusual fatty acid ricinoleate, which has many industrial and medical applications. Castor bean seeds also contain ricin, a highly toxic Type 2 ribosome-inactivating protein, which has gained relevance in recent years due to biosafety concerns. In order to gain knowledge on global genetic diversity in castor bean and to ultimately help the development of breeding and forensic tools, we carried out an extensive chloroplast sequence diversity analysis. Taking advantage of the recently published genome sequence of castor bean, we assembled the chloroplast and mitochondrion genomes extracting selected reads from the available whole genome shotgun reads. Using the chloroplast reference genome we used the methylation filtration technique to readily obtain draft genome sequences of 7 geographically and genetically diverse castor bean accessions. These sequence data were used to identify single nucleotide polymorphism markers and phylogenetic analysis resulted in the identification of two major clades that were not apparent in previous population genetic studies using genetic markers derived from nuclear DNA. Two distinct sub-clades could be defined within each major clade and large-scale genotyping of castor bean populations worldwide confirmed previously observed low levels of genetic diversity and showed a broad geographic distribution of each sub-clade.
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MESH Headings
- Base Sequence
- Ricinus communis/classification
- Ricinus communis/genetics
- Ricinus communis/growth & development
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Genetic Variation
- Genome, Chloroplast/genetics
- Genome, Mitochondrial/genetics
- Genome, Plant/genetics
- Molecular Sequence Data
- Phylogeny
- Polymorphism, Single Nucleotide
- Sequence Analysis, DNA
- Species Specificity
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Affiliation(s)
- Maximo Rivarola
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey T. Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Amber L. Williams
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Danny W. Rice
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Xinyue Liu
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | | | - Heather Huot Creasy
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Daniela Puiu
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - M. J. Rosovitz
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Hoda M. Khouri
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Stephen M. Beckstrom-Sternberg
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
- Pathogen Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Gerard J. Allan
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Pablo D. Rabinowicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- J. Craig Venter Institute, Rockville, Maryland, United States of America
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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32
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Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD. The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 2011; 6:e16404. [PMID: 21283772 PMCID: PMC3024419 DOI: 10.1371/journal.pone.0016404] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 12/18/2010] [Indexed: 11/26/2022] Open
Abstract
The mitochondrial genomes of seed plants are exceptionally fluid in size, structure, and sequence content, with the accumulation and activity of repetitive sequences underlying much of this variation. We report the first fully sequenced mitochondrial genome of a legume, Vigna radiata (mung bean), and show that despite its unexceptional size (401,262 nt), the genome is unusually depauperate in repetitive DNA and "promiscuous" sequences from the chloroplast and nuclear genomes. Although Vigna lacks the large, recombinationally active repeats typical of most other seed plants, a PCR survey of its modest repertoire of short (38–297 nt) repeats nevertheless revealed evidence for recombination across all of them. A set of novel control assays showed, however, that these results could instead reflect, in part or entirely, artifacts of PCR-mediated recombination. Consequently, we recommend that other methods, especially high-depth genome sequencing, be used instead of PCR to infer patterns of plant mitochondrial recombination. The average-sized but repeat- and feature-poor mitochondrial genome of Vigna makes it ever more difficult to generalize about the factors shaping the size and sequence content of plant mitochondrial genomes.
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Affiliation(s)
- Andrew J Alverson
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America.
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33
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Leister D, Kleine T. Role of intercompartmental DNA transfer in producing genetic diversity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 291:73-114. [PMID: 22017974 DOI: 10.1016/b978-0-12-386035-4.00003-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, genes are found in three compartments-the nucleus, mitochondria, and plastids-and extensive gene transfer has occurred between them. Most organellar genes in the nucleus migrated there long ago, but transfer is ongoing and ubiquitous. It now generates mostly noncoding nuclear DNA, can also disrupt gene functions, and reshape genes by adding novel exons. Plastid or nuclear sequences have also contributed to the formation of mitochondrial tRNA genes. It is now clear that organelle-to-nucleus DNA transfer involves the escape of DNA molecules from the organelles at times of stress or at certain developmental stages, and their subsequent incorporation at sites of double-stranded breaks in nuclear DNA by nonhomologous recombination. Intercompartmental DNA transfer thus appears to be an inescapable phenomenon that has had a broad impact on eukaryotic evolution, affecting DNA repair, gene and genome evolution, and redirecting proteins to different target compartments.
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Affiliation(s)
- Dario Leister
- Lehrstuhl für Molekularbiologie der Pflanzen, Department Biologie I, Ludwig-Maximilians-Universität München-LMU, Planegg-Martinsried, Germany
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Sloan DB, Alverson AJ, Storchová H, Palmer JD, Taylor DR. Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol 2010; 10:274. [PMID: 20831793 PMCID: PMC2942850 DOI: 10.1186/1471-2148-10-274] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 09/10/2010] [Indexed: 11/10/2022] Open
Abstract
Background Mitochondrial gene loss and functional transfer to the nucleus is an ongoing process in many lineages of plants, resulting in substantial variation across species in mitochondrial gene content. The Caryophyllaceae represents one lineage that has experienced a particularly high rate of mitochondrial gene loss relative to other angiosperms. Results In this study, we report the first complete mitochondrial genome sequence from a member of this family, Silene latifolia. The genome can be mapped as a 253,413 bp circle, but its structure is complicated by a large repeated region that is present in 6 copies. Active recombination among these copies produces a suite of alternative genome configurations that appear to be at or near "recombinational equilibrium". The genome contains the fewest genes of any angiosperm mitochondrial genome sequenced to date, with intact copies of only 25 of the 41 protein genes inferred to be present in the common ancestor of angiosperms. As observed more broadly in angiosperms, ribosomal proteins have been especially prone to gene loss in the S. latifolia lineage. The genome has also experienced a major reduction in tRNA gene content, including loss of functional tRNAs of both native and chloroplast origin. Even assuming expanded wobble-pairing rules, the mitochondrial genome can support translation of only 17 of the 61 sense codons, which code for only 9 of the 20 amino acids. In addition, genes encoding 18S and, especially, 5S rRNA exhibit exceptional sequence divergence relative to other plants. Divergence in one region of 18S rRNA appears to be the result of a gene conversion event, in which recombination with a homologous gene of chloroplast origin led to the complete replacement of a helix in this ribosomal RNA. Conclusions These findings suggest a markedly expanded role for nuclear gene products in the translation of mitochondrial genes in S. latifolia and raise the possibility of altered selective constraints operating on the mitochondrial translational apparatus in this lineage.
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Affiliation(s)
- Daniel B Sloan
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
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35
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Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome. ACTA ACUST UNITED AC 2010. [DOI: 10.1155/2010/620137] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The angiosperm mitochondrial genome is the largest and least gene-dense among the eukaryotes, because its intergenic regions are expanded. There seems to be no functional constraint on the size of the intergenic regions; angiosperms maintain the large mitochondrial genome size by a currently unknown mechanism. After a brief description of the angiosperm mitochondrial genome, this review focuses on our current knowledge of the mechanisms that control the maintenance and alteration of the genome. In both processes, the control of homologous recombination is crucial in terms of site and frequency. The copy numbers of various types of mitochondrial DNA molecules may also be controlled, especially during transmission of the mitochondrial genome from one generation to the next. An important characteristic of angiosperm mitochondria is that they contain polypeptides that are translated from open reading frames created as byproducts of genome alteration and that are generally nonfunctional. Such polypeptides have potential to evolve into functional ones responsible for mitochondrially encoded traits such as cytoplasmic male sterility or may be remnants of the former functional polypeptides.
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36
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Xue JY, Liu Y, Li L, Wang B, Qiu YL. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet 2009; 56:53-61. [DOI: 10.1007/s00294-009-0279-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/19/2009] [Accepted: 11/21/2009] [Indexed: 10/20/2022]
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37
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Mower JP, Bonen L. Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae. BMC Evol Biol 2009; 9:265. [PMID: 19917118 PMCID: PMC2780418 DOI: 10.1186/1471-2148-9-265] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 11/16/2009] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial genomes of plants generally encode 30-40 identified protein-coding genes and a large number of lineage-specific ORFs. The lack of wide conservation for most ORFs suggests they are unlikely to be functional. However, an ORF, termed orf-bryo1, was recently found to be conserved among bryophytes suggesting that it might indeed encode a functional mitochondrial protein. Results From a broad survey of land plants, we have found that the orf-bryo1 gene is also conserved in the mitochondria of vascular plants and charophycean green algae. This gene is actively transcribed and RNA edited in many flowering plants. Comparative sequence analysis and distribution of editing suggests that it encodes ribosomal protein L10 of the large subunit of the ribosome. In several lineages, such as crucifers and grasses, where the rpl10 gene has been lost from the mitochondrion, we suggest that a copy of the nucleus-encoded chloroplast-derived rpl10 gene may serve as a functional replacement. Conclusion Despite the fact that there are now over 20 mitochondrial genome sequences for land plants and green algae, this gene has remained unidentified and largely undetected until now because of the unlikely coincidence that most of the earlier sequences were from the few lineages that lack the intact gene. These results illustrate the power of comparative sequencing to identify novel genomic features.
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Affiliation(s)
- Jeffrey P Mower
- Department of Agronomy and Horticulture, University of Nebraska, Center for Plant Science Innovation, Lincoln, NE, USA.
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