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Grosser MR, Sites SK, Murata MM, Lopez Y, Chamusco KC, Love Harriage K, Grosser JW, Graham JH, Gmitter FG, Chase CD. Plant mitochondrial introns as genetic markers - conservation and variation. FRONTIERS IN PLANT SCIENCE 2023; 14:1116851. [PMID: 37021319 PMCID: PMC10067590 DOI: 10.3389/fpls.2023.1116851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.
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Affiliation(s)
- Melinda R. Grosser
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Samantha K. Sites
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Mayara M. Murata
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Karen C. Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Kyra Love Harriage
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - James H. Graham
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Fred G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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Xia H, Zhao W, Shi Y, Wang XR, Wang B. Microhomologies Are Associated with Tandem Duplications and Structural Variation in Plant Mitochondrial Genomes. Genome Biol Evol 2021; 12:1965-1974. [PMID: 32790831 PMCID: PMC7643612 DOI: 10.1093/gbe/evaa172] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2020] [Indexed: 12/15/2022] Open
Abstract
Short tandem repeats (STRs) contribute to structural variation in plant mitochondrial genomes, but the mechanisms underlying their formation and expansion are unclear. In this study, we detected high polymorphism in the nad7-1 region of the Pinus tabuliformis mitogenome caused by the rapid accumulation of STRs and rearrangements over a few million years ago. The STRs in nad7-1 have a 7-bp microhomology (TAG7) flanking the repeat array. We then scanned the mitogenomes of 136 seed plants to understand the role of microhomology in the formation of STR and mitogenome evolution. A total of 13,170 STRs were identified, and almost half of them were associated with microhomologies. A substantial amount (1,197) of microhomologies was long enough to mediate structural variation, and the length of microhomology is positively correlated with the length of tandem repeat unit. These results suggest that microhomology may be involved in the formation of tandem repeat via microhomology-mediated pathway, and the formation of longer duplicates required greater length of microhomology. We examined the abundance of these 1,197 microhomologies, and found 75% of them were enriched in the plant mitogenomes. Further analyses of the 400 prevalent microhomologies revealed that 175 of them showed differential enrichment between angiosperms and gymnosperms and 186 differed between angiosperms and conifers, indicating lineage-specific usage and expansion of microhomologies. Our study sheds light on the sources of structural variation in plant mitochondrial genomes and highlights the importance of microhomology in mitochondrial genome evolution.
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Affiliation(s)
- Hanhan Xia
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Zhao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Yong Shi
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Xiao-Ru Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
- Department of Ecology and Environmental Science, UPSC, Umeå University, Umeå, Sweden
| | - Baosheng Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
- Corresponding author: E-mail:
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He W, Chen C, Adedze YMN, Dong X, Xi K, Sun Y, Dang T, Jin D. Multicentric origin and diversification of atp6- orf79-like structures reveal mitochondrial gene flows in Oryza rufipogon and Oryza sativa. Evol Appl 2020; 13:2284-2299. [PMID: 33005224 PMCID: PMC7513716 DOI: 10.1111/eva.13022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/26/2020] [Accepted: 05/13/2020] [Indexed: 11/27/2022] Open
Abstract
Cytoplasmic male sterility (CMS) is a widely used genetic tool in modern hybrid rice breeding. Most genes conferring rice gametophytic CMS are homologous to orf79 and co-transcribe with atp6. However, the origin, differentiation and flow of these mitochondrial genes in wild and cultivated rice species remain unclear. In this study, we performed de novo assembly of the mitochondrial genomes of 221 common wild rice (Oryza rufipogon Griff.) and 369 Asian cultivated rice (Oryza sativa L.) accessions, and identified 16 haplotypes of atp6-orf79-like structures and 11 orf79 alleles. These homologous structures were classified into 4 distinct groups (AO-I, AO-II, AO-III and AO-IV), all of which were observed in O. rufipogon but only AO-I was detected in O. sativa, causing a decrease in the frequency of atp6-orf79-like structures from 19.9% to 8.1%. Phylogenetic and biogeographic analyses revealed that the different groups of these gametophytic CMS-related genes in O. rufipogon evolved in a multicentric pattern. The geographical origin of the atp6-orf79-like structures was further traced back, and a candidate region in north-east of Gangetic Plain on the Indian Peninsula (South Asia) was identified as the origin centre of AO-I. The orf79 alleles were detected in all three cytoplasmic types (Or-CT0, Or-CT1 and Or-CT2) of O. rufipogon, but only two alleles (orf79a and orf79b) were observed in Or-CT0 type of O. sativa, while no orf79 allele was found in other types of O. sativa. Our results also revealed that the orf79 alleles in cultivated rice originated from the wild rice population in South and South-East Asia. In addition, strong positive selection pressure was detected on the sequence variations of orf79 alleles, and a special evolutionary strategy was noted in these gametophytic CMS-related genes, suggesting that their divergence could be beneficial to their survival in evolution.
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Affiliation(s)
- Wenchuang He
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
| | - Caijin Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
- Institute of Biological and Environmental Sciences University of Aberdeen Aberdeen UK
| | | | - Xilong Dong
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
| | - Kun Xi
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
| | - Yongsheng Sun
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
| | - Tengfei Dang
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
| | - Deming Jin
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River College of Plant Science and Technology Huazhong Agricultural University Wuhan China
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Hrivnák M, Paule L, Krajmerová D, Kulaç Ş, Şevik H, Turna İ, Tvauri I, Gömöry D. Genetic variation in Tertiary relics: The case of eastern-Mediterranean Abies (Pinaceae). Ecol Evol 2017; 7:10018-10030. [PMID: 29238533 PMCID: PMC5723589 DOI: 10.1002/ece3.3519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 09/11/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023] Open
Abstract
The eastern‐Mediterranean Abies taxa, which include both widely distributed species and taxa with minuscule ranges, represent a good model to study the impacts of range size and fragmentation on the levels of genetic diversity and differentiation. To assess the patterns of genetic diversity and phylogenetic relationships among eastern‐Mediterranean Abies taxa, genetic variation was assessed by eight nuclear microsatellite loci in 52 populations of Abies taxa with a focus on those distributed in Turkey and the Caucasus. Both at the population and the taxon level, the subspecies or regional populations of Abies nordmanniana s.l. exhibited generally higher allelic richness, private allelic richness, and expected heterozygosity compared with Abies cilicica s.l. Results of both the structure analysis and distance‐based approaches showed a strong differentiation of the two A. cilicica subspecies from the rest as well as from each other, whereas the subspecies of A. nordmanniana were distinct but less differentiated. ABC simulations were run for a set of scenarios of phylogeny and past demographic changes. For A. ×olcayana, the simulation gave a poor support for the hypothesis of being a taxon resulting from a past hybridization, the same is true for Abies equi‐trojani: both they represent evolutionary branches of Abies bornmuelleriana.
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Affiliation(s)
| | | | | | | | - Hakan Şevik
- Faculty of Engineering and Architecture Kastamonu University Kastamonu Turkey
| | - İbrahim Turna
- Faculty of Forestry Karadeniz Technical University Trabzon Turkey
| | - Irina Tvauri
- Scientific-Research Center of Agriculture Tbilisi Georgia.,Vasil Gulisashvili Forest Institute Agricultural University of Georgia Tbilisi Georgia
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Sawicki J, Plášek V, Ochyra R, Szczecińska M, Ślipiko M, Myszczyński K, Kulik T. Mitogenomic analyses support the recent division of the genus Orthotrichum (Orthotrichaceae, Bryophyta). Sci Rep 2017; 7:4408. [PMID: 28667304 PMCID: PMC5493672 DOI: 10.1038/s41598-017-04833-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/22/2017] [Indexed: 11/22/2022] Open
Abstract
A recently presented taxonomical arrangement of the moss genus Orthotrichum Hedw. s.l. substantially changed the traditional view of the taxon that had been accepted throughout the twentieth century. This paper provides the results of mitogenomic studies that strongly support the new taxonomical concept. Comparative analyses presented in this study confirmed the stable structure of moss mitogenomes. Moreover, 17 complete mitogenome sequences were used to identify the major evolutionary groups, including 11 newly sequenced ones, for this study. The analysis of mitochondrial hotspots revealed intron 4 of the cox1 gene to be the most variable non-coding region. The most variable protein-coding genes in the tribe Orthotricheae were ccmFC and tatC. The intergenic and intronic hotspots of Orthotrichum s.l. identified in the present study do not correspond to those described in vascular plant mitogenomes.
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Affiliation(s)
- Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland.
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic.
| | - Vítězslav Plášek
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Ryszard Ochyra
- Laboratory of Bryology, Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Kraków, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
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Hao ZZ, Liu YY, Nazaire M, Wei XX, Wang XQ. Molecular phylogenetics and evolutionary history of sect. Quinquefoliae (Pinus): implications for Northern Hemisphere biogeography. Mol Phylogenet Evol 2015; 87:65-79. [PMID: 25800283 DOI: 10.1016/j.ympev.2015.03.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 02/24/2015] [Accepted: 03/14/2015] [Indexed: 01/15/2023]
Abstract
Climatic changes and tectonic events in the Cenozoic have greatly influenced the evolution and geographic distribution of the temperate flora. Such consequences should be most evident in plant groups that are ancient, widespread, and diverse. As one of the most widespread genera of trees, Pinus provides a good model for investigating the history of species diversification and biogeographic disjunction in the Northern Hemisphere. In this study, we reconstructed the phylogeny and investigated the evolutionary and biogeographic history of sect. Quinquefoliae (Pinus), a species-rich lineage disjunctly distributed in Asia, Europe and North America, based on complete taxon sampling and by using nine DNA fragments from chloroplast (cp), mitochondrial (mt) and nuclear genomes. The monophyly of the three subsections, Krempfianae, Gerardianae, and Strobus, is well-supported by cpDNA and nuclear gene phylogenies. However, neither subsect. Gerardianae nor subsect. Strobus forms a monophyletic group in the mtDNA phylogeny, in which sect. Quinquefoliae was divided into two major clades, one consisting of the North American and northeastern Asian species as well as the European P. peuce of subsect. Strobus, and the other comprising the remaining Eurasian species belonging to three subsections. The significant topological incongruence among the gene trees, in conjunction with divergence time estimation and ancestral area reconstruction, indicates that both ancient and relatively recent introgressive hybridization events occurred in the evolution of sect. Quinquefoliae, particularly in northeastern Asia and northwestern North America. In addition, the phylogenetic analysis suggests that the species of subsect. Strobus from subtropical eastern Asia and neighboring areas may have a single origin, although species non-monophyly is very widespread in the nuclear gene trees. Moreover, our study seems to support a Tethyan origin of sect. Quinquefoliae given the distributions and phylogenetic positions of subsects. Krempfianae and Gerardianae, and also highlights the importance of active mountain buildings and climatic changes during the Late Neogene in shaping the species diversity and geographic distribution of Pinus.
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Affiliation(s)
- Zhen-Zhen Hao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yan-Yan Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Mare Nazaire
- Rancho Santa Ana Botanic Garden, Claremont, CA 91711, USA
| | - Xiao-Xin Wei
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Xiao-Quan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
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Wang B, Wang XR. Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus. Mol Phylogenet Evol 2014; 80:20-30. [PMID: 25106134 DOI: 10.1016/j.ympev.2014.07.014] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 06/18/2014] [Accepted: 07/24/2014] [Indexed: 11/28/2022]
Abstract
The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pinus. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.
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Affiliation(s)
- Baosheng Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden.
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, SE-90187 Umeå, Sweden
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Evolution and biogeography of gymnosperms. Mol Phylogenet Evol 2014; 75:24-40. [DOI: 10.1016/j.ympev.2014.02.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 02/06/2014] [Accepted: 02/10/2014] [Indexed: 11/20/2022]
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Semerikova SA, Semerikov VL. Mitochondrial DNA variation and reticulate evolution of the genus Abies. RUSS J GENET+ 2014. [DOI: 10.1134/s1022795414040139] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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