1
|
Zhou L, Chen T, Qiu X, Liu J, Guo S. Evolutionary differences in gene loss and pseudogenization among mycoheterotrophic orchids in the tribe Vanilleae (subfamily Vanilloideae). FRONTIERS IN PLANT SCIENCE 2023; 14:1160446. [PMID: 37035052 PMCID: PMC10073425 DOI: 10.3389/fpls.2023.1160446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Galeola lindleyana is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae. METHODS In this study, the G. lindleyana plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes. RESULTS The G. lindleyana plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and psaJ in photosystem I. The length of the G. lindleyana plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid's plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two ndhB genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the Cyrtosia septentrionalis plastome which was found to be closest in length to the G. lindleyana plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the psbA, psbK, atpA and psaB retained in the G. lindleyana plastome were missing in the C. septentrionalis plastome, while, the matK, rps16, and atpF were incomplete in the C. septentrionalis plastome, yet still complete in that of the G. lindleyana. Lastly, compared with the G. lindleyana plastome, a 15 kb region located in the SSC area between ndhB-rrn16S was found to be inverted in the C. septentrionalis plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes. DISCUSSION Thus, this study's decoding of the mycoheterotrophic G. lindleyana plastome provides valuable resource data for future research and conservation of endangered orchids.
Collapse
Affiliation(s)
| | | | | | - Jinxin Liu
- *Correspondence: Jinxin Liu, ; Shunxing Guo,
| | | |
Collapse
|
2
|
de Lima Ferreira P, Batista R, Andermann T, Groppo M, Bacon CD, Antonelli A. Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses. Mol Phylogenet Evol 2022; 169:107432. [DOI: 10.1016/j.ympev.2022.107432] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 12/21/2021] [Accepted: 01/14/2022] [Indexed: 11/26/2022]
|
3
|
Thode VA, Oliveira CT, Loeuille B, Siniscalchi CM, Pirani JR. Comparative analyses of Mikania (Asteraceae: Eupatorieae) plastomes and impact of data partitioning and inference methods on phylogenetic relationships. Sci Rep 2021; 11:13267. [PMID: 34168241 PMCID: PMC8225666 DOI: 10.1038/s41598-021-92727-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 06/15/2021] [Indexed: 11/09/2022] Open
Abstract
We assembled new plastomes of 19 species of Mikania and of Ageratina fastigiata, Litothamnus nitidus, and Stevia collina, all belonging to tribe Eupatorieae (Asteraceae). We analyzed the structure and content of the assembled plastomes and used the newly generated sequences to infer phylogenetic relationships and study the effects of different data partitions and inference methods on the topologies. Most phylogenetic studies with plastomes ignore that processes like recombination and biparental inheritance can occur in this organelle, using the whole genome as a single locus. Our study sought to compare this approach with multispecies coalescent methods that assume that different parts of the genome evolve at different rates. We found that the overall gene content, structure, and orientation are very conserved in all plastomes of the studied species. As observed in other Asteraceae, the 22 plastomes assembled here contain two nested inversions in the LSC region. The plastomes show similar length and the same gene content. The two most variable regions within Mikania are rpl32-ndhF and rpl16-rps3, while the three genes with the highest percentage of variable sites are ycf1, rpoA, and psbT. We generated six phylogenetic trees using concatenated maximum likelihood and multispecies coalescent methods and three data partitions: coding and non-coding sequences and both combined. All trees strongly support that the sampled Mikania species form a monophyletic group, which is further subdivided into three clades. The internal relationships within each clade are sensitive to the data partitioning and inference methods employed. The trees resulting from concatenated analysis are more similar among each other than to the correspondent tree generated with the same data partition but a different method. The multispecies coalescent analysis indicate a high level of incongruence between species and gene trees. The lack of resolution and congruence among trees can be explained by the sparse sampling (~ 0.45% of the currently accepted species) and by the low number of informative characters present in the sequences. Our study sheds light into the impact of data partitioning and methods over phylogenetic resolution and brings relevant information for the study of Mikania diversity and evolution, as well as for the Asteraceae family as a whole.
Collapse
Affiliation(s)
- Verônica A Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, Porto Alegre, Rio Grande do Sul, 91501-970, Brazil
| | - Caetano T Oliveira
- Sítio Roberto Burle Marx, Instituto do Patrimônio Histórico e Artístico Nacional, Estrada Roberto Burle Marx, 2019, Barra de Guaratiba, Rio de Janeiro, Rio de Janeiro, 23020-240, Brazil
| | - Benoît Loeuille
- Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Avenida Professor Moraes Rego, 1235, Recife, Pernambuco, 50670-901, Brazil
| | - Carolina M Siniscalchi
- Department of Biological Sciences, Mississippi State University, 295 Lee Blvd, Mississippi State, Mississippi, MS, 39762, USA.
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Tv. 14, São Paulo, São Paulo, 05508-090, Brazil
| |
Collapse
|
4
|
Daniell H, Jin S, Zhu X, Gitzendanner MA, Soltis DE, Soltis PS. Green giant-a tiny chloroplast genome with mighty power to produce high-value proteins: history and phylogeny. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:430-447. [PMID: 33484606 PMCID: PMC7955891 DOI: 10.1111/pbi.13556] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/11/2021] [Accepted: 01/16/2021] [Indexed: 05/04/2023]
Abstract
Free-living cyanobacteria were entrapped by eukaryotic cells ~2 billion years ago, ultimately giving rise to chloroplasts. After a century of debate, the presence of chloroplast DNA was demonstrated in the 1960s. The first chloroplast genomes were sequenced in the 1980s, followed by ~100 vegetable, fruit, cereal, beverage, oil and starch/sugar crop chloroplast genomes in the past three decades. Foreign genes were expressed in isolated chloroplasts or intact plant cells in the late 1980s and stably integrated into chloroplast genomes, with typically maternal inheritance shown in the 1990s. Since then, chloroplast genomes conferred the highest reported levels of tolerance or resistance to biotic or abiotic stress. Although launching products with agronomic traits in important crops using this concept has been elusive, commercial products developed include enzymes used in everyday life from processing fruit juice, to enhancing water absorption of cotton fibre or removal of stains as laundry detergents and in dye removal in the textile industry. Plastid genome sequences have revealed the framework of green plant phylogeny as well as the intricate history of plastid genome transfer events to other eukaryotes. Discordant historical signals among plastid genes suggest possible variable constraints across the plastome and further understanding and mitigation of these constraints may yield new opportunities for bioengineering. In this review, we trace the evolutionary history of chloroplasts, status of autonomy and recent advances in products developed for everyday use or those advanced to the clinic, including treatment of COVID-19 patients and SARS-CoV-2 vaccine.
Collapse
Affiliation(s)
- Henry Daniell
- Department of Basic and Translational SciencesSchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xin‐Guang Zhu
- State Key Laboratory for Plant Molecular Genetics and Center of Excellence for Molecular Plant SciencesChinese Academy of SciencesShanghaiChina
| | | | - Douglas E. Soltis
- Florida Museum of Natural History and Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFLUSA
| |
Collapse
|
5
|
Loeuille B, Thode V, Siniscalchi C, Andrade S, Rossi M, Pirani JR. Extremely low nucleotide diversity among thirty-six new chloroplast genome sequences from Aldama (Heliantheae, Asteraceae) and comparative chloroplast genomics analyses with closely related genera. PeerJ 2021; 9:e10886. [PMID: 33665028 PMCID: PMC7912680 DOI: 10.7717/peerj.10886] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 01/12/2021] [Indexed: 01/23/2023] Open
Abstract
Aldama (Heliantheae, Asteraceae) is a diverse genus in the sunflower family. To date, nearly 200 Asteraceae chloroplast genomes have been sequenced, but the plastomes of Aldama remain undescribed. Plastomes in Asteraceae usually show little sequence divergence, consequently, our hypothesis is that species of Aldama will be overall conserved. In this study, we newly sequenced 36 plastomes of Aldama and of five species belonging to other Heliantheae genera selected as outgroups (i.e., Dimerostemma asperatum, Helianthus tuberosus, Iostephane heterophylla, Pappobolus lanatus var. lanatus, and Tithonia diversifolia). We analyzed the structure and gene content of the assembled plastomes and performed comparative analyses within Aldama and with other closely related genera. As expected, Aldama plastomes are very conserved, with the overall gene content and orientation being similar in all studied species. The length of the plastome is also consistent and the junction between regions usually contain the same genes and have similar lengths. A large ∼20 kb and a small ∼3 kb inversion were detected in the Large Single Copy (LSC) regions of all assembled plastomes, similarly to other Asteraceae species. The nucleotide diversity is very low, with only 1,509 variable sites in 127,466 bp (i.e., 1.18% of the sites in the alignment of 36 Aldama plastomes, with one of the IRs removed, is variable). Only one gene, rbcL, shows signatures of positive selection. The plastomes of the selected outgroups feature a similar gene content and structure compared to Aldama and also present the two inversions in the LSC region. Deletions of different lengths were observed in the gene ycf2. Multiple SSRs were identified for the sequenced Aldama and outgroups. The phylogenetic analysis shows that Aldama is not monophyletic due to the position of the Mexican species A. dentata. All Brazilian species form a strongly supported clade. Our results bring new understandings into the evolution and diversity of plastomes at the species level.
Collapse
Affiliation(s)
- Benoit Loeuille
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Verônica Thode
- Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Carolina Siniscalchi
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, United States of America
| | - Sonia Andrade
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| | - José Rubens Pirani
- Departamento de Botânica, Universidade de São Paulo, São Paulo, São Paulo, Brazil
| |
Collapse
|
6
|
Zhang R, Xu B, Li J, Zhao Z, Han J, Lei Y, Yang Q, Peng F, Liu ZL. Transit From Autotrophism to Heterotrophism: Sequence Variation and Evolution of Chloroplast Genomes in Orobanchaceae Species. Front Genet 2020; 11:542017. [PMID: 33133143 PMCID: PMC7573133 DOI: 10.3389/fgene.2020.542017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/07/2020] [Indexed: 01/15/2023] Open
Abstract
The family Orobanchaceae including autotrophic, hemiparasitic, and holoparasitic species, is becoming a key taxa to study the evolution of chloroplast genomes in different lifestyles. But the early evolutionary trajectory in the transit from autotrophism to hemiparasitism still maintains unclear for the inadequate sampling. In this study, we compared 50 complete chloroplast genomes in Orobanchaceae, containing four newly sequenced plastomes from hemiparasitic Pedicularis, to elucidate the sequence variation patterns in the evolution of plastomes. Contrasted to the sequence and structural hypervariabilities in holoparasites, hemiparasitic plastomes exhibited high similarity to those of autotrophs in gene and GC contents. They are generally characterized with functional or physical loss of ndh/tRNA genes and the inverted small-single-copy region. Gene losses in Orobanchaceae were lineage-specific and convergent, possibly related to structural reconfiguration and expansion/contraction of the inverted region. Pseudogenization of ndh genes was unique in hemiparasites. At least in Pedicularis, the ndhF gene might be most sensitive to the environmental factors and easily pseudogenized when autotrophs transit to hemiparasites. And the changes in gene contents and structural variation potentially deeply rely on the feeding type. Selective pressure, together with mutational bias, was the dominant factor of shaping the codon usage patterns. The relaxed selective constraint, potentially with genome-based GC conversion (gBGC) and preferential codon usage, drive the fluctuation of GC contents among taxa with different lifestyles. Phylogenetic analysis in Orobanchaceae supported that parasitic species were single-originated while holoparasites were multiple-originated. Overall, the comparison of plastomes provided a good opportunity to understand the evolution process in Orobanchaceae with different lifestyles.
Collapse
Affiliation(s)
- Ruiting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Bei Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jianfang Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhe Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Jie Han
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Yunjing Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Qian Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Fangfang Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| | - Zhan-Lin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Science, Northwest University, Xi'an, China
| |
Collapse
|
7
|
Complete chloroplast genome of Sophora alopecuroides (Papilionoideae): molecular structures, comparative genome analysis and phylogenetic analysis. J Genet 2020. [DOI: 10.1007/s12041-019-1173-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
8
|
Liu X, Zhou B, Yang H, Li Y, Yang Q, Lu Y, Gao Y. Sequencing and Analysis of Chrysanthemum carinatum Schousb and Kalimeris indica. The Complete Chloroplast Genomes Reveal Two Inversions and rbcL as Barcoding of the Vegetable. Molecules 2018; 23:E1358. [PMID: 29874832 PMCID: PMC6099409 DOI: 10.3390/molecules23061358] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 05/31/2018] [Accepted: 05/31/2018] [Indexed: 01/28/2023] Open
Abstract
Chrysanthemum carinatum Schousb and Kalimeris indica are widely distributed edible vegetables and the sources of the Chinese medicine Asteraceae. The complete chloroplast (cp) genome of Asteraceae usually occurs in the inversions of two regions. Hence, the cp genome sequences and structures of Asteraceae species are crucial for the cp genome genetic diversity and evolutionary studies. Hence, in this paper, we have sequenced and analyzed for the first time the cp genome size of C. carinatum Schousb and K. indica, which are 149,752 bp and 152,885 bp, with a pair of inverted repeats (IRs) (24,523 bp and 25,003) separated by a large single copy (LSC) region (82,290 bp and 84,610) and a small single copy (SSC) region (18,416 bp and 18,269), respectively. In total, 79 protein-coding genes, 30 distinct transfer RNA (tRNA) genes, four distinct rRNA genes and two pseudogenes were found not only in C. carinatum Schousb but also in the K. indica cp genome. Fifty-two (52) and fifty-nine (59) repeats, and seventy (70) and ninety (90) simple sequence repeats (SSRs) were found in the C. carinatum Schousb and K. indica cp genomes, respectively. Codon usage analysis showed that leucine, isoleucine, and serine are the most frequent amino acids and that the UAA stop codon was the significantly favorite stop codon in both cp genomes. The two inversions, the LSC region ranging from trnC-GCA to trnG-UCC and the whole SSC region were found in both of them. The complete cp genome comparison with other Asteraceae species showed that the coding area is more conservative than the non-coding area. The phylogenetic analysis revealed that the rbcL gene is a good barcoding marker for identifying different vegetables. These results give an insight into the identification, the barcoding, and the understanding of the evolutionary model of the Asteraceae cp genome.
Collapse
Affiliation(s)
- Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Boyang Zhou
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Hongyuan Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Yuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Qian Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Yuzhuo Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| | - Yu Gao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, China.
| |
Collapse
|
9
|
Rieseberg LH, Soltis DE, Palmer JD. A MOLECULAR REEXAMINATION OF INTROGRESSION BETWEEN HELIANTHUS ANNUUS AND H. BOLANDERI (COMPOSITAE). Evolution 2017; 42:227-238. [PMID: 28567846 DOI: 10.1111/j.1558-5646.1988.tb04127.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/1987] [Accepted: 10/27/1987] [Indexed: 11/28/2022]
Abstract
Heiser (1949) hypothesized that a weedy race of Helianthus bolanderi had originated by the introgression of genes from H. annum into a serpentine race of H. bolanderi. Although Heiser's investigation of these species is frequently cited as one of the best examples of introgression in plants, definitive evidence of gene exchange is lacking (Heiser, 1973). To determine whether the weedy race of H. bolanderi actually originated via introgression, we analyzed allozyme, chloroplast-DNA (cpDNA), and nuclear-ribosomal-DNA (rDNA) variation. Evidence from enzyme electrophoresis did not support the proposed introgressive origin of weedy H. bolanderi. We detected a total of 37 low-frequency alleles distinguishing the serpentine race of H. bolanderi from H. annuus. Weedy H. bolanderi possessed only four of the 37 marker alleles. Further analysis demonstrated that serpentine H. bolanderi combined seven of the 35 alleles distinguishing H. annuus from weedy H. bolanderi, indicating that serpentine H. bolanderi shares three more marker alleles with H. annuus than does weedy H. bolanderi. These results are similar to expectations for race divergence from a single common ancestor and suggest that, if introgression occurred, the majority of marker alleles were rapidly lost following the initial hybridization event. Even more compelling evidence opposing Heiser's (1949) hypothesis, however, was from restriction-fragment analysis of cpDNA and nuclear rDNA. We detected a total of 17 cpDNA and five rDNA restriction-site mutations among the 19 populations examined. No parallel or back mutations were observed in phylogenetic trees constructed using either cpDNA or rDNA mutations, and both phylogenies were completely congruent regarding the alignment of all three taxa. In addition, the weedy race of H. bolanderi possessed a unique cpDNA, which was outside the range of variation observed among populations of either of the presumed parental species. Mean sequence divergences between the cpDNAs of weedy H. bolanderi and those of serpentine H. bolanderi and H. annuus were 0.30% and 0.35%, respectively. These estimates are comparable to sequence-divergence values observed between closely related species in other plant groups. Given the lack of parallel or convergent mutations in the cpDNA and rDNA phylogenetic trees, the complete congruence of these trees with flavonoid- and allozyme-variation patterns, and the presence of a unique and divergent chloroplast genome in the weedy race of H. bolanderi, we suggest that the weedy race of H. bolanderi was not derived recently through introgression, as hypothesized, but is relatively ancient in origin.
Collapse
Affiliation(s)
- Loren H Rieseberg
- Department of Botany, Washington State University, Pullman, WA, 99164
| | - Douglas E Soltis
- Department of Botany, Washington State University, Pullman, WA, 99164
| | - Jeffrey D Palmer
- Department of Biology, University of Michigan, Ann Arbor, MI, 48109
| |
Collapse
|
10
|
Soltis DE, Soltis PS, Ness BD. CHLOROPLAST‐DNA VARIATION AND MULTIPLE ORIGINS OF AUTOPOLYPLOIDY IN
HEUCHERA MICRANTHA
(SAXIFRAGACEAE). Evolution 2017; 43:650-656. [DOI: 10.1111/j.1558-5646.1989.tb04260.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/1988] [Accepted: 12/05/1988] [Indexed: 11/30/2022]
Affiliation(s)
| | - Pamela S. Soltis
- Department of Botany Washington State University Pullman WA 99164
| | - Bryan D. Ness
- Department of Botany Washington State University Pullman WA 99164
| |
Collapse
|
11
|
Comes HP, Abbott RJ. THE RELATIVE IMPORTANCE OF HISTORICAL EVENTS AND GENE FLOW ON THE POPULATION STRUCTURE OF A MEDITERRANEAN RAGWORT,SENECIO GALLICUS(ASTERACEAE). Evolution 2017; 52:355-367. [DOI: 10.1111/j.1558-5646.1998.tb01637.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/1997] [Accepted: 11/12/1997] [Indexed: 12/01/2022]
Affiliation(s)
- Hans Peter Comes
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews Fife KY16 9TH United Kingdom
| | - Richard J. Abbott
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews Fife KY16 9TH United Kingdom
| |
Collapse
|
12
|
NUCLEAR RIBOSOMAL DNA VARIATION AMONG RAMETS AND GENETS OF WHITE CLOVER. Evolution 2017; 46:1240-1247. [DOI: 10.1111/j.1558-5646.1992.tb00634.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/1991] [Accepted: 12/30/1991] [Indexed: 11/26/2022]
|
13
|
Spooner DM, Sytsma KJ, Smith JF. A MOLECULAR REEXAMINATION OF DIPLOID HYBRID SPECIATION OF
SOLANUM RAPHANIFOLIUM. Evolution 2017; 45:757-764. [DOI: 10.1111/j.1558-5646.1991.tb04344.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/1989] [Accepted: 09/04/1990] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Spooner
- Cooperative Investigation of the USDA, ARS, and the Department of Botany University of Wisconsin–Madison USA
| | - Kenneth J. Sytsma
- Vegetable Crops Research Unit, Agricultural Research Service, USDA, Department of Horticulture University of Wisconsin–Madison USA
| | - James F. Smith
- Department of Botany University of Wisconsin–Madison Madison WI 53706 USA
| |
Collapse
|
14
|
Jansen RK, Holsinger KE, Michaels HJ, Palmer JD. PHYLOGENETIC ANALYSIS OF CHLOROPLAST DNA RESTRICTION SITE DATA AT HIGHER TAXONOMIC LEVELS: AN EXAMPLE FROM THE ASTERACEAE. Evolution 2017; 44:2089-2105. [DOI: 10.1111/j.1558-5646.1990.tb04314.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/1989] [Accepted: 04/09/1990] [Indexed: 11/30/2022]
Affiliation(s)
- Robert K. Jansen
- Department of Ecology and Evolutionary Biology University of Connecticut Box U‐42 Storrs CT 06269 USA
| | - Kent E. Holsinger
- Department of Ecology and Evolutionary Biology University of Connecticut Box U‐42 Storrs CT 06269 USA
| | | | | |
Collapse
|
15
|
Comes HP, Abbott RJ. POPULATION GENETIC STRUCTURE AND GENE FLOW ACROSS ARID VERSUS MESIC ENVIRONMENTS: A COMPARATIVE STUDY OF TWO PARAPATRICSENECIOSPECIES FROM THE NEAR EAST. Evolution 2017; 53:36-54. [DOI: 10.1111/j.1558-5646.1999.tb05331.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/1997] [Accepted: 09/30/1998] [Indexed: 11/30/2022]
Affiliation(s)
- Hans Peter Comes
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews, Fife KY16 9TH United Kingdom
| | - Richard J. Abbott
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews, Fife KY16 9TH United Kingdom
| |
Collapse
|
16
|
Choi KS, Park S. The complete chloroplast genome sequence of Aster spathulifolius (Asteraceae); genomic features and relationship with Asteraceae. Gene 2015; 572:214-21. [PMID: 26164759 DOI: 10.1016/j.gene.2015.07.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 06/02/2015] [Accepted: 07/06/2015] [Indexed: 11/26/2022]
Abstract
Aster spathulifolius, a member of the Asteraceae family, is distributed along the coast of Japan and Korea. This plant is used for medicinal and ornamental purposes. The complete chloroplast (cp) genome of A. sphathulifolius consists of 149,473 bp that include a pair of inverted repeats of 24,751 bp separated by a large single copy region of 81,998 bp and a small single copy region of 17,973 bp. The chloroplast genome contains 78 coding genes, four rRNA genes and 29 tRNA genes. When compared to other cpDNA sequences of Asteraceae, A. spathulifolius showed the closest relationship with Jacobaea vulgaris, and its atpB gene was found to be a pseudogene, unlike J. vulgaris. Furthermore, evaluation of the gene compositions of J. vulgaris, Helianthus annuus, Guizotia abyssinica and A. spathulifolius revealed that 13.6-kb showed inversion from ndhF to rps15, unlike Lactuca of Asteraceae. Comparison of the synonymous (Ks) and nonsynonymous (Ka) substitution rates with J. vulgaris revealed that synonymous genes related to a small subunit of the ribosome showed the highest value (0.1558), while nonsynonymous rates of genes related to ATP synthase genes were highest (0.0118). These findings revealed that substitution has occurred at similar rates in most genes, and the substitution rates suggested that most genes is a purified selection.
Collapse
Affiliation(s)
- Kyoung Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 712-749, South Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 712-749, South Korea.
| |
Collapse
|
17
|
Prince LM. Plastid primers for angiosperm phylogenetics and phylogeography. APPLICATIONS IN PLANT SCIENCES 2015; 3:apps1400085. [PMID: 26082876 PMCID: PMC4467757 DOI: 10.3732/apps.1400085] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 03/24/2015] [Indexed: 05/12/2023]
Abstract
PREMISE OF THE STUDY PCR primers are available for virtually every region of the plastid genome. Selection of which primer pairs to use is second only to selection of the genic region. This is particularly true for research at the species/population interface. METHODS Primer pairs for 130 regions of the chloroplast genome were evaluated in 12 species distributed across the angiosperms. Likelihood of amplification success was inferred based upon number and location of mismatches to target sequence. Intraspecific sequence variability was evaluated under three different criteria in four species. RESULTS Many published primer pairs should work across all taxa sampled, with the exception of failure due to genomic reorganization events. Universal barcoding primers were the least likely to work (65% success). The list of most variable regions for use within species has little in common with the lists identified in prior studies. DISCUSSION Published primer sequences should amplify a diversity of flowering plant DNAs, even those designed for specific taxonomic groups. "Universal" primers may have extremely limited utility. There was little consistency in likelihood of amplification success for any given publication across lineages or within lineage across publications.
Collapse
Affiliation(s)
- Linda M. Prince
- Department of Botany, The Field Museum, 1400 S. Lake Shore Drive, Chicago, Illinois 60605 USA
- Author for correspondence:
| |
Collapse
|
18
|
Affiliation(s)
- K. Bachmann
- Hugo de Vries Laboratory; University of Amsterdam; Kruislaan 318 NL-1098 SM Amsterdam The Netherlands
| |
Collapse
|
19
|
Walker JF, Zanis MJ, Emery NC. Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae). AMERICAN JOURNAL OF BOTANY 2014; 101:722-9. [PMID: 24699541 DOI: 10.3732/ajb.1400049] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
PREMISE OF THE STUDY Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. METHODS We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. KEY RESULTS The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. CONCLUSIONS Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.
Collapse
Affiliation(s)
- Joseph F Walker
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907 USA
| | | | | |
Collapse
|
20
|
van Heusden AW, Bachmann K. Nuclear DNA Polymorphisms Among Strains ofMicroseris bigelovii(Asteraceae: Lactuceae) Amplified from Arbitrary Primers. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1992.tb00307.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
21
|
Timme RE, Kuehl JV, Boore JL, Jansen RK. A comparative analysis of the Lactuca and Helianthus (Asteraceae) plastid genomes: identification of divergent regions and categorization of shared repeats. AMERICAN JOURNAL OF BOTANY 2007; 94:302-12. [PMID: 21636403 DOI: 10.3732/ajb.94.3.302] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We have sequenced two complete chloroplast genomes in the Asteraceae, Helianthus annuus (sunflower), and Lactuca sativa (lettuce), which belong to the distantly related subfamilies, Asteroideae and Cichorioideae, respectively. The Helianthus chloroplast genome is 151 104 bp and the Lactuca genome is 152 772 bp long, which is within the usual size range for chloroplast genomes in flowering plants. When compared to tobacco, both genomes have two inversions: a large 22.8-kb inversion and a smaller 3.3-kb inversion nested within it. Pairwise sequence divergence across all genes, introns, and spacers in Helianthus and Lactuca has resulted in the discovery of new, fast-evolving DNA sequences for use in species-level phylogenetics, such as the trnY-rpoB, trnL-rpl32, and ndhC-trnV spacers. Analysis and categorization of shared repeats resulted in seven classes useful for future repeat studies: double tandem repeats, three or more tandem repeats, direct repeats dispersed in the genome, repeats found in reverse complement orientation, hairpin loops, runs of A's or T's in excess of 12 bp, and gene or tRNA similarity. Results from BLAST searches of our genomic sequence against expressed sequence tag (EST) databases for both genomes produced eight likely RNA edited sites (C → U changes). These detailed analyses in Asteraceae contribute to a broader understanding of plastid evolution across flowering plants.
Collapse
Affiliation(s)
- Ruth E Timme
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station C0930, Austin, Texas 78712 USA
| | | | | | | |
Collapse
|
22
|
James JK, Abbott RJ. RECENT, ALLOPATRIC, HOMOPLOID HYBRID SPECIATION: THE ORIGIN OF SENECIO SQUALIDUS (ASTERACEAE) IN THE BRITISH ISLES FROM A HYBRID ZONE ON MOUNT ETNA, SICILY. Evolution 2005. [DOI: 10.1111/j.0014-3820.2005.tb00967.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
|
23
|
Lelivelt CLC, McCabe MS, Newell CA, deSnoo CB, van Dun KMP, Birch-Machin I, Gray JC, Mills KHG, Nugent JM. Stable plastid transformation in lettuce (Lactuca sativa L.). PLANT MOLECULAR BIOLOGY 2005; 58:763-774. [PMID: 16240172 DOI: 10.1007/s11103-005-7704-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 05/20/2005] [Indexed: 05/04/2023]
Abstract
Although plastid transformation in higher plants was first demonstrated in the early 1990s it is only recently that the technology is being extended to a broader range of species. To date, the production of fertile transplastomic plants has been reported for tobacco, tomato, petunia, soybean, cotton and Lesquerella fendleri (Brassicaceae). In this study we demonstrate a polyethylene glycol-mediated plastid transformation system for lettuce that generates fertile, homoplasmic, plastid-transformed lines. Transformation was achieved using a vector that targets genes to the trnA/trnI intergenic region of the lettuce plastid genome employing the aadA gene as a selectable marker against spectinomycin. Spectinomycin resistance and heterologous gene transcription were shown in T(1) plants derived from self-pollinated primary regenerants demonstrating transmission of the plastid-encoded transgene to the first seed generation. Crossing with male sterile wild-type lettuce showed that spectinomycin resistance was not transmitted via pollen. Constructs containing the gfp gene showed plastid-based expression of green fluorescent protein. The lettuce plastid could have potential both as a production and a delivery system for edible human therapeutic proteins.
Collapse
Affiliation(s)
- Cilia L C Lelivelt
- Rijk Zwaan Breeding B.V., 1e Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Matthew S McCabe
- Institute of Bioengineering and Agroecology, National University of Ireland, Maynooth, Co. Kildare, Ireland
| | - Christine A Newell
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK
| | - C Bastiaan deSnoo
- Rijk Zwaan Breeding B.V., 1e Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Kees M P van Dun
- Rijk Zwaan Breeding B.V., 1e Kruisweg 9, 4793 RS, Fijnaart, The Netherlands
| | - Ian Birch-Machin
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK
- Department of Anatomy, University of Cambridge, Downing Street, CB2 3DY, Cambridge, UK
| | - John C Gray
- Department of Plant Sciences, University of Cambridge, Downing Street, CB2 3EA, Cambridge, UK
| | | | - Jacqueline M Nugent
- Institute of Bioengineering and Agroecology, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
24
|
Bain JF, Golden JL. Chloroplast haplotype diversity patterns inPackera pauciflora(Asteraceae) are affected by geographical isolation, hybridization, and breeding system. ACTA ACUST UNITED AC 2005. [DOI: 10.1139/b05-063] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Packera pauciflora (Pursh) Löve & Löve is a wide ranging alpine or subalpine species that is disjunct in three regions of North America: the northern Rocky mountains, QuebecLabrador, and the Sierra Nevada of California. It is one of two Packera species known to be self-fertile. We assessed intrapopulational chloroplast haplotype diversity (n) and haplotype nucleotide diversity ([Formula: see text]) and found it was lower and population structure (Φst), higher than all but one of the five other Packera species examined to date. In addition, distinct differences exist between populations from California and those from the Rocky mountains and eastern Canada. Our results suggest that geographical isolation, hybridization, and breeding system have all played a role in the formation of haplotype diversity patterns, and that, in spite of the wide disjunctions, the species is monophyletic.Key words: Asteraceae, cpDNA, haplotypes, Packera, phylogeography, self-fertility.
Collapse
|
25
|
Kim KJ, Choi KS, Jansen RK. Two chloroplast DNA inversions originated simultaneously during the early evolution of the sunflower family (Asteraceae). Mol Biol Evol 2005; 22:1783-92. [PMID: 15917497 DOI: 10.1093/molbev/msi174] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The chloroplast DNA (cpDNA) inversion in the Asteraceae has been cited as a classic example of using genomic rearrangements for defining major lineages of plants. We further characterize cpDNA inversions in the Asteraceae using extensive sequence comparisons among 56 species, including representatives of all major clades of the family and related families. We determine the boundaries of the 22-kb (now known as 22.8 kb) inversion that defines a major split within the Asteraceae, and in the process, we characterize the second and a new, smaller 3.3-kb inversion that occurs at one end of the larger inversion. One end point of the smaller inversion is upstream of the trnE-UUC gene, and the other end point is located between the trnC-GCA and rpoB genes. Although a diverse sampling of Asteraceae experienced substantial length variation and base substitution during the long evolutionary history subsequent to the inversion events, the precise locations of the inversion end points are identified using comparative sequence alignments in the inversion regions. The phylogenetic distribution of two inversions is identical among the members of Asteraceae, suggesting that the inversion events likely occurred simultaneously or within a short time period shortly after the origin of the family. Estimates of divergence times based on ndhF and rbcL sequences suggest that two inversions originated during the late Eocene (38-42 MYA). The divergence time estimates also suggest that the Asteraceae originated in the mid Eocene (42-47 MYA).
Collapse
Affiliation(s)
- Ki-Joong Kim
- School of Life Sciences and Biotechnology, Korea University, Seoul, Korea.
| | | | | |
Collapse
|
26
|
James JK, Abbott RJ. RECENT, ALLOPATRIC, HOMOPLOID HYBRID SPECIATION: THE ORIGIN OF SENECIO SQUALIDUS (ASTERACEAE) IN THE BRITISH ISLES FROM A HYBRID ZONE ON MOUNT ETNA, SICILY. Evolution 2005. [DOI: 10.1554/05-306.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
Milne RI, Abbott RJ. Geographic origin and taxonomic status of the invasive Privet, Ligustrum robustum (Oleaceae), in the Mascarene Islands, determined by chloroplast DNA and RAPDs. Heredity (Edinb) 2003; 92:78-87. [PMID: 14666126 DOI: 10.1038/sj.hdy.6800385] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Information concerning the area of origin, genetic diversity and possible acquisition of germplasm through hybridisation is fundamental to understanding the evolution, ecology and possible control measures for an introduced invasive plant species. Among the most damaging of alien plants that are invading and degrading native vegetation in the Mascarene Islands of the Indian Ocean is the Tree Privet, Ligustrum robustum. Exact information about the geographic source of introduced material of this species is lacking, in part because Ligustrum is a taxonomically difficult genus. Native material of L. robustum ssp. walkeri from Sri Lanka, L. robustum ssp. robustum from northeastern India, and the closely related L. perrottetii from southern India was compared with introduced material from La Réunion and Mauritius using chloroplast DNA RFLP markers and random amplified polymorphic DNA (RAPDs). Sri Lankan and introduced material was monomorphic for the same cpDNA haplotype that was absent from south and northeast Indian Ligustrum. Sri Lankan and introduced material was also clearly distinguished from Indian Ligustrum by RAPDs. It was concluded that material introduced and established in the Mascarene Islands is derived from the Sri Lankan subspecies L. robustum ssp. walkeri. No geographic structuring of genetic variation within Sri Lanka was detected for this taxon, so the location(s) within Sri Lanka from which introduced material is derived could not be pinpointed. RAPDs indicate that L. robustum ssp. walkeri in Sri Lanka is more similar to south Indian L. perrottetii than to northeast Indian L. robustum ssp. robustum. Moreover, RAPDs showed that introduced material in La Réunion has undergone little or no loss of genetic diversity since introduction. However, there was no evidence that it is introgressed with germplasm from two other alien Ligustrum species present on La Réunion.
Collapse
Affiliation(s)
- R I Milne
- Division of Environmental and Evolutionary Biology, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK.
| | | |
Collapse
|
28
|
Caujapé-Castells J, Jansen RK. The influence of the Miocene Mediterranean desiccation on the geographical expansion and genetic variation of Androcymbium gramineum (Cav.) McBride (Colchicaceae). Mol Ecol 2003; 12:1515-25. [PMID: 12755880 DOI: 10.1046/j.1365-294x.2003.01839.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Chloroplast DNA (cpDNA) restriction site and isozyme data were combined to explore the spatial-temporal influence of the Messinian desiccation in the Mediterranean on the disjunct distribution of Androcymbium gramineum in Almería and Morocco (north and south of the straits of Gibraltar, respectively). Lack of evidence for different selective pressures, divergence time estimates based on the calibration of the isozyme molecular clock with the cpDNA data, the basal position of Almerian populations in the A. gramineum clade, and the much higher isozyme polymorphism in Almería suggest that (i) only a southern European range of A. gramineum existed before the Messinian [ approximately 11.2 million years ago (Ma), in the middle Miocene] and (ii) the desiccation of the Mediterranean basin about 5.5-4.5 Ma induced the migration of A. gramineum from Almería to Morocco (between 4.9 and 4.6 Ma, according to our time estimates). After the split into two allopatric units following the refilling of the Mediterranean, the major influence of drift associated with Plio-Pleistocene recurrent glaciation cycles and range expansions/contractions probably fostered the substantial interpopulation genetic differentiation observed within Almería (CGST = 0.41, average DNei = 0.185) and, to a lesser extent, within Morocco (CGST = 0.24, average DNei = 0.089), but did not hinder the maintenance of considerable levels of genetic variation in either geographical area (A = 2.14, HE = 0.230 and A = 1.90, HE = 0.213, respectively).
Collapse
Affiliation(s)
- Juli Caujapé-Castells
- Laboratorio de Biodiversidad Molecular, Jardín Botánico Canario Viera y Clavijo, Ap. de correos 14 de Tafira Alta, 35017 Las Palmas de Gran Canaria, Spain.
| | | |
Collapse
|
29
|
Leino M, Teixeira R, Landgren M, Glimelius K. Brassica napus lines with rearranged Arabidopsis mitochondria display CMS and a range of developmental aberrations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 106:1156-1163. [PMID: 12748764 DOI: 10.1007/s00122-002-1167-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2002] [Accepted: 09/16/2002] [Indexed: 05/24/2023]
Abstract
Numerous Brassica napus (+) Arabidopsis thaliana somatic hybrids were screened for male sterility and aberrant flower phenotypes. Nine hybrids were selected and backcrossed recurrently to B. napus. The resulting lines displayed stable maternal inheritance of flower phenotypes. Nuclear and organellar genomes were characterized molecularly using RFLP analysis. No DNA from A. thaliana was found in the nuclear genome after six back-crosses, whilst the mitochondrial genomes contained rearranged DNA from both A. thaliana and B. napus. Each line tested had a unique RFLP pattern of the mitochondrial DNA (mtDNA) that remained unchanged between the BC(3) and BC(6) generation. The plastid genomes consisted of B. napus DNA. Five lines of the BC(5) generation were subjected to more comprehensive investigations of growth, morphology and fertility. On the basis of these investigations, the five CMS lines could be assigned to two groups, one represented by three lines displaying reduced vegetative development, complete male sterility, and homeotic conversions of stamens into feminized structures. The second group, represented by the other two lines, were not completely male-sterile but still displayed severely affected flower morphologies. These two lines did not display any reduction in vegetative development. For both groups only stamens and petals suffered from the morphological and functional aberrations, while the sepals and pistils displayed normal morphology. All plants were fully female-fertile. Different rearrangements of the mitochondrial genome disturbed nuclear-mitochondrial interactions and led to various types of aberrant growth and flower development. The existence of numerous CMS lines with different mitochondrial patterns involving a species with a sequenced genome offers new opportunities to investigate the genetic regulation of CMS and its associated developmental perturbations.
Collapse
Affiliation(s)
- M Leino
- Department of Plant Biology, Box 7080, Swedish University for Agricultural Sciences, 750 07 Uppsala, Sweden.
| | | | | | | |
Collapse
|
30
|
SEGRAVES KA, THOMPSON JN, SOLTIS PS, SOLTIS DE. Multiple origins of polyploidy and the geographic structure of
Heuchera grossulariifolia. Mol Ecol 2003. [DOI: 10.1046/j.1365-294x.1999.00562.x] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- K. A. SEGRAVES
- Department of Botany, Washington State University, Pullman, WA 99164–4238, USA,,
| | - J. N. THOMPSON
- Department of Botany, Washington State University, Pullman, WA 99164–4238, USA,,
- Department of Zoology, Washington State University, Pullman, WA 99164–4236, USA,
| | - P. S. SOLTIS
- Department of Botany, Washington State University, Pullman, WA 99164–4238, USA,,
| | - D. E. SOLTIS
- Department of Botany, Washington State University, Pullman, WA 99164–4238, USA,,
| |
Collapse
|
31
|
Moore MJ, Francisco-Ortega J, Santos-Guerra A, Jansen RK. Chloroplast DNA evidence for the roles of island colonization and extinction in Tolpis (Asteraceae: Lactuceae). AMERICAN JOURNAL OF BOTANY 2002; 89:518-526. [PMID: 21665651 DOI: 10.3732/ajb.89.3.518] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Tolpis consists of ∼13 species native to Africa, Europe, and Macaronesia, with at least one species endemic to each of the four major archipelagos of the Azores, Madeira Islands, Canary Islands, and Cape Verde Islands. All but two of these species develop woody stems by maturity. Chloroplast DNA restriction site variation was analyzed for all species of Tolpis and four outgroups in order to understand the patterns of island colonization and evolution of woodiness in this genus. Parsimony analyses revealed a strongly supported monophyletic Tolpis. Within the genus, the following three well-supported groups were detected: all species from the Canary Islands and Cape Verde Islands, both Azorean species, and both continental species. The Canary Island/Cape Verde clade was sister to the two continental species, and the Azorean clade was sister to this group. The two Madeiran species of Tolpis occupied the basalmost positions within the genus. When biogeography was mapped onto this phylogeny, nine equally parsimonious reconstructions (five steps each) of dispersal history were detected, which fell into two groups: eight reconstructions implied that Tolpis colonized Madeira from the continent, followed by continental extinction and subsequent continental recolonization, while one reconstruction implied that Tolpis colonized Macaronesia four times. Two of the reconstructions involving continental extinction required the least amount of overall dispersal distance. The cpDNA phylogeny also suggests that woodiness arose in the common ancestor of all extant Tolpis, followed by two independent reversals to an herbaceous habit. Assuming that one of the eight reconstructions favoring continental extinction and recolonization is true, our results suggest that Tolpis may represent the first documented example of a woody plant group in Macaronesia that has recolonized the mainland in herbaceous form.
Collapse
Affiliation(s)
- Michael J Moore
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas, Austin, Texas 78712 USA
| | | | | | | |
Collapse
|
32
|
Comes HP, Abbott RJ. MOLECULAR PHYLOGEOGRAPHY, RETICULATION, AND LINEAGE SORTING IN MEDITERRANEAN SENECIO SECT. SENECIO (ASTERACEAE). Evolution 2001. [DOI: 10.1111/j.0014-3820.2001.tb01312.x] [Citation(s) in RCA: 143] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
33
|
Comes HP, Abbott RJ. MOLECULAR PHYLOGEOGRAPHY, RETICULATION, AND LINEAGE SORTING IN MEDITERRANEAN SENECIO SECT. SENECIO (ASTERACEAE). Evolution 2001. [DOI: 10.1554/0014-3820(2001)055[1943:mprals]2.0.co;2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
34
|
Golden JL, Bain JF. Phylogeographic patterns and high levels of chloroplast DNA diversity in four Packera (asteraceae) species in southwestern Alberta. Evolution 2000; 54:1566-79. [PMID: 11108585 DOI: 10.1111/j.0014-3820.2000.tb00702.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Chloroplast DNA (cpDNA) haplotype variation is compared among alpine and prairie/montane species of Packera from a region in southwestern Alberta that straddles the boundary of Pleistocene glaciation. The phylogeny of the 15 haplotypes identified reveals the presence of two groups: one generally found in coastal and northern species and the other from species in drier habitats. The presence of both groups in all four species and most populations from southwestern Alberta is evidence of past hybridization involving species or lineages that may no longer be present in the region. With the exception of the alpine P. subnuda (phiST = 1.0), interpopulational subdivision of haplotype variation is low (phiST < 0.350), suggesting that interpopulational gene flow is high. However, based on haplotype distribution patterns, we propose that Pleistocene hybridization and incomplete lineage sorting have resulted in reduced subdivision of interpopulational variation so that gene flow may not be as high as indicated. Drift has been more important in the alpine species populations, especially P. subnuda.
Collapse
Affiliation(s)
- J L Golden
- Department of Biological Sciences, University of Lethbridge, Alberta, Canada.
| | | |
Collapse
|
35
|
Milne RI, Abbott RJ. Origin and evolution of invasive naturalized material of Rhododendron ponticum L. in the British isles. Mol Ecol 2000; 9:541-56. [PMID: 10792698 DOI: 10.1046/j.1365-294x.2000.00906.x] [Citation(s) in RCA: 139] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Information concerning the area of origin, genetic diversity and possible acquisition of germplasm through hybridization is fundamental to understanding the evolution, ecology and possible control measures for an introduced invasive plant species. Rhododendron ponticum is extensively naturalized in the British Isles, but it is not known whether native material in Turkey, Spain or Portugal gave rise to the naturalized material, or to what extent introgression has affected this material. Chloroplast (cp) and nuclear ribosomal DNA (rDNA) restriction fragment length polymorphisms (RFLPs) were sought which could distinguish between native material of R. ponticum, and between 15 other Rhododendron species including R. ponticum's closest relatives. Thereafter, a total of 260 naturalized accessions of R. ponticum from throughout the British Isles was examined with respect to informative polymorphisms. It was found that 89% of these accessions possessed a cpDNA haplotype that occurred in native material of R. ponticum derived almost entirely from Spain, while 10% of accessions had a haplotype unique to Portuguese material. These results therefore indicated an Iberian origin for British material. rDNA or cpDNA evidence of introgression from R. catawbiense was found in 27 British accessions of R. ponticum, and such accessions were significantly more abundant in Britain's coldest region, eastern Scotland, than elsewhere. This could indicate that introgression from R. catawbiense confers improved cold tolerance. Introgression from R. maximum and an unidentified species was also detected.
Collapse
Affiliation(s)
- R I Milne
- Division of Environmental & Evolutionary Biology, School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH, UK
| | | |
Collapse
|
36
|
Golden JL, Bain JF. PHYLOGEOGRAPHIC PATTERNS AND HIGH LEVELS OF CHLOROPLAST DNA DIVERSITY IN FOUR PACKERA (ASTERACEAE) SPECIES IN SOUTHWESTERN ALBERTA. Evolution 2000. [DOI: 10.1554/0014-3820(2000)054[1566:ppahlo]2.0.co;2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
37
|
Gould KR, Jansen RK. Taxonomy and Phylogeny of a Gulf Coast Disjunct Group ofSpigelia(Loganiaceae Sensu Lato). ACTA ACUST UNITED AC 1999. [DOI: 10.25224/1097-993x-2.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Katherine R. Gould
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
- Present address: Brooklyn Botanic Garden, 1000 Washington Ave., Brooklyn, New York 11225
| | - Robert K. Jansen
- Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
| |
Collapse
|
38
|
Bain JF, Jansen RK. Numerous chloroplast DNA polymorphisms are shared among different populations and species in the aureoid Senecio (Packera) complex. ACTA ACUST UNITED AC 1996. [DOI: 10.1139/b96-209] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Species boundaries within the aureoid Senecio complex (Packera) are poorly defined, possibly as a result of hybridization and introgression. The results of restriction site analysis of cpDNA using 16 enzymes and hybridization with lettuce probes representing over 95% of the chloroplast genome reveal a high level of intrapopulational polymorphism combined with a relatively low level of interspecific variation. Forty-nine populations representing 23 different species were examined, and only 20 variable restriction sites were identified. Eleven of the 20 variable sites were polymorphic in at least one population, and 14 of the 23 species were polymorphic for at least one site. The polymorphisms are widespread and are found in species representing all of the previously recognized subgroups of the aureoid complex. Individuals analyzed separately were shown to possess only a single haplorype. Although the polymorphisms may be the result of hybridization and introgression, it is difficult to explain the geographical patterns based on the current distribution of species. It is possible that the aureoid complex represents a single, polymorphic biological species. Keywords: Asteraceae, Senecio, aureoid complex, Packera, cpDNA, molecular systematics.
Collapse
|
39
|
Lashermes P, Cros J, Combes MC, Trouslot P, Anthony F, Hamon S, Charrier A. Inheritance and restriction fragment length polymorphism of chloroplast DNA in the genus Coffea L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1996; 93:626-632. [PMID: 24162358 DOI: 10.1007/bf00417958] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/1996] [Accepted: 04/26/1996] [Indexed: 06/02/2023]
Abstract
CpDNA variation among 52 tree samples belonging to 25 different taxa of Coffea and two species of Psilanthus was assessed by RFLP analysis on both the total chloroplast genome and the atpB-rbcL intergenic region. Twelve variable characters were distinguished allowing the identification of 12 different plastomes. The low sequence divergence observed might suggest that Coffea is a young genus. The results were in contradiction with the present classification into two genera. Additionally, cpDNA inheritance was studied in interspecific hybrids between C. arabica and C. canephora, and in an intraspecific progeny of C. canephora, using PCR-based markers. Both studies showed exclusively maternal inheritance of cpDNA.
Collapse
Affiliation(s)
- P Lashermes
- ORSTOM, Laboratoire de ressources génétiques et d'amélioration des plantes tropicales, BP 5045, F-34032, Montpellier, France
| | | | | | | | | | | | | |
Collapse
|
40
|
Wallace RS, Cota JH. An intron loss in the chloroplast gene rpoC1 supports a monophyletic origin for the subfamily Cactoideae of the Cactaceae. Curr Genet 1996; 29:275-81. [PMID: 8595674 DOI: 10.1007/bf02221558] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The deletion of an approximately 700-bp intron in the chloroplast-encoded gene rpoC1 was shown in 21 representative species of the subfamily Cactoideae of the angiosperm family Cactaceae. Members of the subfamilies Pereskioideae and Opuntioideae were found to possess the intron, as did members of the related families Aizoaceae, Basellaceae, Didiereaceae, Phytolaccaceae, and Portulacaceae. These results support a monophyletic origin for the most-speciose subfamily of the cactus family, and represent a first report of the loss of this intron in dicots.
Collapse
Affiliation(s)
- R S Wallace
- Department of Botany, Iowa State University, Ames, IA 50011-1020, USA
| | | |
Collapse
|
41
|
O'Kane SL. Clone bank and physical map of Lopezia miniata Lag. ex DC. ssp. miniata (Onagraceae) chloroplast DNA. BIOCHEM SYST ECOL 1995. [DOI: 10.1016/0305-1978(95)00041-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
42
|
Whitton J, Wallace RS, Jansen RK. Phylogenetic relationships and patterns of character change in the tribe Lactuceae (Asteraceae) based on chloroplast DNA restriction site variation. ACTA ACUST UNITED AC 1995. [DOI: 10.1139/b95-115] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Lactuceae is perhaps the most easily recognizable tribe in the Asteraceae, distinguished by the presence of milky latex and of ligulate florets in the inflorescence. Three existing taxonomic treatments of the tribe establish subtribal classifications but fail to resolve relationships among major lineages. Our study of chloroplast DNA restriction site variation sampled 60 Lactuceae taxa. We detected 1268 mutations, 612 of which are phylogenetically informative. Despite the large amount of variation detected, little resolution of relationships among major lineages was obtained from parsimony analyses, although the monophyly of many groups is strongly supported. These results, when considered along with data from morphological analyses of other workers, suggest that rapid diversification played an important role in early stages of the tribe's evolution. Our examination of character change further reveals that as noted by other workers, restriction site variation is not evenly distributed across the chloroplast genome and that regions with higher levels of variation do not necessarily have higher amounts of homoplasy. This is somewhat surprising, since we found that amounts of homoplasy along terminal branches of our phylogenetic tree are related to levels of divergence. Key words: Asteraceae, chloroplast DNA, homoplasy, Lactuceae, phylogeny, restriction site variation.
Collapse
|
43
|
|
44
|
Mayer MS, Soltis PS. Chloroplast DNA phylogeny of Lens (Leguminosae): origin and diversity of the cultivated lentil. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 87:773-781. [PMID: 24190462 DOI: 10.1007/bf00221128] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/1992] [Accepted: 06/28/1993] [Indexed: 06/02/2023]
Abstract
A restriction-site analysis of chloroplast DNA (cpDNA) variation in Lens was conducted to: (1) assess the levels of variation in Lens culinaris ssp. culinaris (the domesticated lentil), (2) identify the wild progenitor of the domesticated lentil, and (3) construct a cpDNA phylogeny of the genus. We analyzed 399 restriction sites in 114 cultivated accessions and 11 wild accessions. All but three accessions of the cultivar had identical cpDNAs. Two accessions exhibited a single shared restriction-site loss, and a small insertion was observed in the cpDNA of a third accession. We detected 19 restriction-site mutations and two length mutations among accessions of the wild taxa. Three of the four accessions of L. culinaris ssp. orientalis were identical to the cultivars at every restriction site, clearly identifying ssp. orientalis as the progenitor of the cultivated lentil. Because of its limited cpDNA diversity, we conclude that either the cultivated lentil has passed through a genetic bottleneck during domestication and lost most of its cytoplasmic variability or else was domesticated from an ancestor that was naturally depauperate in cpDNA restriction-site variation. However, because we had access to only a small number of populations of the wild taxa, the levels of variation present in ssp. orientalis can only be estimated, and the extent of such a domestication bottleneck, if applicable, cannot be evaluated. The cpDNA-based phylogeny portrays Lens as quite distinct from its putative closest relative, Vicia montbretii. L. culinaris ssp. odemensis is the sister of L. nigricans; L. culinaris is therefore paraphyletic given the current taxonomic placement of ssp. odemensis. Lens nigricans ssp. nigricans is by far the most divergent taxon of the genus, exhibiting ten autapomorphic restriction-site mutations.
Collapse
Affiliation(s)
- M S Mayer
- Department of Botany, Washington State University, 99164-4238, Pullman, WA, USA
| | | |
Collapse
|
45
|
Fahleson J, Eriksson I, Landgren M, Stymne S, Glimelius K. Intertribal somatic hybrids between Brassica napus and Thlaspi perfoliatum with high content of the T. perfoliatum-specific nervonic acid. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1994; 87:795-804. [PMID: 24190465 DOI: 10.1007/bf00221131] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/1993] [Accepted: 06/16/1993] [Indexed: 05/11/2023]
Abstract
Protoplast fusions were performed between hypocotyl protoplasts of Brassica napus and mesophyll protoplasts of Thlaspi perfoliatum. The two species are members of the Lepidieae and Brassiceae tribes, respectively, in the family of Brassicaceae. Seeds of T. perfoliatum are rich in the fatty acid C24∶1 (nervonic acid), an oil valuable for technical purposes. In the search for renewable oils to replace the mineral oils, plant breeders have been trying to develop oil crops with a high content of long-chain fatty acids. After fusion of B. napus protoplasts with non-irradiated as well as irradiated protoplasts of T. perfoliatum selection was carried out by flow cytometry and cell sorting. Of the shoots regenerated from different calli 27 were verified as hybrids or partial hybrids using the isoenzyme phosphoglucose isomerase (PGI) as a marker. Another 6 plants were identified as partial hybrids using a T. perfoliatum-specific repetitive DNA sequence. Slot blot experiments were performed to estimate the copy number of the repetitive DNA sequence in the parental species and in the hybrids. In T. perfoliatum there were approximately 10(5) copies per haploid genome, and the range in the hybrids was 1-37% of the value in T. perfoliatum. When the nuclear DNA content of the regenerated shoots was analysed we found partial as well as symmetric hybrids. Even though the rooting and establishment of hybrid shoots in the greenhouse were difficult, resulting in the death of many plants, 19 plants were cultured to full maturity. Seeds obtained from 15 plants were analysed to determine whether they contained nervonic acid, and 5 of the hybrids were found to contain significantly greater amounts of nervonic acid than B. napus.
Collapse
Affiliation(s)
- J Fahleson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 7003, S-750 07, Uppsala, Sweden
| | | | | | | | | |
Collapse
|
46
|
Hasebe M, Iwatsuki K. Gene localization on the chloroplast DNA of the maiden hair fern;Adiantum capillus-veneris. ACTA ACUST UNITED AC 1992. [DOI: 10.1007/bf02497656] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
47
|
Wilson HD, Doebley J, Duvall M. Chloroplast DNA diversity among wild and cultivated members of Cucurbita (Cucurbitaceae). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1992; 84:859-65. [PMID: 24201487 DOI: 10.1007/bf00227397] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/1991] [Accepted: 02/26/1992] [Indexed: 05/27/2023]
Abstract
Cladistic analysis of 86 chloroplast DNA restriction-site mutations among 30 samples representing 15 species of Cucurbita indicates that annual species of the genus are derived from perennials. The Malabar Gourd, C. ficifolia, is placed as a basal, sister taxon relative to other domesticated species and allied wild-types. The pattern of variation supports three species groups as monophyletic: (1) C. fraterna, C. pepo, and C. texana, (2) C. lundelliana, C. martinezii, C. mixta, C. moschata and C. sororia, and (3) C. foetidissima and C. pedatifolia. Domesticated samples representing subspecies of C. pepo are divided into two concordant groups, one of which is allied to wild-types referable to C. texana and C. fraterna. The data failed to resolve relationships among cultivars of C. moschata and C. mixta and their association to the wild C. sororia. The South American domesticate, C. maxima, and its companion weed, C. andreana, show close affinity and alliance to C. equadorensis.
Collapse
Affiliation(s)
- H D Wilson
- Department of Biology, Texas A and M University, 77843, College Station, TX, USA
| | | | | |
Collapse
|
48
|
Harris SA, Ingram R. Molecular systematics of the genus Senecio L. II: The origin of S. vulgaris L. Heredity (Edinb) 1992. [DOI: 10.1038/hdy.1992.103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
49
|
Harris SA, Ingram R. Molecular systematics of the genus Senecio L. I: Hybridization in a British polyploid complex. Heredity (Edinb) 1992. [DOI: 10.1038/hdy.1992.88] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
50
|
Wimpee CF, Morgan R, Wrobel RL. Loss of transfer RNA genes from the plastid 16S-23S ribosomal RNA gene spacer in a parasitic plant. Curr Genet 1992; 21:417-22. [PMID: 1525868 DOI: 10.1007/bf00351704] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The plastid 16S-23S intergenic spacer region in Conopholis americana, a totally heterotrophic angiosperm in the family Orobanchaceae, has undergone large deletions, including the entire tRNA(Ile) gene and all but small remnants of the tRNA(Ala) gene. The length of the region is less than 20% of that of other land plants which have been investigated, making it the smallest 16S-23S intergenic spacer reported thus far for any land plant. The remaining sequences in the spacer are 90.1% identical to tobacco, indicating that, while the region is well conserved at the sequence level, it is evolving rapidly by deletion. Experiments using the polymerase chain reaction and hybridization to DNA gel blots have failed to reveal either of the two missing tRNA genes elsewhere in the Conopholis cell.
Collapse
Affiliation(s)
- C F Wimpee
- Department of Biological Sciences, University of Wisconsin, Milwaukee 53201
| | | | | |
Collapse
|