1
|
Wang R, Liu K, Zhang XJ, Chen WL, Qu XJ, Fan SJ. Comparative Plastomes and Phylogenetic Analysis of Cleistogenes and Closely Related Genera (Poaceae). FRONTIERS IN PLANT SCIENCE 2021; 12:638597. [PMID: 33841465 PMCID: PMC8030268 DOI: 10.3389/fpls.2021.638597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Cleistogenes (Orininae, Cynodonteae, Chloridoideae, Poaceae) is an ecologically important genus. The phylogenetic placement of Cleistogenes and phylogenetic relationships among Cleistogenes taxa remain controversial for a long time. To resolve the intra- and inter-generic relationships of Cleistogenes, the plastomes of 12 Cleistogenes taxa (including 8 species and 4 varieties), one Orinus species, 15 Triodia species, two Tripogon species, and two Aeluropus species were included in the present study. All the taxa showed a similar pattern in plastome structure, gene order, gene content, and IR boundaries. The number of simple sequence repeats ranged from 145 (O. kokonorica) to 161 (T. plurinervata and T. schinzii). Moreover, 1,687 repeats were identified in these taxa, including 1,012 forward, 650 palindromic, 24 reverse, and one complement. Codon usage analysis revealed that these plastomes contained 16,633 (T. stipoides) to 16,678 (T. tomentosa) codons. Sequence divergence analysis among Cleistogenes and closely related genera identified five non-coding regions (trnS-UGA-psbZ, rpl32-trnL-UAG, trnQ-UUG-psbK, trnD-GUC-psbM, trnT-GGU-trnE-UUC). Phylogenetic analysis of complete plastomes indicated that Cleistogenes is sister to a clade composed of Orinus and Triodia, whereas it did not support the sister relationship between the recently proposed subtribe Orininae (Cleistogenes and Orinus) and Triodia. The subtribe Orininae was not supported by our complete plastome data. The split between Cleistogenes and Orinus-Triodia clade go back to 14.01 Ma. Besides, our findings suggested that C. squarrosa and C. songorica are the successive early diverging groups in the phylogenetic analysis. The other 10 taxa are divided into two groups: a monophyletic group composed of Cleistogenes sp. nov. and C. caespitosa var. ramosa is sister to other eight Cleistogenes taxa. Cleistogenes was estimated to have experienced rapid divergence within a short period, which could be a major obstacle in resolving phylogenetic relationships within Cleistogenes. Collectively, our results provided valuable insights into the phylogenetic study of grass species.
Collapse
Affiliation(s)
- Rong Wang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Kuan Liu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Xue-Jie Zhang
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Wen-Li Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Shou-Jin Fan
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| |
Collapse
|
2
|
Liu K, Wang R, Guo XX, Zhang XJ, Qu XJ, Fan SJ. Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae). PLANTS 2021; 10:plants10010109. [PMID: 33419221 PMCID: PMC7825611 DOI: 10.3390/plants10010109] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 11/24/2022]
Abstract
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnG–UCC-trnT–GGU, ndhF–rpl32, ycf4–cemA, rpl32–trnL–UAG, trnG–GCC–trnfM–CAU, and ccsA–ndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae.
Collapse
Affiliation(s)
| | | | | | | | - Xiao-Jian Qu
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
| | - Shou-Jin Fan
- Correspondence: (X.-J.Q.); (S.-J.F.); Tel.: +86-0531-8618-0718 (S.-J.F.)
| |
Collapse
|
3
|
Huang YY, Cho ST, Haryono M, Kuo CH. Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae. PLoS One 2017; 12:e0179055. [PMID: 28617867 PMCID: PMC5472289 DOI: 10.1371/journal.pone.0179055] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 05/23/2017] [Indexed: 02/02/2023] Open
Abstract
Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.
Collapse
Affiliation(s)
- Ya-Yi Huang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Mindia Haryono
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- * E-mail:
| |
Collapse
|
4
|
Wysocki WP, Burke SV, Swingley WD, Duvall MR. The First Complete Plastid Genome from Joinvilleaceae (J. ascendens; Poales) Shows Unique and Unpredicted Rearrangements. PLoS One 2016; 11:e0163218. [PMID: 27658044 PMCID: PMC5033401 DOI: 10.1371/journal.pone.0163218] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 09/06/2016] [Indexed: 11/19/2022] Open
Abstract
Joinvilleaceae is a family of tropical grass-like monocots that comprises only the genus Joinvillea. Previous studies have placed Joinvilleaceae in close phylogenetic proximity to the well-studied grass family. A full plastome sequence was determined and characterized for J. ascendens. The plastome was sequenced with next generation methods, fully assembled de novo and annotated. The assembly revealed two novel inversions specific to the Joinvilleaceae lineage and at least one novel plastid inversion in the Joinvilleaceae-Poaceae lineage. Two previously documented inversions in the Joinvilleaceae-Poaceae lineage and one previously documented inversion in the Poaceae lineage were also verified. Inversion events were identified visually and verified computationally by simulation mutations. Additionally, the loss and subsequent degradation of the accD gene in order Poales was explored extensively in Poaceae and J. ascendens. The two novel inversions along with changes in gene composition between families better delimited lineages in the Poales. The presence of large inversions and subsequent reversals in this small family suggested a high potential for large-scale rearrangements to occur in plastid genomes.
Collapse
Affiliation(s)
- William P. Wysocki
- Center for Data Intensive Sciences, University of Chicago, 5454 South Shore Dr., Chicago, IL 60615, United States of America
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
- * E-mail:
| | - Sean V. Burke
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
| | - Wesley D. Swingley
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
| | - Melvin R. Duvall
- Northern Illinois University; 1425 W. Lincoln Hwy, DeKalb, IL 60115, United States of America
| |
Collapse
|
5
|
Weng ML, Blazier JC, Govindu M, Jansen RK. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates. Mol Biol Evol 2013; 31:645-59. [PMID: 24336877 DOI: 10.1093/molbev/mst257] [Citation(s) in RCA: 217] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed.
Collapse
Affiliation(s)
- Mao-Lun Weng
- Department of Integrative Biology, University of Texas, Austin
| | | | | | | |
Collapse
|
6
|
Martin G, Baurens FC, Cardi C, Aury JM, D’Hont A. The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution. PLoS One 2013; 8:e67350. [PMID: 23840670 PMCID: PMC3696114 DOI: 10.1371/journal.pone.0067350] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 05/16/2013] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. METHODOLOGY/PRINCIPAL FINDINGS The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. CONCLUSION The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.
Collapse
Affiliation(s)
- Guillaume Martin
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, Montpellier, France
| | - Franc-Christophe Baurens
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, Montpellier, France
| | - Céline Cardi
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, Montpellier, France
| | | | - Angélique D’Hont
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP, Montpellier, France
| |
Collapse
|
7
|
Kwanda N, Noikotr K, Sudmoon R, Tanee T, Chaveerach A. Medicinal parasitic plants on diverse hosts with their usages and barcodes. J Nat Med 2012; 67:438-45. [DOI: 10.1007/s11418-012-0695-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 07/11/2012] [Indexed: 11/28/2022]
|
8
|
Chaveerach A, Tanee T, Sudmoon R. Molecular identification and barcodes for the genus Nymphaea. ACTA BIOLOGICA HUNGARICA 2011; 62:328-40. [PMID: 21840834 DOI: 10.1556/abiol.62.2011.3.11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Nymphaea species, the most popular decorative plants, were collected for specificity of inter-simple sequence repeat (ISSR) analyses in species identification and differentiation of cultivars and natural populations. Dendrogram constructed from ISSR analyses separated out wild species, namely Nymphaea cyanea, N. nouchali, N. capensis, N. lotus and an outgroup N. mexicana, and cultivars. The dendrogram indicates that the cultivars should be differentiated from N. capensis, as they are sister individuals of N. capensis. The ISSR banding data and the dendrogram are concordantly concluded that wild N. capensis would be an effective type species for producing different cultivars. After plant identification by ISSR markers, DNA barcodes of all sample materials were done to provide species specific markers which can be used for rapid and accurate further plant identification without morphological characters. DNA barcoding sequence analysis indicates genetic distance values. All sequences were recorded in GenBank database.
Collapse
|
9
|
Morris LM, Duvall MR. The chloroplast genome of Anomochloa marantoidea (Anomochlooideae; Poaceae) comprises a mixture of grass-like and unique features. AMERICAN JOURNAL OF BOTANY 2010; 97:620-7. [PMID: 21622424 DOI: 10.3732/ajb.0900226] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Features in the complete plastome of Anomochloa marantoidea (Poaceae) were investigated. This species is one of four of Anomochlooideae, the crown node of which diverged before those of any other grass subfamily. The plastome was sequenced from overlapping amplicons using previously designed primers. The plastome of A. marantoidea is 138412 bp long with a typical gene content for Poaceae. Five regions were examined in detail because of prior surveys that identified structural alterations among graminoid Poales. Anomochloa marantoidea was found to have an intron in rpoC1, unlike other Poaceae. The insertion region of rpoC2 is unusually short in A. marantoidea compared with those of other grasses, but with atypically long subrepeats. Both ycf1 and ycf2 are nonfunctional as is typical in grasses, but A. marantoidea has a uniquely long ψycf1. Finally, the rbcL-psaI spacer in A. marantoidea is atypically short with no evidence of the ψrpl23 locus found in all other Poaceae. Some of these features are of noteworthy dissimilarity between A. marantoidea and those crown grasses for which entire plastomes have been sequenced. Complete plastome sequences of other Anomochlooideae and outgroups will further advance our understanding of the evolutionary events in the plastome that accompanied graminoid diversification.
Collapse
Affiliation(s)
- Leah M Morris
- Department of Biological Sciences, 1425 W. Lincoln Hwy, Northern Illinois University, DeKalb, Illinois USA 60115-2861
| | | |
Collapse
|
10
|
Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK. Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae. J Mol Evol 2010; 70:149-66. [PMID: 20091301 PMCID: PMC2825539 DOI: 10.1007/s00239-009-9317-3] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 12/16/2009] [Indexed: 11/21/2022]
Abstract
Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.
Collapse
Affiliation(s)
- Mary M Guisinger
- Section of Integrative Biology, University of Texas, Austin, TX 78712, USA.
| | | | | | | | | |
Collapse
|
11
|
Thiede J, Schmidt SA, Rudolph B. Phylogenetic implication of the chloroplast rpoC1 intron loss in the Aizoaceae (Caryophyllales). BIOCHEM SYST ECOL 2007. [DOI: 10.1016/j.bse.2006.12.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
12
|
Katayama H, Uematsu C. Structural analysis of chloroplast DNA in Prunus (Rosaceae): evolution, genetic diversity and unequal mutations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1430-9. [PMID: 16142464 DOI: 10.1007/s00122-005-0075-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 08/03/2005] [Indexed: 05/04/2023]
Abstract
In order to understand the evolutionary aspects of the chloroplast DNA (cpDNA) structures in Rosaceous plants, a physical map of peach (Prunus persica cv. Hakuhou) cpDNA was constructed. Fourteen lambda phage clones which covered the entire sequence of the peach cpDNA were digested by restriction enzymes (SalI, XhoI, BamHI, SacI, and PstI) used singly or in combination. The molecular size of peach cpDNA was estimated to be about 152 kb. The gene order and contents were revealed to be equivalent to those of standard type of angiosperms by the localization of 31 genes on the physical map. Eighteen accessions from 14 Prunus species (P. persica, P. mira, P. davidiana, P. cerasis, P. cerasifera, P. domestica, P. insititia, P. spinosa, P. salicina, P. maritima, P. armeniaca, P. mume, P. tomentosa, P. zippeliana, and P. salicifolia) and one interspecific hybrid were used for the structural analysis of cpDNAs. Seventeen mutations (16 recognition site changes and one length mutation) were found in the cpDNA of these 18 accessions by RFLP analysis allowing a classification into 11 genome types. Although the base substitution rate in the recognition site (100p = 0.72) of cpDNA in Prunus was similar to that of other plants, i.e., Triticum-Aegilops, Brassica, and Pisum, it differed from Pyrus (100p = 0.15) in Rosaceae. Seven mutations including one length mutation were densely located within a region of about 9.1 kb which includes psbA and atpA in the left border of a large single-copy region of Prunus cpDNAs. The length mutation was detected only in P. persica and consisted of a 277 bp deletion which occurred in a spacer region between the trnS and trnG genes within the 9.1 kb region. Additional fragment length mutations (insertion/deletion), which were not detected by RFLP analysis, were revealed by PCR and sequence analyses in P. zippeliana and P. salicifolia. All of these length mutations occurred within the 9.1 kb region between psbA and atpA. This region could be an intra-molecular recombinational hotspot in Prunus species.
Collapse
Affiliation(s)
- H Katayama
- Food Resources Education and Research Center, Kobe University, 675-2103 Hyogo, Japan.
| | | |
Collapse
|
13
|
Katayama H, Ogihara Y. Phylogenetic affinities of the grasses to other monocots as revealed by molecular analysis of chloroplast DNA. Curr Genet 1996; 29:572-81. [PMID: 8662197 DOI: 10.1007/bf02426962] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The distribution of structural alterations of the chloroplast genome found in grass chloroplast (cp) DNA in comparison with that of tobacco was systematically surveyed in the cpDNAs of monocots. Southern hybridization and/or PCR analyses for the detection of (1) three inversions in the large single-copy region, (2) loss of an intron in the rpoC1 gene, (3) an extra-sequence insertion in the rpoC2 gene, (4) the deletion of ORF2280, (5) rearrangements of the accD (ORF512) gene, and (6) non-reciprocal translocation of the rpl23 gene, were carried out on cpDNAs isolated from 58 species, 22 families, and 11 orders, which covered almost all families of monocots. These structural alterations of cpDNA mostly occurred at the family level. However, only part of the Restionaceae possessed the inversion that characterizes the lineage of grass differentiation. The order of mutational events made it possible to reconstruct grass phylogeny in monocots. Since no variations in structural alterations of the cpDNA were found among the Poaceae, grass plants were inferred to have originated from an ancestor harboring these structural alterations of the chloroplast genome. These phylogenetic relationships were supported by the sequence data of rbcL.
Collapse
Affiliation(s)
- H Katayama
- Kihara Institute for Biological Research, Yokohama City University, Maioka-cho 641-12, Yokohama 244, Japan
| | | |
Collapse
|
14
|
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
|
15
|
Watanabe N, Nakazono M, Kanno A, Tsutsumi N, Hirai A. Evolutionary variations in DNA sequences transferred from chloroplast genomes to mitochondrial genomes in the Gramineae. Curr Genet 1994; 26:512-8. [PMID: 7874746 DOI: 10.1007/bf00309942] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The transfer of fragments of DNA from chloroplast genomes to mitochondrial genomes is considered to be a general phenomenon in higher plants. In the present study, Southern hybridization, together with amplification by PCR and DNA sequencing techniques, was used to examine the regions homologous to chloroplast rps19 in the mitochondrial genomes of several gramineous plants. In all the mitochondrial DNAs from the gramineous plants examined, except for that from wheat, the transferred fragments of chloroplast DNA were found to be maintained and the same junctions of mitochondrion-specific and chloroplast-like sequences were found at one terminus. This finding indicates that the transfer of the chloroplast sequence occurred in the distant past during the evolution of gramineous plants. Subsequent analysis revealed that the fragments had been variously rearranged among species with respect to the other terminus. Considering the current diversity of this one particular transferred fragment of chloroplast DNA, we propose that chloroplast-derived DNA sequences that have lost their original functions tend to be rearranged during evolution in mitochondrial genomes.
Collapse
Affiliation(s)
- N Watanabe
- Laboratory of Radiation Genetics, Faculty of Agriculture, University of Tokyo, Japan
| | | | | | | | | |
Collapse
|
16
|
OGIHARA Y, ISONO K, SAITO A. Toward construction of synteny maps among cereal genomes. I. Molecular characterization of cereal genomes as probed by rice genomic clones. ACTA ACUST UNITED AC 1994. [DOI: 10.1266/jjg.69.347] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Yasunari OGIHARA
- Kihara Institute for Biological Research, Yokohama City University
| | - Kazuhiro ISONO
- Kihara Institute for Biological Research, Yokohama City University
| | - Akira SAITO
- National Institute of Agrobiological Resources
| |
Collapse
|
17
|
OGIHARA Y, ISONO K, SAITO A. Toward construction of synteny maps among cereal genomes. I. Molecular characterization of cereal genomes as probed by rice genomic clones. Genes Genet Syst 1994. [DOI: 10.1266/ggs.69.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|