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1.
Mol Phylogenet Evol ; 22(1): 31-42, 2002 Jan.
Article En | MEDLINE | ID: mdl-11796027

We investigated the origin of Hawaiian Pittosporum and their relationship to other South Pacific Pittosporum species using internal transcribed spacer sequences of nuclear ribosomal DNA. We performed both maximum-parsimony and maximum-likelihood analyses, which produced congruent results. Sequence divergence was 0.0% between Hawaiian members of Pittosporum. These taxa formed a strongly supported clade, suggesting a single colonization event followed by phyletic radiation. Sister to the Hawaiian clade were two South Pacific species, P. yunckeri from Tonga and P. rhytidocarpum from Fiji. This result presents convincing evidence for a South Pacific origin of Hawaiian Pittosporum. Our results also identify a monophyletic group comprising three species representing the Fijian Province and East Polynesia, two introductions onto New Caledonia, and at least one (but possibly two) introduction(s) onto New Zealand. Whether the New Zealand taxa form a monophyletic group is unclear from these data. Previous morphologically based hypotheses, however, suggest the presence of four different lineages occupying New Zealand. The nonmonophyly of the New Caledonian species was not surprising based on the extent of their morphological diversity. Although this latter result is not strongly supported, these species are morphologically complex and are currently the subject of taxonomic revision and molecular systematic analyses.


Magnoliopsida/genetics , Base Sequence , DNA, Plant/genetics , DNA, Ribosomal Spacer/genetics , Evolution, Molecular , Hawaii , Magnoliopsida/classification , Phylogeny , Species Specificity
2.
Syst Biol ; 50(6): 926-44, 2001.
Article En | MEDLINE | ID: mdl-12116641

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.


Evolution, Molecular , Zingiberales/classification , Zingiberales/genetics , DNA, Plant/genetics , Databases, Factual , Databases, Genetic , Fossils , Genes, Plant , Models, Genetic , Phylogeny , RNA, Ribosomal, 18S/genetics , Ribulose-Bisphosphate Carboxylase/genetics , Zingiberales/anatomy & histology
3.
Mol Phylogenet Evol ; 15(3): 419-39, 2000 Jun.
Article En | MEDLINE | ID: mdl-10860651

Phylogenetic analysis of ribosomal DNA internal transcribed spacer sequences from 35 members of western American Portulacaceae plus seven Portulacaceae outgroups generally supports morphologically based interpretations of multiple intercontinental disjunctions. The data neither support nor refute monophyly of the western American group but strongly support a group comprising the western American taxa plus Phemeranthus, the only strictly American genus of the morphology-based eastern American/African group of Portulacaceae, along with the Australian genus Parakeelya. Support is strong for the monophyly of Calandrinia, Montiopsis, Lewisia, Claytonia, and Montia, along with a sister relationship of the last two. The data neither strongly support nor refute the morphologically based diagnosis of Cistanthe, but they strongly support a clade including the North American Cistanthe section Calyptridium and the South American Cistanthe sections Amarantoideae and Philippiamra. The internal transcribed spacer data fail to resolve the phylogenetic relationships among most of the western American lineages, suggesting either rapid radiation or, alternatively, erratic evolution of the internal transcribed spacer. The internal transcribed spacer and morphological evidence together suggest that in this group there have been 8-13 dispersal and colonization events across >2000 km (1 for every 15-26 extant species in this group). The internal transcribed spacer data document complex molecular evolutionary patterns, including strong substitution biases, among-site rate heterogeneity, positional bias for deamination-type substitutions, nonstationarity, and variable rates of insertion/deletion. Our phylogenetic conclusions, however, do not appear to be sensitive to these patterns.


DNA, Ribosomal/genetics , Magnoliopsida/classification , Magnoliopsida/genetics , Base Sequence , Evolution, Molecular , Genes, Plant/genetics , Genetic Variation , Likelihood Functions , Mitosis/genetics , Molecular Sequence Data , North America , Phylogeny , Sequence Homology, Nucleic Acid , South America
4.
Nature ; 402(6760): 404-7, 1999 Nov 25.
Article En | MEDLINE | ID: mdl-10586879

Angiosperms have dominated the Earth's vegetation since the mid-Cretaceous (90 million years ago), providing much of our food, fibre, medicine and timber, yet their origin and early evolution have remained enigmatic for over a century. One part of the enigma lies in the difficulty of identifying the earliest angiosperms; the other involves the uncertainty regarding the sister group of angiosperms among extant and fossil gymnosperms. Here we report a phylogenetic analysis of DNA sequences of five mitochondrial, plastid and nuclear genes (total aligned length 8,733 base pairs), from all basal angiosperm and gymnosperm lineages (105 species, 103 genera and 63 families). Our study demonstrates that Amborella, Nymphaeales and Illiciales-Trimeniaceae-Austrobaileya represent the first stage of angiosperm evolution, with Amborella being sister to all other angiosperms. We also show that Gnetales are related to the conifers and are not sister to the angiosperms, thus refuting the Anthophyte Hypothesis. These results have far-reaching implications for our understanding of diversification, adaptation, genome evolution and development of the angiosperms.


Genome, Plant , Magnoliopsida/classification , Phylogeny , Biological Evolution , Cell Nucleus/classification , Cell Nucleus/genetics , DNA, Plant , Genes, Plant , Magnoliopsida/genetics , Mitochondria/classification , Mitochondria/genetics , Molecular Sequence Data , Plastids/classification , Plastids/genetics , Sequence Alignment
5.
Mol Phylogenet Evol ; 11(2): 261-72, 1999 Mar.
Article En | MEDLINE | ID: mdl-10191070

The phylogenetic relationships of some angiosperm families have remained enigmatic despite broad phylogenetic analyses of rbcL sequences. One example is the aquatic family Podostemaceae, the relationships of which have long been controversial because of major morphological modifications associated with their aquatic habit. Podostemaceae have variously been associated with Piperaceae, Nepenthaceae, Polygonaceae, Caryophyllaceae, Scrophulariaceae, Rosaceae, Crassulaceae, and Saxifragaceae. Two recent analyses of rbcL sequences suggest a possible sister-group relationship of Podostemaceae to Crassulaceae (Saxifragales). However, the branch leading to Podostemaceae was long, and use of different outgroups resulted in alternative placements. We explored the phylogenetic relationships of Podostemaceae using 18S rDNA sequences and a combined rbcL + 18S rDNA matrix representing over 250 angiosperms. In analyses based on 18S rDNA data, Podostemaceae are not characterized by a long branch; the family consistently appears as part of a Malpighiales clade that also includes Malpighiaceae, Turneraceae, Passifloraceae, Salicaceae, Euphorbiaceae, Violaceae, Linaceae, Chrysobalanaceae, Trigoniaceae, Humiriaceae, and Ochnaceae. Phylogenetic analyses based on a combined 18S rDNA + rbcL data set (223 ingroup taxa) with basal angiosperms as the outgroup also suggest that Podostemaceae are part of a Malpighiales clade. These searches swapped to completion, and the shortest trees showed enhanced resolution and increased internal support compared to those based on 18S rDNA or rbcL alone. However, when Gnetales are used as the outgroup, Podostemaceae appear with members of the nitrogen fixing clade (e.g., Elaeagnaceae, Ulmaceae, Rhamnaceae, Cannabaceae, Moraceae, and Urticaceae). None of the relationships suggested here for Podostemaceae receives strong bootstrap support. Our analyses indicate that Podostemaceae are not closely allied with Crassulaceae or with other members of the Saxifragales clade; their closest relatives, although still uncertain, appear to lie elsewhere in the rosids.


DNA, Ribosomal/genetics , Magnoliopsida/genetics , Phylogeny , Plant Proteins/genetics , Ribulose-Bisphosphate Carboxylase , Magnoliopsida/classification , Models, Biological
6.
Mol Biol Evol ; 15(3): 251-63, 1998 Mar.
Article En | MEDLINE | ID: mdl-9501492

18S ribosomal RNA genes are the most widely used nuclear sequences for phylogeny reconstruction at higher taxonomic levels in plants. However, due to a conservative rate of evolution, 18S rDNA alone sometimes provides too few phylogenetically informative characters to resolve relationships adequately. Previous studies using partial sequences have suggested the potential of 26S or large-subunit (LSU) rDNA for phylogeny retrieval at taxonomic levels comparable to those investigated with 18S rDNA. Here we explore the patterns of molecular evolution of entire 26S rDNA sequences and their impact on phylogeny retrieval. We present a protocol for PCR amplification and sequencing of entire (approximately 3.4 kb) 26S rDNA sequences as single amplicons, as well as primers that can be used for amplification and sequencing. These primers proved useful in angiosperms and Gnetales and likely have broader applicability. With these protocols and primers, entire 26S rDNA sequences were generated for a diverse array of 15 seed plants, including basal eudicots, monocots, and higher eudicots, plus two representatives of Gnetales. Comparisons of sequence dissimilarity indicate that expansion segments (or divergence domains) evolve 6.4 to 10.2 times as fast as conserved core regions of 26S rDNA sequences in plants. Additional comparisons indicate that 26S rDNA evolves 1.6 to 2.2 times as fast as and provides 3.3 times as many phylogenetically informative characters as 18S rDNA; compared to the chloroplast gene rbcL, 26S rDNA evolves at 0.44 to 1.0 times its rate and provides 2.0 times as many phylogenetically informative characters. Expansion segment sequences analyzed here evolve 1.2 to 3.0 times faster than rbcL, providing 1.5 times the number of informative characters. Plant expansion segments have a pattern of evolution distinct from that found in animals, exhibiting less cryptic sequence simplicity, a lower frequency of insertion and deletion, and greater phylogenetic potential.


DNA, Plant/genetics , DNA, Ribosomal/genetics , Evolution, Molecular , Phylogeny , RNA, Ribosomal/genetics , Base Composition , Base Sequence , Conserved Sequence/genetics , DNA Primers , Genetic Variation/genetics , Molecular Sequence Data , Polymerase Chain Reaction/methods , Sequence Analysis, DNA/methods
7.
Mol Phylogenet Evol ; 6(2): 167-77, 1996 Oct.
Article En | MEDLINE | ID: mdl-8899721

Panax, the ginseng genus, is one of the most medicinally important genera in the Orient and demonstrates a classical eastern Asian and eastern North American disjunct distributional pattern. Sequences of the internal transcribed spacers (ITS) and the 5.8S coding region of the nuclear ribosomal DNA repeat were obtained for the 12 species of Panax to reconstruct phylogenetic relationships. Of the 2 eastern North American species, P. quinquefolius and P. trifolius, P. quinquefolius was suggested to be more closely related to the eastern Asian species in the ITS tree, while P. trifolius was phylogenetically isolated. Monophyly of the three medicinally most important species, P. ginseng, P. notoginseng, and P. quinquefolius, suggested by previous workers, was not supported by the ITS data. A close phylogenetic relationship between Panax and Aralia was supported. Several biogeographical implications were inferred: (1) two divergence events have produced the eastern Asian and eastern North American disjunct distribution in Panax, (2) no intercontinental species pairs are found in Panax; (3) a discrepancy between the sequence divergence pattern and the phylogenetic pattern was observed in Panax, suggesting the need for caution in using sequence divergence data alone in inferring biogeographical patterns; (4) the Himalayas and central and western China are the current centers of diversity of the ginseng genus; and (5) the low ITS sequence divergence and a close relationship among species in that region suggest that rapid evolutionary radiation may have created such a diversity of Panax in the Himalayas and in central and western China.


Panax/classification , Plants, Medicinal , Asia , DNA, Plant , DNA, Ribosomal , Molecular Sequence Data , North America , Panax/genetics , Phylogeny , Repetitive Sequences, Nucleic Acid
8.
Nucleic Acids Res ; 24(15): 2857-67, 1996 Aug 01.
Article En | MEDLINE | ID: mdl-8760866

The two internal transcribed spacers (ITS1 and ITS2) of nuclear ribosomal DNA have become commonly exploited sources of informative variation for interspecific-/intergeneric-level phylogenetic analyses among angiosperms and other eukaryotes. We present an alignment in which one-third to one-half of the ITS2 sequence is alignable above the family level in angiosperms and a phenetic analysis showing that ITS2 contains information sufficient to diagnose lineages at several hierarchical levels. Base compositional analysis shows that angiosperm ITS2 is inherently GC-rich, and that the proportion of T is much more variable than that for other bases. We propose a general model of angiosperm ITS2 secondary structure that shows common pairing relationships for most of the conserved sequence tracts. Variations in our secondary structure predictions for sequences from different taxa indicate that compensatory mutation is not limited to paired positions.


Conserved Sequence , DNA, Ribosomal/genetics , Nucleic Acid Conformation , Phylogeny , Plants/genetics , Base Composition , Base Sequence , Computer Simulation , DNA, Ribosomal/classification , Models, Chemical , Molecular Sequence Data , Plants/classification , Sequence Alignment , Sequence Analysis, DNA , Sequence Homology, Nucleic Acid
9.
Mol Phylogenet Evol ; 3(4): 322-43, 1994 Dec.
Article En | MEDLINE | ID: mdl-7697190

Phylogenetic hypotheses generated from cladistic analysis of organismal and molecular data are shown to be generally congruent and/or complementary for comparisons of unicellular and colonial green algae in the Chlorophyceae. Cladistic analysis of organismal character data corroborates the alliance of colonial Stephanosphaera with unicellular Haematococcus (Haematococcaceae sensu Smith), inferred from previous studies of nuclear-encoded rRNA sequence data. The organismal data also support monophyly of the colonial Volvocaceae (sensu Smith). Alliances of other unicellular taxa, including those ascribed to the "Euchlamydomonas" Hauptgruppe (sensu Ettl), are not resolved by organismal characters principally because the structure of the data is skewed to shared ancestral characters (symplesiomorphies) and unique characters (autapomorphies) which define individual taxa only. Reanalysis of rRNA sequence data, with additional sequence data for critical taxa, does not support monophyly of the colonial Volvocaceae (sensu Smith). However, these data are weak in the support of the alternate hypothesis of nonmonophyly. In contrast, relationships among most unicellular flagellates are unambiguously resolved by the molecular data. Although the failure of the sequence data to resolve relationships among colonial flagellates appears to be due to a sampling of conservative sequences, an ancient, rapid radiation event or taxon sampling bias may also be contributing to the ambiguity problem. Results from analysis of a combined data set (organismal and molecular) are generally consistent with the inferences of the organismal character data regarding the colonial flagellates and are also consistent with the inferences of the sequence data regarding the unicellular taxa.


DNA, Protozoan/genetics , DNA, Ribosomal/genetics , Eukaryota/classification , Phylogeny , RNA, Protozoan/genetics , RNA, Ribosomal/genetics , Animals , Base Sequence , Chlamydomonas/classification , Chlamydomonas/genetics , Classification , Eukaryota/genetics , Molecular Sequence Data , Sequence Alignment , Sequence Homology, Nucleic Acid , Species Specificity , Volvocida/classification , Volvocida/genetics
10.
EXS ; 69: 607-16, 1994.
Article En | MEDLINE | ID: mdl-7994127

The first three decades of the subdiscipline of biology known as "molecular evolution" have generated large amounts of new information that illuminate the nature of evolutionary pattern and process. Major progress has been made in identifying primary sequence variation in genes and their protein products, initially from biochemically tractable systems (from large or culturable organisms and from highly-reiterated genes or highly-expressed gene products). In the 1980s, these techniques that had been limited to specialists, to relatively few representatives of the diversity of life, and to a small number of those organisms' genes, were extended through advances in molecular genetics and biochemistry, resulting in an explosion of molecular information and a proliferation of molecular trees. Studies of variation in molecular characters also were rarely linked with studies of anatomical, behavioral or ecological diversity. More sophisticated molecular genetic and biochemical techniques, currently being applied to long-standing questions in cell and developmental biology in model systems, should be applicable to more diverse lineages in the next decade. Molecular trees produced from one or more "housekeeping genes" can identify key lineages (species, populations, genomes or gene families) which, by comparison to model systems, may illuminate important aspects of higher level variability. Thus, the next phase of research in the field of molecular evolution should see greater linkage between studies of simple molecular and more complex developmental characters, and increased functional testing of genes and gene products in an evolutionary context. This review highlights some comparative experimental approaches that I believe will be most effective in extending our understanding of molecular evolution and better linking the field to other areas of science in the next few years.


Biological Evolution , Molecular Biology/trends , Animals , Phylogeny
11.
Mol Phylogenet Evol ; 2(2): 132-42, 1993 Jun.
Article En | MEDLINE | ID: mdl-8025720

Phylogenetic relationships of 19 species representing nine holometabolous insect orders and three outgroup orders were examined using sequence data from two-thirds of the 18S nuclear ribosomal RNA molecule. Of 1330 aligned nucleotide sites in 19 taxa, 460 were variable and used for phylogenetic analysis. Parsimony analyses resolved relationships in a few groups but left the most controversial questions regarding relationships among major lineages unresolved. All analyses supported a clade with Lepidoptera and Trichoptera as sister taxa most closely related to Diptera. Mecoptera and Siphonaptera were most often linked basally to this group, supporting the existence of the Mecopterida superorder. Phylogenetic affinities of this superorder and remaining lineages, Coleoptera, Hymenoptera, and neuropterids, were ambiguous. In contrast, distance analysis produced a tree supporting one of three morphologically based hypotheses. Neuroptera and Hymenoptera were placed as sister taxa ancestral to Mecopterida, with Coleoptera basal to all orders. The inability of the 18S molecule to resolve ancient divergence events may be due to the rapid divergence of holometabolous orders, resulting in few synapomorphies.


Insecta/classification , Phylogeny , RNA, Ribosomal, 18S/genetics , Animals , Base Sequence , Conserved Sequence , DNA , Genetic Variation , Insecta/genetics , Molecular Sequence Data , Sequence Alignment
12.
Plant Mol Biol ; 21(5): 805-21, 1993 Mar.
Article En | MEDLINE | ID: mdl-8096771

An Eco RI polymorphism, present in the 26S ribosomal RNA gene (rDNA) of the maize hybrid Sx19 (B73 x Mo17), was utilized to correlate DNaseI sensitivity, undermethylation and expression in rDNA. We have previously shown that in double digest experiments with methylation-sensitive restriction enzymes and Eco RI, Sx19 rDNA fragments originating from repeat units with two Eco RI sites (8.0 kb) are undermethylated, whereas the fragments originating from repeat units with a single Eco RI site (9.1 kb) are completely methylated. In the present study, Sx19 rDNA chromatin structure was examined by purifying intact nuclei and digesting them briefly with increasing amounts of DNaseI. Analysis of this DNA with Eco RI showed that the 8.0 kb rDNA fragments are extremely sensitive to DNaseI digestion, while the 9.1 kb rDNA fragments are relatively resistant to digestion even at high levels of DNaseI. Specific sites hypersensitive to DNaseI cleavage were mapped to a region in the intergenic spacer (IGS) near the major undermethylated site. Analysis of polymerase chain reaction (PCR) products synthesized using Sx19, B73, and Mo17 DNAs as templates indicated that the Eco RI polymorphism is due to a base change in the recognition site. Direct rRNA sequencing identified a single-base change in Mo17 rRNA relative to B73 rRNA. Allele-specific oligonucleotide probes containing the region surrounding and including the Eco RI polymorphic site were utilized to detect a nucleolar dominance effect by quantitating levels of rRNA transcripts in Sx19 and the reciprocal cross. Results from these single-base-pair mismatch hybridization experiments indicate that the majority of the rRNA transcripts in Sx19 originate from the DNaseI-sensitive, undermethylated, Eco RI-polymorphic rDNA repeat units.


DNA, Ribosomal/genetics , Zea mays/genetics , Alleles , Base Sequence , Chimera , Deoxyribonuclease EcoRI , Deoxyribonuclease I , Methylation , Molecular Sequence Data , Polymerase Chain Reaction , Polymorphism, Restriction Fragment Length , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , RNA, Ribosomal, 18S/genetics , RNA, Ribosomal, 18S/metabolism , Restriction Mapping
15.
Obstet Gynecol ; 77(6): 885-8, 1991 Jun.
Article En | MEDLINE | ID: mdl-2030862

A cross-sectional transvaginal ultrasound study was conducted in 137 normal pregnancies with gestational ages ranging from 5-12 weeks. Several biometric measurements were obtained throughout pregnancy, including the three diameters of the gestational sac, the crown-rump length, and the yolk sac. In addition, the appearance of the embryo heartbeat and embryo body movements were evaluated. Linear relationships were found between the mean gestational sac diameters and gestational age (r = 0.911; P less than .00001) and between mean gestational sac growth and crown-rump length growth (r = 0.926; P less than .0001). A gestational sac could be identified at 5 weeks' gestation; embryo heartbeat was imaged when the mean gestational sac diameter measured 2 cm, and embryo body movements could be seen when the mean gestational sac diameter reached 3 cm. In the present study, embryo heartbeat was identifiable after 6 weeks and 4 days with a sensitivity of 100%, specificity of 93.1%, positive predictive value of 96.9%, and negative predictive value of 100%. The embryo body movements, which were absent before 7 weeks' gestation, were observed after 8 weeks' gestation with a sensitivity of 100%, specificity of 92.8%, positive predictive value of 94.3%, and negative predictive value of 100%. With identification by transvaginal sonographic evaluation, the following can serve as markers of normal embryo growth: a mean gestational sac diameter greater than 2 cm in the presence of the embryo heartbeat, or a mean sac diameter measurement greater than 3 cm in the presence of embryo movement.


Extraembryonic Membranes/diagnostic imaging , Extraembryonic Membranes/growth & development , Fetal Movement/physiology , Heart Rate, Fetal/physiology , Ultrasonography, Prenatal/methods , Female , Humans , Pregnancy , Pregnancy Trimester, First , Regression Analysis , Sensitivity and Specificity , Vagina
16.
Plant Mol Biol ; 14(3): 333-47, 1990 Mar.
Article En | MEDLINE | ID: mdl-1715206

The restriction endonucleases Hpa II and Msp I were used to examine cytosine methylation in the ribosomal RNA genes (rDNA) of inbred lines of maize and species of teosinte. In all of the rDNAs examined, Msp I (not sensitive to mCpG) digestion yielded a distribution of lower molecular weight fragments indicative of multiple recognition sites. The majority of the rDNA arrays in an individual were inaccessible to Hpa II (sensitive to mCpG) cleavage, but a significant fraction (10-25%) was cleaved at least once by Hpa II into repeat unit length fragments (9.1 kbp). In some maize inbred lines, one or two additional fragment populations (less than 9.1 kbp in length) were also produced by Hpa II digestion. All of the unmethylated Hpa II sites mapped to the intergenic spacer (IGS), and the major unmethylated site was located approximately 800 bp 5' to the start of the 18S RNA coding sequence. An Eco RI polymorphism, present in the 26S gene of certain inbred lines and hybrids, was utilized to investigate the organization of unmethylated repeat units in the rDNA array. In double digest experiments with Hpa II/Eco RI, the fragments from repeat units with two Eco RI sites were sensitive to Hpa II digestion, whereas, the fragments from repeat units with a single Eco RI site were almost completely resistant to Hpa II digestion. Similar digestion patterns were also observed in Eco RII (sensitive to mCNG)/Eco RI digests. These results suggest that unmethylated and Eco RI polymorphic sites occur in the same repeat units.


DNA, Ribosomal/genetics , Plants/genetics , Base Sequence , Deoxyribonuclease HpaII , Deoxyribonucleases, Type II Site-Specific , Introns , Methylation , Repetitive Sequences, Nucleic Acid , Species Specificity , Zea mays/genetics
17.
Theor Appl Genet ; 77(6): 844-50, 1989 Jun.
Article En | MEDLINE | ID: mdl-24232902

The structure and organization of the ribosomal DNA (rDNA) of sorghum (Sorghum bicolor) and several closely related grasses were determined by gel blot hybridization to cloned maize rDNA. Monocots of the genus Sorghum (sorghum, shattercane, Sudangrass, and Johnsongrass) and the genus Saccharum (sugarcane species) were observed to organize their rDNA as direct tandem repeats of several thousand rDNA monomer units. For the eight restriction enzymes and 14 cleavage sites examined, no variations were seen within all of the S. bicolor races and other Sorghum species investigated. Sorghum, maize, and sugarcane were observed to have very similar rDNA monomer sizes and restriction maps, befitting their close common ancestry. The restriction site variability seen between these three genera demonstrated that sorghum and sugarcane are more closely related to each other than either is to maize. Variation in rDNA monomer lengths were observed frequently within the Sorghum genus. These size variations were localized to the intergenic spacer region of the rDNA monomer. Unlike many maize inbreds, all inbred Sorghum diploids were found to contain only one rDNA monomer size in an individual plant. These results are discussed in light of the comparative timing, rates, and modes of evolutionary events in Sorghum and other grasses. Spacer size variation was found to provide a highly sensitive assay for the genetic contribution of different S. bicolor races and other Sorghum species to a Sorghum population.

18.
Genetics ; 120(4): 1125-36, 1988 Dec.
Article En | MEDLINE | ID: mdl-2906307

We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.


RNA, Ribosomal/genetics , Zea mays/genetics , Blotting, Southern , Crosses, Genetic , DNA/genetics , DNA Probes , Edible Grain/genetics , Genetic Variation , Polymorphism, Restriction Fragment Length , RNA, Ribosomal, 18S/genetics , RNA, Ribosomal, 5.8S/genetics , Repetitive Sequences, Nucleic Acid , Restriction Mapping , Zea mays/classification
19.
Biosystems ; 21(3-4): 223-30, 1988.
Article En | MEDLINE | ID: mdl-2840134

The nuclear ribosomal RNA genes (rDNA) of Chlamydomonas reinhardtii, C. moewusii and C. eugametos were examined with restriction endonuclease fragment and direct rRNA sequencing analyses. These comparative molecular data confirm similarity between C. moewusii and C. eugametos, and dissimilarity between the strains and C. reinhardtii. For C. moewusii and C. eugametos, the fragment analysis of digests with 16 (six base pair recognition site) restriction endonucleases revealed either no or minor differences. These minor differences appear to be confined to length and site variation in the rapidly evolving intergenic spacer region of the algal rDNA repeat unit. In contrast, patterns of digests for C. reinhardtii were completely different from those of C. moewusii and C. eugametos for all enzymes tested. Over two regions of the 18S ribosomal RNA (spanning approx. 300 bases) in C. moewusii and C. eugametos, we observed three possible base substitutions and no insertion/deletion events. The same comparison between C. reinhardtii and C. moewusii (or C. eugametos) revealed 31 base substitutions and eight insertion/deletion events. Overall, the rDNA comparisons support the proposed conspecificity of C. moewusii and C. eugametos, as well as the hypothesis that intraspecific variation in the algal ribosomal RNA coding region is minimal and that comparisons of rDNA sequences at higher taxonomic levels can be useful indicators of algal phylogeny. The degree of difference in the sequences of the 18S coding region between C. reinhardtii and C. moewusii or C. eugametos is comparable to that between an angiosperm and Equisetum and may reflect an ancient divergence between two species in one algal genus.(ABSTRACT TRUNCATED AT 250 WORDS)


Chlamydomonas/genetics , Eukaryota/genetics , Genes , Phylogeny , RNA, Ribosomal/genetics , Cell Nucleus/physiology , DNA Restriction Enzymes , DNA, Ribosomal/genetics , Species Specificity
20.
Cell ; 25(3): 737-41, 1981 Sep.
Article En | MEDLINE | ID: mdl-7285116

We have sequenced the 3' and 5' untranslated regions of beta-globin mRNAs from cebus monkey, rhesus monkey and chimpanzee. A comparison with the corresponding human sequences reveals that the rate of sequence divergence among the higher primates is the same in the 3' and 5' noncoding regions and that this rate is several times lower than the rate for silent substitutions in the coding regions. In addition, the rate of sequence divergence in the 3' untranslated region of the primate beta-globin nRNA is several times lower than the rate calculated for this region from other comparisons. The low rate of sequence divergence in the noncoding 3' end of the primate beta-globin mRNAs may indicate a specialized and significant function for this region in the higher primates.


Biological Evolution , Globins/genetics , Primates/genetics , RNA, Messenger/genetics , Animals , Base Sequence , Humans , Protein Biosynthesis , RNA, Messenger/physiology , Structure-Activity Relationship
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