Inferences on the origins of polyploid Turnera species (Passifloraceae) based on molecular data

Botany ◽  
2013 ◽  
Vol 91 (3) ◽  
pp. 167-175 ◽  
Author(s):  
Alicia López ◽  
Aveliano Fernández ◽  
Joel S. Shore
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Diploid Species ◽  
Nuclear Genome ◽  
Molecular Data ◽  
Genome Donor ◽  
A Genome ◽  
Cytogenetic Studies ◽  
C Genome ◽  
Nuclear Its

We explore the evolution of polyploids in subseries Turnera, testing hypotheses on their origins using DNA sequences (partial ndhF and trnT-L) from the plastid genome, as well as sequences of the nuclear ribosomal internal transcribed spacer (ITS). We construct phylogenies (with both Bayesian and maximum parsimony methods) using both the plastid and ITS sequences. We test hypotheses concerning the genome contributors to polyploids where previous cytogenetic studies had designated various diploid species as possessing A or C genomes and had proposed various genomic constitutions for the polyploids. Our analyses support the occurrence of a C genome clade of species and the origin of autooctoploid T. fernandezii Arbo from T. grandiflora (Urb.) Arbo (a C genome diploid). Nuclear ITS data support the hypothesis that T. concinna Arbo (an A genome species) contributed a genome to the segmental allotetraploid T. grandidentata (Urb.) Arbo, whereas analyses of ndhF and trnT-L sequences did not lead to identification of the plastid (or additional nuclear genome) donor. Our analyses support the origins of allooctoploids T. aurelii Arbo and T. cuneiformis Poir. from hexaploid T. orientalis (Urb.) Arbo. We found no evidence that hexaploid T. velutina Presl. possesses a C genome. We provide evidence, using Bayes factors, supporting the hypothesis that the segmental allohexaploids have had independent origins.

The use of double fluorescence in situ hybridization to physically map the positions of 5S rDNA genes in relation to the chromosomal location of 18S–5.8S–26S rDNA and a C genome specific DNA sequence in the genus Avena

Genome ◽  
1996 ◽  
Vol 39 (3) ◽  
pp. 535-542 ◽  
Author(s):  
Concha Linares ◽  
Juan González ◽  
Esther Ferrer ◽  
Araceli Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequence ◽  
Diploid Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
26S Rdna ◽  
A Genome ◽  
Rdna Loci ◽  
C Genome

A physical map of the locations of the 5S rDNA genes and their relative positions with respect to 18S–5.8S–26S rDNA genes and a C genome specific repetitive DNA sequence was produced for the chromosomes of diploid, tetraploid, and hexaploid oat species using in situ hybridization. The A genome diploid species showed two pairs of rDNA loci and two pairs of 5S loci located on both arms of one pair of satellited chromosomes. The C genome diploid species showed two major pairs and one minor pair of rDNA loci. One pair of subtelocentric chromosomes carried rDNA and 5S loci physically separated on the long arm. The tetraploid species (AACC genomes) arising from these diploid ancestors showed two pairs of rDNA loci and three pairs of 5S loci. Two pairs of rDNA loci and 2 pairs of 5S loci were arranged as in the A genome diploid species. The third pair of 5S loci was located on one pair of A–C translocated chromosomes using simultaneous in situ hybridization with 5S rDNA genes and a C genome specific repetitive DNA sequence. The hexaploid species (AACCDD genomes) showed three pairs of rDNA loci and six pairs of 5S loci. One pair of 5S loci was located on each of two pairs of C–A/D translocated chromosomes. Comparative studies of the physical arrangement of rDNA and 5S loci in polyploid oats and the putative A and C genome progenitor species suggests that A genome diploid species could be the donor of both A and D genomes of polyploid oats. Key words : oats, 5S rDNA genes, 18S–5.8S–26S rDNA genes, C genome specific repetitive DNA sequence, in situ hybridization, genome evolution.

Phylogenetic relationships of the monogenomic species of the wheat tribe, Triticeae (Poaceae), inferred from nuclear rDNA (internal transcribed spacer) sequences

Genome ◽  
1995 ◽  
Vol 38 (2) ◽  
pp. 211-223 ◽  
Author(s):  
C. Hsiao ◽  
N. J. Chatterton ◽  
K. H. Asay ◽  
K. B. Jensen
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Parallel Evolution ◽  
Diploid Species ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
The Arctic ◽  
Cytogenetic Evidence

Phylogenetic relationships of 30 diploid species of Triticeae (Poaceae) representing 19 genomes were estimated from the sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. The ITS sequence phylogeny indicated that: (i) each genome group of species is monophyletic, concordant with cytogenetic evidence; (ii) Hordeum (I) and Critesion (H) are basal; (iii) Australopyrum (W) is closely related to Agropyron (P); (iv) Peridictyon (G), Heteranthelium (Q), and Dasypyrum (V) are closely related to Pseudoroegneria (S); (v) most of the annuals, Triticum s.l. (A, B, D), Crithopsis (K), Taeniatherum (T), Eremopyrum (F), Henrardia (O), Secale (R), and two perennials, Thinopyrum (J) and Lophopyrum (E), all of Mediterranean origin, are a monophyletic group. However, phylogenetic trees based on morphology group these Mediteranean species with various perennial lineages of the Arctic-temperate region. The molecular data and biogeography of the tribe suggest that the Mediterranean lineage is derived from the Arctic-temperate lineage and that the two lineages have evolved in parallel. Extensive morphological parallelism apparently obscures the true genealogical history of the tribe when only morphology is considered.Key words: Poaceae, Triticeae, rDNA sequence, molecular phylogeny, parallel evolution.

scholarly journals A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

IMA Fungus ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Kai Wang ◽  
Timo Sipilä ◽  
Kirk Overmyer
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Host Plants ◽  
Sequence Data ◽  
Nuclear Gene ◽  
Molecular Data ◽  
Rapid Identification ◽  
Nuclear Ribosomal Dna ◽  
Species Relationships ◽  
Internal Transcribed Spacer Sequences

AbstractProtomyces is an understudied genus of yeast-like fungi currently defined as phytopathogens of only Umbelliferae and Compositae. Species relationships and boundaries remain controversial and molecular data are lacking. Of the 82 named Protomyces, we found few recent studies and six available cultures. We previously isolated Protomyces strains from wild Arabidopsis thaliana, a member of Brassicaceae, a family distant from accepted Protomyces hosts. We previously sequenced the genomes of all available Protomyces species, and P. arabidopsidicola sp. nov. strain C29, from Arabidopsis. Phylogenomics suggests this new species occupied a unique position in the genus. Genomic, morphological, and physiological characteristics distinguished P. arabidopsidicola sp. nov. from other Protomyces. Nuclear gene phylogenetic marker analysis suggests actin1 gene DNA sequences could be used with nuclear ribosomal DNA internal transcribed spacer sequences for rapid identification of Protomyces species. Previous studies demonstrated P. arabidopsidicola sp. nov. could persist on the Arabidopsis phyllosphere and Protomyces sequences were discovered on Arabidopsis at multiple sites in different countries. We conclude that the strain C29 represents a novel Protomyces species and propose the name of P. arabidopsidicola sp. nov. Consequently, we propose that Protomyces is not strictly associated only with the previously recognized host plants.

ANALYSIS OF SPECIES RELATIONSHIPS IN AVENAE BY THIN-LAYER CHROMATOGRAPHY AND DISC ELECTROPHORESIS

1972 ◽  
Vol 14 (2) ◽  
pp. 305-316 ◽  
Author(s):  
H. C. Dass
Keyword(s):  
Thin Layer ◽  
Diploid Species ◽  
Disc Electrophoresis ◽  
Tetraploid Species ◽  
Species Relationships ◽  
D Genome ◽  
Genome Donor ◽  
A Genome ◽  
Layer Chromatography ◽  
Esterase Patterns

Thin-layer chromatographic studies on flavonoids, and disc electrophoretic studies on proteins and esterase isoenzymes were conducted with Avena to determine species relationships and genome homologies. Distinctness of Avena ventricosa and A. pilosa was observed in comparison to other diploid species. Closeness of the diploid species of the A. strigosa group (including hirtula and wiestii) was evident from the similarity of their protein and esterase spectra. The tetraploid species, A. barbata and A. abyssinica, were found to be very close to A. hirtula and A. strigosa, respectively, by TLC studies. Proteins and esterases also showed that the tetraploid species are very close to the A. strigosa group of diploid species. The contribution of a genome by the A. strigosa group to the tetraploids and hexaploids was confirmed. The hexaploids showed different protein and esterase patterns. The involvement of A. ventricosa as the C genome donor to the hexaploids was shown by the protein and esterase spectra. A few extra protein bands observed may have been from the D genome.

Fluorescence in situ hybridization mapping of Avena sativa L. cv. SunII and its monosomic lines using cloned repetitive DNA sequences

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1230-1237 ◽  
Author(s):  
M L Irigoyen ◽  
C Linares ◽  
E Ferrer ◽  
A Fominaya
Keyword(s):  
In Situ Hybridization ◽  
Dna Sequences ◽  
Avena Sativa ◽  
Meiotic Chromosome ◽  
D Genome ◽  
Fish Mapping ◽  
Intergenomic Translocations ◽  
A Genome ◽  
C Genome

Fluorescent in situ hybridization (FISH) employing multiple probes was used with mitotic or meiotic chromosome spreads of Avena sativa L. cv. SunII and its monosomic lines to produce physical chromosome maps. The probes used were Avena strigosa pAs120a (which hybridizes exclusively to A-genome chromosomes), Avena murphyi pAm1 (which hybridizes exclusively to C-genome chromosomes), A. strigosa pAs121 (which hybridizes exclusively to A- and D-genome chromosomes), and the wheat rDNA probes pTa71 and pTa794. Simultaneous and sequential FISH employing two-by-two combinations of these probes allowed the unequivocal identification and genome assignation of all chromosomes. Ten pairs were found carrying intergenomic translocations: (i) between the A and C genomes (chromosome pair 5A); (ii) between the C and D genomes (pairs 1C, 2C, 4C, 10C, and 16C); and (iii) between the D and C genomes (pairs 9D, 11D, 13D, and 14D). The existence of a reciprocal intergenomic translocation (10C–14D) is also proposed. Comparing these results with those of other hexaploids, three intergenomic translocations (10C, 9D, and 14D) were found to be unique to A. sativa cv. SunII, supporting the view that 'SunII' is genetically distinct from other hexaploid Avena species and from cultivars of the A. sativa species. FISH mapping using meiotic and mitotic metaphases facilitated the genomic and chromosomal identification of the aneuploid chromosome in each monosomic line. Of the 18 analyzed, only 11 distinct monosomic lines were actually found, corresponding to 5 lines of the A genome, 2 lines of the C genome, and 4 lines of the D genome. The presence or absence of the 10C–14D interchange was also monitored in these lines.Key words: Avena sativa, monosomics, FISH mapping, genomic identification, intergenomic translocations.

scholarly journals Phylogenetic Trees of Aecial-Stage Rust Fungus, Puccinia paederiae (Dietel) Gorlenko Causing Gall on Paederia linearis Hook f.

2017 ◽  
Vol 15 (10) ◽  
pp. 739-752
Author(s):  
Wuttiwat JITJAK ◽  
Niwat SANOAMUANG
Keyword(s):  
Bayesian Methods ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Rust Fungus ◽  
Large Subunit ◽  
Molecular Data ◽  
Small Subunit ◽  
Phylogenetic Study ◽  
Internal Transcribed Spacer Region

A rust fungus, Puccinia paederiae (Dietel) Gorlenko causing galls on the stem of the skunk vine (Paederia linearis Hook. f. var. linealis and P. linealis var. palida (Craib) Puff) was collected for phylogenetic study as no molecular data was exclusively available for this fungus. Three regions of ribosomal DNA sequences, small subunit (SSU), large subunit (LSU) and internal transcribed spacer region 1 (ITS1) were employed. The results of maximum parsimony and Bayesian methods suggested that among the trees with these sequences, this fungus was nested in Pucciniaceae clades and Puccinia species with supportive statistical values. This is the first report on the phylogenetic analysis using multiple genes of the rust, P. paederiae.

Three new species of northern Australian Glycine (Fabaceae, Phaseolae), G. gracei, G. montis-douglas and G. syndetika

2006 ◽  
Vol 19 (3) ◽  
pp. 245 ◽  
Author(s):  
B. E. Pfeil ◽  
L. A. Craven ◽  
A. H. D. Brown ◽  
B. G. Murray ◽  
J. J. Doyle
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Species Complex ◽  
Diploid Species ◽  
Northern Territory ◽  
Crossing Experiments ◽  
Diploid Parent ◽  
The Third ◽  
A Genome ◽  
Three New Species

Three new Australian diploid species in Glycine Willd. are described. Two of these (Glycine gracei B.E.Pfeil & Craven and Glycine montis-douglas B.E.Pfeil & Craven) are endemic to the Northern Territory whereas the third (Glycine syndetika B.E.Pfeil & Craven) is endemic to Queensland. G. montis-douglas is only known from one locality. The genetic affinities of G. gracei and G. syndetika are with other A genome species. The species G. syndetika is the closest relative of a diploid parent of the T2 allotetraploid race of the G. tomentella s.l. Hayata species complex, as well as of allotetraploid G. pescadrensis Hayata, which is here formally reinstated from synonymy. Images are included of the leaflet venation for several species discussed in the paper. Thus, the treatment incorporates evidence from morphology, cytology, DNA sequences and crossing experiments. A key to the subgenera and to the species within Glycine subgenus Glycine is provided, which includes all 25 described Australian taxa.

Nitrate Reductase Phylogeny of Potato (Solanum sect. Petota) Genomes with Emphasis on the Origins of the Polyploid Species

2009 ◽  
Vol 34 (1) ◽  
pp. 207-219 ◽  
Author(s):  
Flor Rodríguez ◽  
David M. Spooner
Keyword(s):  
Nitrate Reductase ◽  
Sequence Data ◽  
Diploid Species ◽  
Polyploid Species ◽  
Genome Species ◽  
The North ◽  
Potato Germplasm ◽  
Maternal Genome ◽  
Genome Donor ◽  
A Genome

Solanum section Petota is taxonomically difficult, partly because of interspecific hybridization at both the diploid and polyploid levels. There is much disagreement regarding species boundaries and affiliation of species to series. Elucidating the phylogenetic relationships within the polyploids is crucial for an effective taxonomic treatment of the section and for the utilization of wild potato germplasm in breeding programs. We here infer relationships among the potato diploids and polyploids using nitrate reductase (NIA) sequence data in comparison to prior plastid phylogenies and: 1) examine genome types within section Petota, 2) show species in the polyploid series Conicibaccata, Longipedicellata, and in the Iopetalum group to be derived from allopolyploidization, 3) support an earlier hypothesis by confirming S. verrucosum as the maternal genome donor for the polyploid species S. demissum as well as species in the Iopetalum Group, 4) demonstrate that S. verrucosum is the closest relative to the maternal genome donor for species in ser. Longipedicellata, 5) support the close relationship between S. acaule and diploid species from series Megistacroloba and Tuberosa, and 6) show the North and Central American B genome species to be well distinguished from the A genome species of South America.

scholarly journals Genome size variation in the genus Avena

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 209-220 ◽  
Author(s):  
Honghai Yan ◽  
Sara L. Martin ◽  
Wubishet A. Bekele ◽  
Robert G. Latta ◽  
Axel Diederichsen ◽  
...  
Keyword(s):  
Genome Size ◽  
Diploid Species ◽  
Size Variation ◽  
Evolutionary Distance ◽  
Polyploid Species ◽  
Genome Size Variation ◽  
Similar Morphology ◽  
Germplasm Collections ◽  
A Genome ◽  
C Genome

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

A new pratylenchid nematode, Hoplotylus japonicus n. sp. (Tylenchina: Pratylenchidae) from the rhizosphere of Japanese maple, Acer palmatum (Thumb.)

Nematology ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. 1131-1140
Author(s):  
Jianfeng Gu ◽  
Munawar Maria ◽  
Yiwu Fang ◽  
Majid Pedram
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Anterior Margin ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Dorsal Side ◽  
Lateral View ◽  
Molecular Phylogenetic ◽  
A New Species

Summary During quarantine inspections, a new species of Hoplotylus was detected from the rhizosphere of the Japanese maple, Acer palmatum, imported into China from Japan. Hoplotylus japonicus n. sp. is characterised by a stout 431-602 μm long body, well-developed 20.0-24.5 μm long stylet with tulip-shaped knobs having rounded sides in lateral view and a rounded anterior margin, excretory pore located slightly posterior to the hemizonid, usually empty, spermatheca, conical tail with a spike-like projection, which is distally smooth on the dorsal side, and males not found. It was morphologically compared with four currently known species of the genus, viz., H. femina, H. montanus, H. silvaticus, and H. sjacobi. In molecular phylogenetic analyses using 18S, 28S and internal transcribed spacer (ITS) ribosomal DNA sequences, the new species formed a clade with the only currently sequenced species of the genus, H. femina, in all phylogenies. This is the second species of the genus characterised by molecular data and the second species recovered from Japan.

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