Phylogenetic reconstruction based on low copy DNA sequence data in an allopolyploid: The B genome of wheat

Genome ◽  
1999 ◽  
Vol 42 (2) ◽  
pp. 351-360 ◽  
Author(s):  
Nancy K Blake ◽  
Ben R Lehfeldt ◽  
Matt Lavin ◽  
Luther E Talbert
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Diploid Species ◽  
Single Copy ◽  
Wheat Evolution ◽  
Polyploid Evolution ◽  
B Genome ◽  
Genome Donor ◽  
Copy Dna

Study of bread wheat (Triticum aestivum) may help to resolve several questions related to polyploid evolution. One such question regards the possibility that the component genomes of polyploids may themselves be polyphyletic, resulting from hybridization and introgression among different polyploid species sharing a single genome. We used the B genome of wheat as a model system to test hypotheses that bear on the monophyly or polyphyly of the individual constituent genomes. By using aneuploid wheat stocks, combined with PCR-based cloning strategies, we cloned and sequenced two single-copy-DNA sequences from each of the seven chromosomes of the wheat B genome and the homologous sequences from representatives of the five diploid species in section Sitopsis previously suggested as sister groups to the B genome. Phylogenetic comparisons of sequence data suggested that the B genome of wheat underwent a genetic bottleneck and has diverged from the diploid B genome donor. The extent of genetic diversity among the Sitopsis diploids and the failure of any of the Sitopsis species to group with the wheat B genome indicated that these species have also diverged from the ancestral B genome donor. Our results support monophyly of the wheat B genome.Key words: wheat evolution, phylogenetics, DNA sequencing.

Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

scholarly journals Sequence organization and developmental expression of an interspersed, repetitive element and associated single-copy DNA sequences in Dictyostelium discoideum.

1985 ◽  
Vol 5 (8) ◽  
pp. 2123-2130 ◽  
Author(s):  
A R Kimmel ◽  
R A Firtel
Keyword(s):  
Dna Sequences ◽  
Transcription Initiation ◽  
Sequence Data ◽  
Single Copy ◽  
Developmental Expression ◽  
Cdna Clones ◽  
Base Pairs ◽  
Sequence Element ◽  
Copy Dna ◽  
Single Copy Dna

We have examined the genomic organization and developmental expression pattern of a short, transcribed, interspersed repeat element and its associated single-copy sequences. We have previously shown that 1% of the polyadenylated [poly(A)+] RNA from vegetative cells contains sequences that hybridize to this repeat. The complementary RNA is heterogeneous in size, and 90% of its mass hybridizes to single-copy DNA. In this study, we examined a series of genomic DNAs and cDNAs derived from poly(A)+ RNAs which are complementary to the repeat. Comparisons of sequence data from various genomic and cDNA clones indicated that (AAC)n X (GTT)n is the common sequence element. The tandem repeat occurred in approximately 100 short segments (approximately 35 to 150 base pairs) per haploid genome interspersed with single-copy DNA. Probes from regions adjacent to this element hybridized to unique restriction fragments on DNA blots and unique poly(A)+ RNA species on RNA blots. The (AAC)n X (GTT)n sequence was asymmetrically transcribed with only (AAC)n sequences represented in RNA. The repeat was localized within the transcribed regions of several genes and 70 base pairs 5' to the transcription initiation site of another gene. Individual (AAC)n-containing RNAs exhibited a developmental pattern of expression suggestive of the coordinate expression of many AAC gene family members.

Electron microscopy of Achlya deoxyribonucleic acid sequence organization

1981 ◽  
Vol 1 (2) ◽  
pp. 136-143
Author(s):  
M Pellegrini ◽  
W E Timberlake ◽  
R B Goldberg
Keyword(s):  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Microscopic Analysis ◽  
Single Copy ◽  
Electron Microscopic ◽  
Sequence Organization ◽  
Double Stranded Dna ◽  
Copy Dna ◽  
Gene 32 ◽  
Single Copy Dna

Electron microscopic analysis of reassociated deoxyribonucleic acid (DNA) from the aquatic fungus Achlya bisexualis revealed details of the sequence arrangement of the inverted repeats and both the highly and moderately repetitive sequence clusters. We used the gene 32 protein-ethidium bromide technique for visualizing the DNA molecules, a procedure which provides excellent contrast between single- and double-stranded DNA regions. Long (greater than 6-kilobase) DNA fragments were isolated after reannealing to two different repetitive C0t values, and the renatured structures were then visualized in an electron microscope. Our results showed that the inverted repeat sequences were short (0.5 kilobase, number-average) and separated by nonhomologous DNA of various lengths. These pairs of sequences were not clustered within the genome. Both highly repetitive and moderately repetitive DNA sequences were organized as tandem arrays of precisely paired, regularly repeating units. No permuted clusters of repeating sequences were observed, nor was there evidence of interspersion of repetitive with single-copy DNA sequences in the Achlya genome.

scholarly journals The Complete Plastid Genome of Magnolia zenii and Genetic Comparison to Magnoliaceae species

Molecules ◽  
2019 ◽  
Vol 24 (2) ◽  
pp. 261 ◽  
Author(s):  
Yongfu Li ◽  
Steven Paul Sylvester ◽  
Meng Li ◽  
Cheng Zhang ◽  
Xuan Li ◽  
...  
Keyword(s):  
Plastid Genome ◽  
Sequence Data ◽  
Genome Structure ◽  
Phylogenetic Reconstruction ◽  
Strong Support ◽  
Gc Content ◽  
Single Copy ◽  
Protein Coding ◽  
Critically Endangered Species ◽  
Genomic Study

Magnolia zenii is a critically endangered species known from only 18 trees that survive on Baohua Mountain in Jiangsu province, China. Little information is available regarding its molecular biology, with no genomic study performed on M. zenii until now. We determined the complete plastid genome of M. zenii and identified microsatellites. Whole sequence alignment and phylogenetic analysis using BI and ML methods were also conducted. The plastome of M. zenii was 160,048 bp long with 39.2% GC content and included a pair of inverted repeats (IRs) of 26,596 bp that separated a large single-copy (LSC) region of 88,098 bp and a small single-copy (SSC) region of 18,757 bp. One hundred thirty genes were identified, of which 79 were protein-coding genes, 37 were transfer RNAs, and eight were ribosomal RNAs. Thirty seven simple sequence repeats (SSRs) were also identified. Comparative analyses of genome structure and sequence data of closely-related species revealed five mutation hotspots, useful for future phylogenetic research. Magnolia zenii was placed as sister to M. biondii with strong support in all analyses. Overall, this study providing M. zenii genomic resources will be beneficial for the evolutionary study and phylogenetic reconstruction of Magnoliaceae.

More than one origin of hexaploid wheat is indicated by sequence comparison of low-copy DNA

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 402-407 ◽  
Author(s):  
L E Talbert ◽  
L Y Smith ◽  
N K Blake
Keyword(s):  
Dna Sequences ◽  
Hexaploid Wheat ◽  
Restriction Site ◽  
Cereal Crop ◽  
Crop Species ◽  
Wheat Evolution ◽  
D Genome ◽  
Restriction Site Variation ◽  
Site Variation ◽  
Copy Dna

Allohexaploid bread wheat is grown on more acreage than any other cereal crop, yet variation at the DNA level seems to be less than that observed in many diploid crop species. A common explanation for the small amount of DNA-level variation is that a severe bottleneck event resulted from the polyploidization events that gave rise to hexaploid wheat, whereby wheat was genetically separated from its progenitors. In this report, we test the extent of the bottleneck separating wheat from its D-genome progenitor, Triticum tauschii, by comparative DNA sequence analysis. Restriction site variation of low-copy DNA sequences amplified by PCR showed an average of 2.9 and 2.4 alleles per primer set in T. tauschii and wheat, respectively. Two different restriction patterns were present in T. tauschii for DNA amplified with a primer set for the A1 locus. Both alleles were also present in wheat. Alleles at the A1 locus were cloned and 527 bp of sequence obtained from 12 and 13 diverse accessions of wheat and T. tauschii, respectively. Average genetic distance among the wheat alleles was similar to that among the T. tauschii alleles (0.0127 and 0.0133, respectively). Nucleotide differences indicated that two distinct alleles existed in T. tauschii, both of which were present in wheat. These data suggest that hexaploid wheat formed at least twice, and that the bottleneck separating wheat from T. tauschii may be less constrictive than previously supposed.Key words: wheat, evolution, DNA.

scholarly journals Genomic distribution of repeated and single copy DNA sequences inPenicillium funiculosum

1987 ◽  
Vol 40 (2-3) ◽  
pp. 315-319 ◽  
Author(s):  
N.A. Sahasrabudhe ◽  
M.N. Sainani ◽  
V.S. Gupta ◽  
P.K. Ranjekar
Keyword(s):  
Dna Sequences ◽  
Single Copy ◽  
Genomic Distribution ◽  
Copy Dna ◽  
Single Copy Dna
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