The evolution of intergenic spacers of the 5S rDNA genes in the Drosophila obscura group: Are these sequences suitable for phylogenetic analyses?

1997 ◽  
Vol 25 (2) ◽  
pp. 131-139 ◽  
Author(s):  
Roger Grau ◽  
Lutz Bachmann
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rdna Genes ◽  
Intergenic Spacers ◽  
Obscura Group

The molecular diversity of the 5S rRNA gene in barley (Hordeum vulgare)

Genome ◽  
1994 ◽  
Vol 37 (6) ◽  
pp. 992-998 ◽  
Author(s):  
Bernard R. Baum ◽  
D. A. Johnson
Keyword(s):  
Hordeum Vulgare ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Sequence Diversity ◽  
Rrna Gene ◽  
Rdna Genes ◽  
Short Repeat ◽  
Repeat Class ◽  
Cultivated Barley

The 5S rDNA genes from several accessions of cultivated barley, Hordeum vulgare L., were amplified by the polymerase chain reaction, cloned, and sequenced. Analysis of the aligned sequences, followed by principal coordinate analysis, support the recognition of at least two distinct classes of 5S rDNA genes. The short repeat class corresponds to the 300-bp tandem repeat defined by E.V. Ananiev as containing several TAG repeating units. The long repeat class contains long tandem repeats and lacks the TAG repeating unit. Sequences in each class can be further subdivided, with the long repeat class containing two groups and the short repeat class containing two and possibly three groups. These results suggest that in cultivated barley the sequence diversity found within the 5S rDNA non-transcribed spacer region may be encoded by three or more loci and may be useful for phylogenetic analyses provided that orthology can be established.Key words: 5S rDNA, sequence diversity, barley, phylogenetic analysis.

scholarly journals Comparative Chloroplast Genomics of Litsea Lam. (Lauraceae) and Its Phylogenetic Implications

Forests ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 744
Author(s):  
Yunyan Zhang ◽  
Yongjing Tian ◽  
David Y. P. Tng ◽  
Jingbo Zhou ◽  
Yuntian Zhang ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
Phylogenetic Analyses ◽  
Eastern China ◽  
Chloroplast Microsatellites ◽  
Endangered Tree ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Chloroplast Genomes ◽  
Phylogenetic Implications ◽  
Chloroplast Genome Sequence

Litsea Lam. is an ecological and economic important genus of the “core Lauraceae” group in the Lauraceae. The few studies to date on the comparative chloroplast genomics and phylogenomics of Litsea have been conducted as part of other studies on the Lauraceae. Here, we sequenced the whole chloroplast genome sequence of Litsea auriculata, an endangered tree endemic to eastern China, and compared this with previously published chloroplast genome sequences of 11 other Litsea species. The chloroplast genomes of the 12 Litsea species ranged from 152,132 (L. szemaois) to 154,011 bp (L. garrettii) and exhibited a typical quadripartite structure with conserved genome arrangement and content, with length variations in the inverted repeat regions (IRs). No codon usage preferences were detected within the 30 codons used in the chloroplast genomes, indicating a conserved evolution model for the genus. Ten intergenic spacers (psbE–petL, trnH–psbA, petA–psbJ, ndhF–rpl32, ycf4–cemA, rpl32–trnL, ndhG–ndhI, psbC–trnS, trnE–trnT, and psbM–trnD) and five protein coding genes (ndhD, matK, ccsA, ycf1, and ndhF) were identified as divergence hotspot regions and DNA barcodes of Litsea species. In total, 876 chloroplast microsatellites were located within the 12 chloroplast genomes. Phylogenetic analyses conducted using the 51 additional complete chloroplast genomes of “core Lauraceae” species demonstrated that the 12 Litsea species grouped into four sub-clades within the Laurus-Neolitsea clade, and that Litsea is polyphyletic and closely related to the genera Lindera and Laurus. Our phylogeny strongly supported the monophyly of the following three clades (Laurus–Neolitsea, Cinnamomum–Ocotea, and Machilus–Persea) among the above investigated “core Lauraceae” species. Overall, our study highlighted the taxonomic utility of chloroplast genomes in Litsea, and the genetic markers identified here will facilitate future studies on the evolution, conservation, population genetics, and phylogeography of L. auriculata and other Litsea species.

Codependence of repetitive sequence classes in genomes: phylogenetic analysis of 5S rDNA families in Hordeum (Triticeae: Poaceae)

Genome ◽  
2010 ◽  
Vol 53 (3) ◽  
pp. 180-202 ◽  
Author(s):  
Bernard R. Baum ◽  
Tara Edwards ◽  
Douglas A. Johnson
Keyword(s):  
Phylogenetic Analyses ◽  
5S Rdna ◽  
Rrna Gene ◽  
Consensus Sequences ◽  
Rdna Sequences ◽  
Unit Classes ◽  
Unit Class ◽  
Comprehensive Picture ◽  
Host Parasite

To complete our study of the genus Hordeum and to elaborate a phylogeny of species based upon 5S rDNA sequences, we have cloned and sequenced PCR amplicons from seven American polyploid species to generate 164 new 5S rRNA gene sequences. These sequences were analysed along with the more than 2000 5S rDNA sequences previously generated from the majority of species in Hordeum to provide a comprehensive picture of the distribution (presence or absence) of 5S rDNA unit classes (orthologous groups) in this genus as well as insights into the phylogeny of Hordeum. Testing of substitution models for each unit class based upon the consensus sequences of all the taxa as well as for each unit class within the genus found that the general best fit was TPM3uf+G, from which a maximum-likelihood tree was calculated. A novel application of cophylogenetic analysis, where relationships among unit classes were treated as host–parasite interactions, depicted some significant pair links under tests of randomness indicative of nonrandom codivergence among several unit classes within the same taxon. The previous classification of four genomic groups is reflected in combinations of unit classes, and it is proposed that current taxa developed from ancient diploidized paleopolyploids and that some were subjected to gene loss, i.e., unit class loss. Finally, separate phylogenetic analyses performed for the tetraploid and hexaploid species were used to derive a working model describing the phylogeny of the polyploid taxa from their putative diploid ancestry.

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.

scholarly journals Phylogenomic and Comparative Analyses of Complete Plastomes of Croomia and Stemona (Stemonaceae)

2018 ◽  
Vol 19 (8) ◽  
pp. 2383 ◽  
Author(s):  
Qixiang Lu ◽  
Wenqing Ye ◽  
Ruisen Lu ◽  
Wuqin Xu ◽  
Yingxiong Qiu
Keyword(s):  
Gene Order ◽  
Phylogenetic Analyses ◽  
Sequence Divergence ◽  
Early Pleistocene ◽  
Disjunct Distribution ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Intergenic Spacers ◽  
Protein Coding Genes

The monocot genus Croomia (Stemonaceae) comprises three herbaceous perennial species that exhibit EA (Eastern Asian)–ENA (Eastern North American) disjunct distribution. However, due to the lack of effective genomic resources, its evolutionary history is still weakly resolved. In the present study, we conducted comparative analysis of the complete chloroplast (cp) genomes of three Croomia species and two Stemona species. These five cp genomes proved highly similar in overall size (154,407–155,261 bp), structure, gene order and content. All five cp genomes contained the same 114 unique genes consisting of 80 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Gene content, gene order, AT content and IR/SC boundary structures were almost the same among the five Stemonaceae cp genomes, except that the Stemona cp genome was found to contain an inversion in cemA and petA. The lengths of five genomes varied due to contraction/expansion of the IR/SC borders. A/T mononucleotides were the richest Simple Sequence Repeats (SSRs). A total of 46, 48, 47, 61 and 60 repeats were identified in C. japonica, C. heterosepala, C. pauciflora, S. japonica and S. mairei, respectively. A comparison of pairwise sequence divergence values across all introns and intergenic spacers revealed that the ndhF–rpl32, psbM–trnD and trnS–trnG regions are the fastest-evolving regions. These regions are therefore likely to be the best choices for molecular evolutionary and systematic studies at low taxonomic levels in Stemonaceae. Phylogenetic analyses of the complete cp genomes and 78 protein-coding genes strongly supported the monophyly of Croomia. Two Asian species were identified as sisters that likely diverged in the Early Pleistocene (1.62 Mya, 95% HPD: 1.125–2.251 Mya), whereas the divergence of C. pauciflora dated back to the Late Miocene (4.77 Mya, 95% HPD: 3.626–6.162 Mya). The availability of these cp genomes will provide valuable genetic resources for further population genetics and phylogeographic studies on Croomia.

scholarly journals A cytomegalovirus DNA sequence containing tracts of tandemly repeated CA dinucleotides hybridizes to highly repetitive dispersed elements in mammalian cell genomes.

1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402 ◽  
Author(s):  
K T Jeang ◽  
G S Hayward
Keyword(s):  
Plasmid Dna ◽  
Genomic Library ◽  
Mammalian Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
Left Handed ◽  
Mammalian Genomes ◽  
Genomic Dnas ◽  
Human And Mouse ◽  
Mouse Genomic

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.

A cytomegalovirus DNA sequence containing tracts of tandemly repeated CA dinucleotides hybridizes to highly repetitive dispersed elements in mammalian cell genomes

1983 ◽  
Vol 3 (8) ◽  
pp. 1389-1402
Author(s):  
K T Jeang ◽  
G S Hayward
Keyword(s):  
Plasmid Dna ◽  
Genomic Library ◽  
Mammalian Species ◽  
5S Rdna ◽  
Rdna Genes ◽  
Left Handed ◽  
Mammalian Genomes ◽  
Genomic Dnas ◽  
Human And Mouse ◽  
Mouse Genomic

A single 880-base-pair region within the genome of simian cytomegalovirus strain Colburn contains sequences that hybridize intensely with both human and mouse total genome DNA probes. This sequence was also found in a second simian cytomegalovirus isolate and was retained in both plaque-purified virus subclones and in plasmid DNA clones containing the SalI P fragment. Cleaved genomic DNAs from several mammalian species all exhibited strong dispersed hybridization with the SalI-P probes, and over 70% of the lambda clones in a mouse genomic library plus several selected clones containing globin, 45S rDNA, or 5S rDNA genes all formed hybrids with SalI-P. The appropriate region of cytomegalovirus SalI-P contains relatively A + T-rich unique sequences interrupted by three stretches of the simple alternating dinucleotides, (CA)15, (CA)22, and (CA)21, which we show to be responsible for most of the cell-virus homology. We conclude that discrete, tandemly repeated (CA) dinucleotide tracts capable of forming left-handed Z-DNA helices punctuate mammalian genomes at greater than 10(5) copies per cell and that three adjacent copies of what appear to be a family of interspersed repetitive elements containing these (CA)n stretches are carried in the genomes of simian cytomegaloviruses.

scholarly journals First chromosome data on Steindachneridion doceanum (Siluriformes: Pimelodidae): a critically endangered catfish endemic of the Doce River basin, Brazil

2018 ◽  
Vol 16 (4) ◽  
Author(s):  
Ana Claudia Swarça ◽  
Mário Luis Orsi ◽  
Fábio Hiroshi Takagui ◽  
Ana Lucia Dias ◽  
Jorge Abdala Dergam ◽  
...  
Keyword(s):  
Secondary Constriction ◽  
Extinction Risk ◽  
Present Report ◽  
5S Rdna ◽  
Rdna Genes ◽  
C Banding ◽  
Endemic Taxon ◽  
Acrocentric Chromosomes ◽  
Doce River ◽  
Submetacentric Pair

ABSTRACT The present report represents the first cytogenetic description of Steindachneridion doceanum, great catfish which is currently at high extinction risk and it is listed as threatened on the red list of the Brazilian Ministry of the Environment, also are suggested karyotype relationships with other species of the same genus endemic from other river basins. The results revealed a diploid number of 2n = 56 and the karyotype composed of 18 metacentric, 20 submetacentric, 10 subtelocentric and 8 acrocentric chromosomes (NF = 104). The AgNORs and CMA3 signals were coincident in location occupying the short arm of an acrocentric chromosome pair (25th), in a secondary constriction. The 5S rDNA genes were localized on the short arms of one subtelocentric pair. C-banding revealed terminal blocks on the short arms on many chromosomes as well as terminal positive bands at the both ends of a submetacentric pair. C banding also revealed a large heterochromatic block in the secondary constriction (25th) region that was coincident with the AgNORs sites and CMA3+ bright bands. In spite S. doceanum represent an endemic taxon, in spite their geographic isolation their cytogenetic characteristics show similarities with other species of the genus.

scholarly journals Heat Shock Protein 70 and 90 Genes in the Harmful DinoflagellateCochlodinium polykrikoides: Genomic Structures and Transcriptional Responses to Environmental Stresses

2015 ◽  
Vol 2015 ◽  
pp. 1-12 ◽  
Author(s):  
Ruoyu Guo ◽  
Seok Hyun Youn ◽  
Jang-Seu Ki
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Harmful Algal Blooms ◽  
Algal Blooms ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Environmental Stresses ◽  
Transcriptional Responses ◽  
Intergenic Spacers

The marine dinoflagellateCochlodinium polykrikoidesis responsible for harmful algal blooms in aquatic environments and has spread into the world’s oceans. As a microeukaryote, it seems to have distinct genomic characteristics, like gene structure and regulation. In the present study, we characterized heat shock protein (HSP) 70/90 ofC. polykrikoidesand evaluated their transcriptional responses to environmental stresses. Both HSPs contained the conserved motif patterns, showing the highest homology with those of other dinoflagellates. Genomic analysis showed that theCpHSP70had no intron but was encoded by tandem arrangement manner with separation of intergenic spacers. However,CpHSP90had one intron in the coding genomic regions, and no intergenic region was found. Phylogenetic analyses of separate HSPs showed that CpHSP70 was closely related with the dinoflagellateCrypthecodinium cohniiand CpHSP90 with other Gymnodiniales in dinoflagellates. Gene expression analyses showed that bothHSPgenes were upregulated by the treatments of separate algicides CuSO4and NaOCl; however, they displayed downregulation pattern with PCB treatment. The transcription ofCpHSP90andCpHSP70showed similar expression patterns under the same toxicant treatment, suggesting that both genes might have cooperative functions for the toxicant induced gene regulation in the dinoflagellate.

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