An evaluation of rDNA variation in Lolium species (ryegrass)

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 307-311 ◽  
Author(s):  
KMF Warpeha ◽  
T J Gilliland ◽  
I Capesius
Keyword(s):  
Genomic Dna ◽  
Parental Species ◽  
Repeat Unit ◽  
Intergenic Spacer ◽  
Reproductive Mode ◽  
Sinapis Alba ◽  
Species Relationships ◽  
The Status ◽  
Rdna Variation ◽  
Ribosomal Repeat

Species of the genus Lolium are important fodder and turf grasses for agricultural and amenity use world-wide. Difficulties currently exist regarding the taxonomy of Lolium species and also in the demarcation between Lolium and the genus Festuca, with the debate focusing on the status of Festuca pratensis and its relations. The diversity in ribosomal DNA (rDNA) in Lolium was investigated. Cloned probes for rDNA, derived from the intergenic spacer (IGS-M) and transcribed regions (COD-M) of mustard (Sinapis alba) were used to investigate species relationships. Genomic DNA from seven Lolium taxa, F. pratensis, and xFestulolium braunii, were assessed for variation in rDNA by RFLP. Data support continued recognition of existing Lolium species' demarcations, and provided more taxonomic insight between allogamous Lolium taxa and F. pratensis. The COD-M and IGS-M probes grouped taxa by reproductive mode. The IGS-M probe distinguished all species as unique entities and established that hybrids, xFestulolium braunii and Lolium xboucheanum, had rDNA phenotypes that were composites of their parental species. The evolution of the ribosomal repeat unit is discussed and the potential for further rDNA taxonomic study in Lolium is considered.Key words: Lolium, variation, ribosomal, rDNA, RFLP.

Species relationships in the dasyurid marsupial genus Pseudantechinus (Marsupialia : Dasyuridae): a re-examination of the taxonomic status of Pseudantechinus roryi

2017 ◽  
Vol 65 (4) ◽  
pp. 240 ◽  
Author(s):  
L. S. Umbrello ◽  
P. A. Woolley ◽  
M. Westerman
Keyword(s):  
Dna Sequences ◽  
Isolation By Distance ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Taxonomic Status ◽  
Museum Collections ◽  
Species Relationships ◽  
Type Specimens ◽  
Network Analyses ◽  
The Status

The status of Pseudantechinus roryi relative to its congeners has been determined from DNA sequences obtained from both nuclear and mitochondrial gene loci. Although all other recognised species of Pseudantechinus form reciprocally monophyletic lineages in phylogenetic analyses, individuals identified in museum collections as Ps. roryi (including type specimens) were indistinguishable from those identified as Ps. macdonnellensis. Ps. roryi is thus considered to be a synonym of Ps. macdonnellensis. Neighbour-joining network analyses failed to reveal any clear biogeographic differences between populations of Ps. macdonnellensis other than some evidence of isolation by distance.

scholarly journals Molecular Diversity of Renibacterium salmoninarum Isolates Determined by Randomly Amplified Polymorphic DNA Analysis

2000 ◽  
Vol 66 (1) ◽  
pp. 435-438 ◽  
Author(s):  
T. Hilton Grayson ◽  
Franck A. Atienzar ◽  
Sarah M. Alexander ◽  
Lynne F. Cooper ◽  
Martyn L. Gilpin
Keyword(s):  
Molecular Diversity ◽  
Dna Analysis ◽  
Repeat Unit ◽  
Intergenic Spacer ◽  
23S Rrna ◽  
Sequence Variant ◽  
Randomly Amplified Polymorphic Dna ◽  
Renibacterium Salmoninarum ◽  
Its1 Sequence ◽  
Biological Source

ABSTRACT The molecular diversity among 60 isolates of Renibacterium salmoninarum which differ in place and date of isolation was investigated by using randomly amplified polymorphic DNA (RAPD) analysis. Isolates were grouped into 21 banding patterns which did not reflect the biological source. Four 16S-23S rRNA intergenic spacer (ITS1) sequence variations and two alleles of an exact tandem repeat locus, ETR-A, were the bases for formation of distinct groups within the RAPD clusters. This study provides evidence that the most common ITS1 sequence variant, SV1, possesses two copies of a 51-bp repeat unit at ETR-A and has been widely dispersed among countries which are associated with mainstream intensive salmonid culture.

scholarly journals Genome-specific histories of divergence and introgression between an allopolyploid unisexual salamander lineage and two sexual species

2018 ◽  
Author(s):  
Robert D. Denton ◽  
Ariadna E. Morales ◽  
H. Lisle Gibbs
Keyword(s):  
Genetic Variation ◽  
Evolutionary History ◽  
Parental Species ◽  
Extended Period ◽  
Reproductive Mode ◽  
Mapping Method ◽  
Genetic Introgression ◽  
Sexual Species ◽  
History Of ◽  
Genomic Material

AbstractQuantifying genetic introgression between sexual species and polyploid lineages traditionally thought to be asexual is an important step in understanding what factors drive the longevity of putatively asexual groups. However, the presence of multiple distinct subgenomes within a single lineage provides a significant logistical challenge to evaluating the origin of genetic variation in most polyploids. Here, we capitalize on three recent innovations—variation generated from ultraconserved elements (UCEs), bioinformatic techniques for assessing variation in polyploids, and model-based methods for evaluating historical gene flow—to measure the extent and tempo of introgression over the evolutionary history of an allopolyploid lineage of all-female salamanders and two ancestral sexual species. We first analyzed variation from more than a thousand UCEs using a reference mapping method developed for polyploids to infer subgenome specific patterns of variation in the all-female lineage. We then used PHRAPL to choose between sets of historical models that reflected different patterns of introgression and divergence between the genomes of the parental species and the same genomes found within the polyploids. Our analyses support a scenario in which the genomes sampled in unisexuals salamanders were present in the lineage ∼3.4 million years ago, followed by an extended period of divergence from their parental species. Recent secondary introgression has occurred at different times between each sexual species and their representative genomes within the unisexuals during the last 500,000 years. Sustained introgression of sexual genomes into the unisexual lineage has been the defining characteristic of their reproductive mode, but this study provides the first evidence that unisexual genomes have also undergone long periods of divergence without introgression. Unlike other unisexual, sperm-dependent taxa in which introgression is rare, the alternating periods of divergence and introgression between unisexual salamanders and their sexual relatives could reveal the scenarios in which the influx of novel genomic material is favored and potentially explain why these salamanders are among the oldest described unisexual animals.

scholarly journals Comparative analysis of the ribosomal DNA repeat unit (rDNA) of Perna viridis (Linnaeus, 1758) and Perna canaliculus (Gmelin, 1791)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7644
Author(s):  
Zhansheng Guo ◽  
Leng Han ◽  
Zhenlin Liang ◽  
Xuguang Hou
Keyword(s):  
Ribosomal Dna ◽  
Phylogenetic Trees ◽  
Repeat Unit ◽  
Cpg Islands ◽  
Intergenic Spacer ◽  
Initiation Site ◽  
Perna Viridis ◽  
28S Rrna ◽  
Important Species ◽  
Perna Canaliculus

Perna viridis and P. canaliculus are economically and ecologically important species of shellfish. In this study, the complete ribosomal DNA (rDNA) unit sequences of these species were determined for the first time. The gene order, 18S rRNA–internal transcribed spacer (ITS) 1–5.8S rRNA–ITS2–28S rRNA–intergenic spacer (IGS), was similar to that observed in other eukaryotes. The lengths of the P. viridis and P. canaliculus rDNA sequences ranged from 8,432 to 8,616 bp and from 7,597 to 7,610 bp, respectively, this variability was mainly attributable to the IGS region. The putative transcription termination site and initiation site were confirmed. Perna viridis and P. canaliculus rDNA contained two (length: 93 and 40 bp) and one (length: 131 bp) repeat motifs, respectively. Individual intra-species differences mainly involved the copy number of repeat units. In P. viridis, three cytosine-guanine (CpG) sites with sizes of 440, 1,075 and 537 bp were found to cover nearly the entire IGS sequence, whereas in P. canaliculus, two CpG islands with sizes of 361 and 484 bp were identified. The phylogenetic trees constructed with maximum likelihood and neighbour-joining methods and based on ITS sequences were identical and included three major clusters. Species of the same genus were easily clustered together.

scholarly journals Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina Japonica

2021 ◽  
Author(s):  
Peng-Fei Liu ◽  
Yan-Hui Bi ◽  
Li Liu ◽  
Zhi-Gang Zhou
Keyword(s):  
Physical Map ◽  
Repeat Unit ◽  
Gc Content ◽  
Intergenic Spacer ◽  
Saccharina Japonica ◽  
Fish Analysis ◽  
45S Rdna ◽  
Rdna Repeat ◽  
Bac Clone ◽  
Rdna Repeat Unit

Abstract IGS is abundant in polymorphism, which is widely used in the analysis of intraspecific genetic diversity and phylogenetic relationships among geographical populations. In this study, the 45S rDNA repeat unit of Saccharina japonica was obtained for the first time by BAC clone sequencing. The total length of 45S rDNA repeat unit of S. japonica was 8995 bp, including 5420 bp of 18s-5.8s-25s rDNA and 3575 bp of IGS (Intergenic Spacer), with the GC content of 51.4%. IGS was composed of 465 bp 3’-outer transcribed spacer (ETS), 874 bp 5’-ETS, and 2236 bp non transcribed spacer (NTS), with the GC content of 50.1%.Fiber-FISH (fiber-fluorescence in situ hybridization, fiber-FISH) analysis of 45S rDNA on the BAC molecule of female gametophytes of S. japonica illustrated that each fiber had at least five continuous moniliform hybridization signal points, indicating the distribution of 45S rDNA repeat unit on the bacterial artificial chromosome. This study provided a new candidate molecular marker for detecting intraspecific polymorphisms of S. japonica, and the successful fiber-FISH analysis of 45S rDNA on BAC molecule would contribute to the construction of the physical map and Map-based cloning of this kelp.

Tandem repeat DNA localizing on the proximal DAPI bands of chromosomes in Larix, Pinaceae

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 777-783 ◽  
Author(s):  
Masahiro Hizume ◽  
Fukashi Shibata ◽  
Ayako Matsumoto ◽  
Yukie Maruyama ◽  
Eiji Hayashi ◽  
...  
Keyword(s):  
In Situ Hybridization ◽  
Fluorescence In Situ Hybridization ◽  
Repetitive Dna ◽  
Genomic Dna ◽  
Repeat Unit ◽  
Blot Hybridization ◽  
Southern Blot Hybridization ◽  
Repeat Sequence ◽  
Proximal Region

Repetitive DNA was cloned from HindIII-digested genomic DNA of Larix leptolepis. The repetitive DNA was about 170 bp long, had an AT content of 67%, and was organized tandemly in the genome. Using fluorescence in situ hybridization and subsequent DAPI banding, the repetitive DNA was localized in DAPI bands at the proximal region of one arm of chromosomes in L. leptolepis and Larix chinensis. Southern blot hybridization to genomic DNA of seven species and five varieties probed with cloned repetitive DNA showed that the repetitive DNA family was present in a tandem organization in genomes of all Larix taxa examined. In addition to the 170-bp sequence, a 220-bp sequence belonging to the same DNA family was also present in 10 taxa. The 220-bp repeat unit was a partial duplication of the 170-bp repeat unit. The 220-bp repeat unit was more abundant in L. chinensis and Larix potaninii var. macrocarpa than in other taxa. The repetitive DNA composed 2.0–3.4% of the genome in most taxa and 0.3 and 0.5% of the genome in L. chinensis and L. potaninii var. macrocarpa, respectively. The unique distribution of the 220-bp repeat unit in Larix indicates the close relationship of these two species. In the family Pinaceae, the LPD (Larix proximal DAPI band specific repeat sequence family) family sequence is widely distributed, but their amount is very small except in the genus Larix. The abundant LPD family in Larix will occur after its speciation.Key words: AT-rich tandem repetitive DNA, fluorescence in situ hybridization, Larix, proximal DAPI band.

Design of plant-specific PCR primers for the ETS region with enhanced specificity for tribe Bromeae and their application to other grasses (Poaceae)

Botany ◽  
2014 ◽  
Vol 92 (10) ◽  
pp. 693-699 ◽  
Author(s):  
Alicia Alonso ◽  
Roger D. Bull ◽  
Carmen Acedo ◽  
Lynn J. Gillespie
Keyword(s):  
Repeat Unit ◽  
Pcr Primers ◽  
Nuclear Ribosomal Dna ◽  
Chain Reaction ◽  
Internal Transcribed Spacer Region ◽  
Specific Pcr ◽  
External Transcribed Spacer ◽  
Preliminary Study ◽  
Polymerase Chain ◽  
Ribosomal Repeat

Selective primers were developed for the amplification via polymerase chain reaction (PCR) of the external transcribed spacer (ETS) region in the nuclear ribosomal repeat unit. These primers were intended to be specific to the Poaceae tribe Bromeae but were found to function broadly across subfamily Pooideae. ETS primers previously developed for grasses were unable to amplify tribe Bromeae taxa because of ETS variability and several subrepeats. After detailed analysis, a region was chosen and four candidate primers were designed to amplify and sequence the ETS fragment. This fragment of approximately 800–900 bp is located in the 3′ region of the ETS of 18S–26S nuclear ribosomal DNA. A preliminary study with these primers was conducted in eight samples of Bromus. The best two primers showed strong amplification and successful sequencing for all samples tested. We also tested the specificity of these two primers in samples belonging to all large taxa of Bromeae, including all three genera and five subgenera and samples of eight tribes and 15 subtribes of the subfamily Pooideae, and both worked for most of the taxa tested. Our results demonstrate that the ETS region is more informative for resolving relationships at different taxonomic levels than internal transcribed spacer region. Also, these results indicate the utility of these new primers for studying the ETS region in the tribe Bromeae as well as across the subfamily Pooideae.

Restriction fragment length polymorphisms within the ribosomal DNA repeat unit of British entomopathogenic nematodes (Rhabditida: Steinernematidae)

Parasitology ◽  
1992 ◽  
Vol 105 (2) ◽  
pp. 317-323 ◽  
Author(s):  
A. P. Reid ◽  
W. M. Hominick
Keyword(s):  
Restriction Fragment ◽  
Ribosomal Dna ◽  
Fragment Length ◽  
Genomic Dna ◽  
Entomopathogenic Nematodes ◽  
Repeat Unit ◽  
Geographical Location ◽  
Steinernema Feltiae ◽  
Dna Repeat ◽  
Restriction Fragment Length

SUMMARYGenomic DNA extracted from entomopathogenic nematodes isolated from 89 soil samples taken throughout the United Kingdom was hybridized with the ribosomal DNA clone from Caenorhabditis elegans (pCe7). When the DNA was digested with EcoR I and Hind III in a double digest, 5 distinct RFLP (restriction fragment length polymorphism) types were observed. While the prevalence of the 5 types was not equal, no correlation with geographical location, soil type or habitat could be detected. Subsequent hybridizations of total genomic DNA from the various RFLP types divided them into 2 groups. The most prevalent group, identified as Steinernema feltiae ( = bibionis), contained 2 of the RFLP types (Al and A2). The other group contained the remaining 3 RFLP types (B1, B2 and B3). Although similar to S. feltiae ( = bibionis), the members of the B-types can be distinguished from this species on morphological grounds and preliminary crossbreeding experiments have demonstrated that the 2 groups are reproductively isolated.

scholarly journals Bayesian phylogenetic analysis for diploid and allotetraploid species networks

2017 ◽  
Author(s):  
Graham Jones
Keyword(s):  
Phylogenetic Analysis ◽  
Parental Species ◽  
Incomplete Lineage Sorting ◽  
Reversible Jump ◽  
Mcmc Algorithm ◽  
Species Relationships ◽  
Lineage Sorting ◽  
Genome Doubling ◽  
Bayesian Phylogenetic Analysis ◽  
Allotetraploid Species

AbstractAllopolyploid species are formed by genome doubling after hybridization between otherwise intersterile parental species. Allopolyploidy is a common speciation mechanism in land plants. Here we describe and evaluate a Bayesian approach to the phylogenetic analysis of species relationships when both ordinary speciation and allopolyploidy are present. The approach takes incomplete lineage sorting into account using the multi-species coalescent model, and extends this to deal with the extra complications due to allopolyploidy. The number of hybridizations is not assumed, which means that the number of parameters varies and a reversible-jump MCMC algorithm is needed to sample from the posterior. The main restriction is that only diploids and allotetraploids are considered. The model is implemented in the BEAST framework and is an extension of Jones et al. (2013). Simulations show that the topology of the network can be reliably inferred along with estimates of other parameters.

Self-amplification of satellite DNA in vitro

Genome ◽  
1998 ◽  
Vol 41 (3) ◽  
pp. 429-434 ◽  
Author(s):  
J B Buntjer ◽  
J A Lenstra
Keyword(s):  
Tandem Repeat ◽  
Satellite Dna ◽  
Genomic Dna ◽  
Tandem Repeats ◽  
Repeat Unit ◽  
Dna Amplification ◽  
Repeat Units ◽  
Rapid Amplification ◽  
Species Specific

We describe a PCR-like reaction in which genomic DNA acts as a template as well as a primer. Interaction between genomic tandem repeat units leads to self-amplification of satellite DNA. This genomic self-priming PCR (GSP-PCR) allowed the rapid amplification of species-specific tandem repeats of horse, cattle, dolphin, and chicken. A novel specific satellite of ostrich with a repeat unit of 60 bp was isolated using this method.Key words: satellite DNA, amplification, isolation, species-specific probes.

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