scholarly journals Satellite DNA Mapping in Pseudis fusca (Hylidae, Pseudinae) Provides New Insights into Sex Chromosome Evolution in Paradoxical Frogs

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 160
Author(s):  
Kaleb Gatto ◽  
Karin Seger ◽  
Paulo Garcia ◽  
Luciana Lourenço
Keyword(s):  
Satellite Dna ◽  
Chromosome Evolution ◽  
Common Ancestor ◽  
Sex Chromosome ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Undescribed Species ◽  
The Common

In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was inferred to have occurred during W chromosome evolution, moving a chromosomal cluster enriched by the PcP190 from the short arm (as observed in P. bolbodactyla) to the NOR-bearing long arm (as observed in P. tocantins). However, whether such an inversion happened in P. tocantins or in the common ancestor of Pseudis fusca and P. tocantins remained unclear. To assess this question, we mapped PcP190 in the karyotype of P. fusca from three distinct localities. Southern blotting was used to compare males and females. The mitochondrial H1 fragment (which contains the 12S ribosomal RNA (rRNA), tRNAval, and 16S rRNA genes) and cytochrome b gene were partially sequenced, and a species tree was inferred to guide our analysis. Pseudis fusca specimens were placed together as the sister group of P. tocantins, but based on genetic distance, one of the analyzed populations is probably an undescribed species. A cluster of PcP190, located in the long arm of chromosome 7, is sex linked in this putative new species but not in the remaining P. fusca. We could infer that the pericentromeric inversion that moved the PcP190 site to the NOR-bearing chromosome arm (long arm) occurred in the common ancestor of P. fusca, the putative undescribed species, and P. tocantins.

Evolutionary Relationships among Boulengerella Species (Ctenoluciidae, Characiformes): Genomic Organization of Repetitive DNAs and Highly Conserved Karyotypes

2017 ◽  
Vol 152 (4) ◽  
pp. 194-203 ◽  
Author(s):  
José F. de Souza e Sousa ◽  
Patrik F. Viana ◽  
Luiz A.C. Bertollo ◽  
Marcelo B. Cioffi ◽  
Eliana Feldberg
Keyword(s):  
18S Rdna ◽  
Sex Chromosome ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Fish Family ◽  
Telomeric Sequences ◽  
5S Rrna Genes ◽  
Species Specific

Ctenoluciidae is a Neotropical freshwater fish family whose representatives are known as bicudas. The genus Boulengerella contains 5 species, and 4 of them (B. cuvieri, B. lateristriga, B. lucius, and B. maculata) were cytogenetically analyzed in the present study by conventional and molecular procedures. All 4 species have a very similar karyotype, with 2n = 36 chromosomes (14 metacentrics + 16 submetacentrics + 6 subtelocentrics; FN = 72). However, the heterochromatin distribution pattern is species-specific. In all 4 species, the nucleolus organizer region is located in pair 18, as also confirmed by cytogenetic mapping of 18S rDNA. In turn, 5S rRNA genes are present in 2 chromosome pairs: in pair 1 of all 4 species, and in pair 10 of B. lateristriga, B. maculata, and B. cuvieri, but in pair 4 of B. lucius. The telomeric probe highlighted terminal regions in all chromosomes, as well as an interstitial centromeric sequence in pair 3 of the 3 first-mentioned species. Notably, a conspicuous heteromorphic secondary constriction in chromosomes 18 was found only in the males of the 3 species, rendering one of the homologs much larger than the other one. This feature, associated with a large 18S rDNA block and accumulation of telomeric sequences, suggests the presence of an XX/XY sex chromosome system in the analyzed Boulengerella species.

scholarly journals Discovery of Putative XX/XY Male Heterogamety in Emydura subglobosa Turtles Exposes a Novel Trajectory of Sex Chromosome Evolution in Emydura

2019 ◽  
Vol 158 (3) ◽  
pp. 160-169 ◽  
Author(s):  
LingSze Lee ◽  
Eugenia E. Montiel ◽  
Nicole Valenzuela
Keyword(s):  
Sex Determination ◽  
Sex Chromosome ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Molecular Cytogenetics ◽  
Nucleolus Organizer ◽  
Model Organisms ◽  
Comparative Genome Hybridization ◽  
Evolutionary Trajectory ◽  
Genotypic Sex Determination

The discovery of sex chromosome systems in non-model organisms has elicited growing recognition that sex chromosomes evolved via diverse paths that are not fully elucidated. Lineages with labile sex determination, such as turtles, hold critical cues, yet data are skewed toward hide-neck turtles (suborder Cryptodira) and scant for side-neck turtles (suborder Pleurodira). Here, we used classic and molecular cytogenetics to investigate Emydura subglobosa (ESU), an unstudied side-neck turtle with genotypic sex determination from the family Chelidae, where extensive morphological divergence exists among XX/XY systems. Our data represent the first cytogenetic description for ESU. Similarities were found between ESU and E. macquarii (EMA), such as identical chromosome number (2n = 50), a single and dimorphic nucleolus organizer region (NOR) localized in a microchromosome pair (ESU14) of both sexes (detected via FISH of 18S rDNA). Only the larger NOR is active (detected by silver staining). As in EMA, comparative genome hybridization revealed putative macro XX/XY chromosomes in ESU (the 4th largest pair). Our comparative analyses and revaluation of previous data strongly support the hypothesis that Emydura's XX/XY system evolved via fusion of an ancestral micro-Y (retained by Chelodina longicollis) onto a macro-autosome. This evolutionary trajectory differs from the purported independent evolution of XX/XY from separate ancestral autosomes in Chelodina and Emydura that was previously reported. Our data permit dating this Y-autosome fusion to at least the split of Emydura around 45 Mya and add critical information about the evolution of the remarkable diversity of sex-determining mechanisms in turtles, reptiles, and vertebrates.

Molecular and cytological characterization of ribosomal RNA genes in Chenopodium quinoa and Chenopodium berlandieri

Genome ◽  
2006 ◽  
Vol 49 (7) ◽  
pp. 825-839 ◽  
Author(s):  
P J Maughan ◽  
B A Kolano ◽  
J Maluszynska ◽  
N D Coles ◽  
A Bonifacio ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Chenopodium Quinoa ◽  
Nucleolus Organizer ◽  
5S Rrna ◽  
Rrna Genes ◽  
Fish Analysis ◽  
General Sequence ◽  
Sequence Composition

The nucleolus organizer region (NOR) and 5S ribosomal RNA (rRNA) genes are valuable as chromosome landmarks and in evolutionary studies. The NOR intergenic spacers (IGS) and 5S rRNA nontranscribed spacers (NTS) were PCR-amplified and sequenced from 5 cultivars of the Andean grain crop quinoa (Chenopodium quinoa Willd., 2n = 4x = 36) and a related wild ancestor (C. berlandieri Moq. subsp. zschackei (Murr) A. Zobel, 2n = 4x = 36). Length heterogeneity observed in the IGS resulted from copy number difference in subrepeat elements, small re arrangements, and species-specific indels, though the general sequence composition of the 2 species was highly similar. Fifteen of the 41 sequence polymorphisms identified among the C. quinoa lines were synapomorphic and clearly differentiated the highland and lowland ecotypes. Analysis of the NTS sequences revealed 2 basic NTS sequence classes that likely originated from the 2 allopolyploid subgenomes of C. quinoa. Fluorescence in situ hybridization (FISH) analysis showed that C. quinoa possesses an interstitial and a terminal pair of 5S rRNA loci and only 1 pair of NOR, suggesting a reduction in the number of rRNA loci during the evolution of this species. C. berlandieri exhibited variation in both NOR and 5S rRNA loci without changes in ploidy.Key words: rDNA, NOR, IGS, 5S NTS, FISH, Chenopodium.

Genetic control of 1R nucleolus organizer region expression in the presence of wheat genomes

Genome ◽  
1990 ◽  
Vol 33 (5) ◽  
pp. 713-718 ◽  
Author(s):  
Rita Vieira ◽  
Álvaro Queiroz ◽  
Leonor Morais ◽  
Augusta Barão ◽  
T. Mello-Sampayo ◽  
...  
Keyword(s):  
Genetic Control ◽  
Hexaploid Wheat ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Root Tip ◽  
Region Gene ◽  
Nucleolar Dominance ◽  
Chromosome 1R

The expression of rRNA genes located in the nucleolar organizing region (NOR) present on the short arm of chromosome 1R from rye (Secale cereale L.) was examined in several hexaploid (Triticum aestivum L.) and tetraploid wheats (Triticum turgidum L.) containing the entire chromosome 1R from rye (disomic substitution 1B(1R)), its full haploid genome (hexaploid wheat–rye F1 hybrid), or only its short arm translocated to the long arms of wheat chromosomes from the homoeologous group 1 (disomic translocations 1AL/1RS, 1BL/1RS, or 1DL/1RS) or added to the complete hexaploid wheat genotype (monotelosomic addition 1RS). By silver staining and determination of the number of Ag-NORs and the average number of nucleoli per root-tip cell it became apparent that the expression of 1R NORs, in the presence of wheat genomes, depends on the absence of the long arm of rye chromosome 1R. In wheat-rye F1 hybrids and in hexaploid wheat with a disomic substitution 1B(1R), 1R NOR was morphologically absent, even when only one wheat major NOR was present, in contrast with its frequent expression in wheat–rye translocation or addition lines where only its short arm was added. It is suggested that wheat nucleolar dominance over rye as expressed by heterochromatic and silent NOR in 1RS is under a complex genetic control which involves interaction between 1RL and unidentified wheat genes.Key words: 1R nucleolus organizer region, gene activity, amphiplasty.

scholarly journals Dix-seq: An integrated pipeline for fast amplicon data analysis

2020 ◽  
Author(s):  
Yongjun wei ◽  
Tianqi Ren ◽  
Lei Zhang
Keyword(s):  
Sequence Data ◽  
Gene Diversity ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Technologies ◽  
Functional Gene Diversity ◽  
Internal Transcribed Spacer Sequences ◽  
The Common ◽  
18S Rrna Genes ◽  
Multiple Samples

AbstractThe amplicon derived from 16S rRNA genes, 18S rRNA genes, internal transcribed spacer sequences or other functional genes can be used to infer and evaluate microbial diversity or functional gene diversity. With the development of sequencing technologies, large amounts of amplicon data were generated. Several different software or pipelines had been developed for amplicon data analyses. However, most current software/pipelines require multistep and advanced programming skills. Moreover, they are often complex and time-consuming. Here, we introduced an integrated pipeline named Dix-seq for high-throughput amplicon sequence data processing (https://github.com/jameslz/dix-seq). Dix-seq integrates several different amplicon analysis algorithms and software for diversity analyses of multiple samples. Dix-seq analyzes amplicon sequences efficiently, and exports abundant visual results automatically with only one command in Linux environment. In summary, Dix-seq enables the common/advanced users to generate amplicon analysis results easily and offers a versatile and convenient tool for researchers.

scholarly journals A dual sequence and culture-based survey of maize rhizosphere protists reveals dominant, plant-enriched, and culturable community members

2021 ◽  
Author(s):  
Stephen J Taerum ◽  
Jamie Micciulla ◽  
Gabrielle Corso ◽  
Blaire Steven ◽  
Daniel J. Gage ◽  
...  
Keyword(s):  
Bacterial Abundance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Field Site ◽  
Community Members ◽  
Abundance Patterns ◽  
Maize Roots ◽  
The Common ◽  
And Function ◽  
Dual Sequence

Protists play important roles in shaping the microbial community of the rhizosphere. However, there is still a limited understanding of how plants shape the protist community, and how well protist isolate collections might represent rhizosphere protist composition and function in downstream studies. We sought to determine whether maize roots select for a distinct protist community in the field, and whether the common or dominant members of that community are readily culturable using standard protist isolation methods. We sequenced 18S and 16S rRNA genes from the rhizospheres of maize grown in two sites, and isolated 103 protists into culture from the same roots. While field site had the greatest effect, rhizospheres in both sites had distinct protist composition from the bulk soils, and certain taxa were enriched in both sites. Enriched taxa were correlated to bacterial abundance patterns. The isolated protists represented six supergroups, and the majority corresponded to taxa found in the sequencing survey. Twenty-six isolates matched eight of the 89 core rhizosphere taxa. This study demonstrates that maize roots select for a distinct protist community, but also illustrate the potential challenges in understanding the function of the dominant protist groups in the rhizosphere.

scholarly journals Rapid evolution of complete dosage compensation in Poecilia

2021 ◽  
Author(s):  
David C.H. Metzger ◽  
Benjamin A. Sandkam ◽  
Iulia Darolti ◽  
Judith E. Mank
Keyword(s):  
Gene Expression ◽  
Dosage Compensation ◽  
Sex Chromosomes ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Sex Chromosome ◽  
Close Relative ◽  
Y Chromosomes ◽  
Compensation Mechanisms ◽  
The Common

ABSTRACTDosage compensation balances gene expression between the sexes in systems with diverged heterogametic sex chromosomes. Theory predicts that dosage compensation should rapidly evolve in parallel with the divergence of sex chromosomes to prevent the deleterious effects of dosage imbalances that occur as a result of sex chromosome divergence. Examples of complete dosage compensation, where gene expression of the entire sex chromosome is compensated, are rare and have only been found in relatively ancient sex chromosome systems. Consequently, very little is known about the evolutionary dynamics of complete dosage compensation systems. We recently found the first example of complete dosage compensation in a fish, Poecilia picta. We also found that the Y chromosome degraded substantially in the common ancestor of P. picta and their close relative Poecilia parae. In this study we find that P. parae also have complete dosage compensation, thus complete dosage compensation likely evolved in the short (∼3.7 my) interval after the split of the ancestor of these two species from P. reticulata, but before they diverged from each other. These data suggest that novel dosage compensation mechanisms can evolve rapidly, thus supporting the longstanding theoretical prediction that such mechanisms arise in parallel with rapidly diverging sex chromosomes.SIGNIFICANCE STATEMENTIn species with XY sex chromosomes, females (XX) have as many copies of X-linked genes compared to males (XY), leading to unbalanced expression between the sexes. Theory predicts that dosage compensation mechanisms should evolve rapidly as X and Y chromosomes diverge, but examples of complete dosage compensation in recently diverged sex chromosomes are scarce, making this theory difficult to test. Across Poeciliid species the X and Y chromosomes have recently diversified. Here we find complete dosage compensation evolved rapidly as the X and Y diverged in the common ancestor of Poecilia parae and P. picta, supporting that novel dosage compensation mechanisms can evolve rapidly in tandem with diverging sex chromosomes. These data confirm longstanding theoretical predictions of sex chromosome evolution.

scholarly journals Phylogenetic Evidence for the Existence of Novel Thermophilic Bacteria in Hot Spring Sulfur-Turf Microbial Mats in Japan

1998 ◽  
Vol 64 (5) ◽  
pp. 1680-1687 ◽  
Author(s):  
Hiroyuki Yamamoto ◽  
Akira Hiraishi ◽  
Kenji Kato ◽  
Hiroshi X. Chiura ◽  
Yonosuke Maki ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Mats ◽  
Hot Springs ◽  
Hot Spring ◽  
Thermophilic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rdna Sequences ◽  
Major Cluster ◽  
The Common

ABSTRACT So-called sulfur-turf microbial mats, which are macroscopic white filaments or bundles consisting of large sausage-shaped bacteria and elemental sulfur particles, occur in sulfide-containing hot springs in Japan. However, no thermophiles from sulfur-turf mats have yet been isolated as cultivable strains. This study was undertaken to determine the phylogenetic positions of the sausage-shaped bacteria in sulfur-turf mats by direct cloning and sequencing of 16S rRNA genes amplified from the bulk DNAs of the mats. Common clones with 16S rDNA sequences with similarity levels of 94.8 to 99% were isolated from sulfur-turf mat samples from two geographically remote hot springs. Phylogenetic analysis showed that the phylotypes of the common clones formed a major cluster with members of theAquifex-Hydrogenobacter complex, which represents the most deeply branching lineage of the domain bacteria. Furthermore, the bacteria of the sulfur-turf mat phylotypes formed a clade distinguishable from that of other members of theAquifex-Hydrogenobacter complex at the order or subclass level. In situ hybridization with clone-specific probes for 16S rRNA revealed that the common phylotype of sulfur-turf mat bacteria is that of the predominant sausage-shaped bacteria.

scholarly journals Historical biogeography of early diverging termite lineages (Isoptera: Teletisoptera)

2021 ◽  
Author(s):  
Menglin Wang ◽  
Simon Hellemans ◽  
Jan Šobotník ◽  
Jigyasa Arora ◽  
Aleš Buček ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Continental Drift ◽  
Historical Biogeography ◽  
Rrna Genes ◽  
Recent Common Ancestor ◽  
Land Bridge ◽  
Most Recent Common Ancestor ◽  
The Family ◽  
The Common ◽  
Warm Temperate

AbstractTermites are social cockroaches distributed throughout warm temperate and tropical ecosystems. The ancestor of modern termites (crown-Isoptera) occurred during the earliest Cretaceous, approximately 140 million years ago, suggesting that both vicariance through continental drift and overseas dispersal may have shaped the distribution of early diverging termite lineages. We reconstruct the historical biogeography of three early diverging termite families – Stolotermitidae, Hodotermitidae, and Archotermopsidae – using the nuclear rRNA genes and mitochondrial genomes of 27 samples. Our analyses confirmed the monophyly of Stolotermitidae + Hodotermitidae + Archotermopsidae (clade Teletisoptera), with Stolotermitidae diverging from a monophyletic Hodotermitidae + Archotermopsidae approximately 100.3 Ma (94.3–110.4 Ma, 95% HPD), and with Archotermopsidae paraphyletic to a monophyletic Hodotermitidae. The Oriental Archotermopsis and the Nearctic Zootermopsis diverged 50.8 Ma (40.7–61.4 Ma, 95% HPD) before land connections between the Palearctic region and North America ceased to exist. The African Hodotermes + Microhodotermes diverged from Anacanthotermes, a genus found in Africa and Asia, 32.1 Ma (24.8–39.9 Ma, 95% HPD), and the most recent common ancestor of Anacanthotermes lived 10.7 Ma (7.3–14.3 Ma, 95% HPD), suggesting that Anacanthotermes dispersed to Asia using the land bridge connecting Africa and Eurasia ∼18–20 Ma. In contrast, the common ancestors of modern Porotermes and Stolotermes lived 20.2 Ma (15.7–25.1 Ma, 95% HPD) and 26.6 Ma (18.3–35.6 Ma, 95% HPD), respectively, indicating that the presence of these genera in South America, Africa, and Australia involved over-water dispersals. Our results suggest that early diverging termite lineages acquired their current distribution through a combination of over-water dispersals and dispersal via land bridges. We clarify the classification by resolving the paraphyly of Archotermopsidae, restricting the family to Archotermopsis and Zootermopsis, and elevating Hodotermopsinae (Hodotermopsis) as Hodotermopsidae (status novum).

1R chromosome nucleolus organizer region activation by 5-azacytidine in wheat × rye hybrids

Genome ◽  
1990 ◽  
Vol 33 (5) ◽  
pp. 707-712 ◽  
Author(s):  
Rita Vieira ◽  
Álvaro Queiroz ◽  
Leonor Morais ◽  
Augusta Barão ◽  
T. Mello-Sampayo ◽  
...  
Keyword(s):  
Triticum Turgidum ◽  
Organizer Region ◽  
Nucleolus Organizer Region ◽  
Nucleolar Organizer ◽  
Pyrimidine Ring ◽  
Nucleolus Organizer ◽  
Rrna Genes ◽  
Root Tip ◽  
Root Tips ◽  
Nucleolar Dominance

Nucleolar activity was studied in several lines of Triticum aestivum cv. Chinese Spring, Triticum turgidum cv. Durum, and F1 hybrids from euploid and aneuploid lines of T. aestivum and Secale cereale cv. Centeio do Alto, in cells from root tips of seeds germinated in water or in 5-azacytidine. 5-Azacytidine, an analog of cytidine modified in the 5 position of the pyrimidine ring, inhibits DNA methylation. By using silver staining to determine the number of nucleolus organizer regions and the average number of nucleoli per root-tip cell from seeds germinated in both situations, it became apparent that the presence of 5-azacytidine during germination allowed for the expression of the nucleolus organizer region locus belonging to the rye genome, in contrast to the usual observed cytological absence of the rye nucleolus organizer region in wheat–rye hybrids. It is suggested that wheat nucleolar dominance in wheat–rye hybrids is mainly a consequence of methylation of rRNA genes or its regulators located on the 1R chromosome of rye.Key words: 1R nucleolar organizer, wheat–rye hybrids, methylation, Ag-NOR.

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