scholarly journals Comparative genomics of Glandirana rugosa using unsupervised AI reveals a high CG frequency

2021 ◽  
Vol 4 (5) ◽  
pp. e202000905
Author(s):  
Yukako Katsura ◽  
Toshimichi Ikemura ◽  
Rei Kajitani ◽  
Atsushi Toyoda ◽  
Takehiko Itoh ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Sex Chromosomes ◽  
Self Organizing Map ◽  
High Identity ◽  
Rhinella Marina ◽  
Short Oligonucleotide ◽  
Repeat Sequences ◽  
Large Size ◽  
Short Period ◽  
Frog Species

The Japanese wrinkled frog (Glandirana rugosa) is unique in having both XX-XY and ZZ-ZW types of sex chromosomes within the species. The genome sequencing and comparative genomics with other frogs should be important to understand mechanisms of turnover of sex chromosomes within one species or during a short period. In this study, we analyzed the newly sequenced genome of G. rugosa using a batch-learning self-organizing map which is unsupervised artificial intelligence for oligonucleotide compositions. To clarify genome characteristics of G. rugosa, we compared its short oligonucleotide compositions in all 1-Mb genomic fragments with those of other six frog species (Pyxicephalus adspersus, Rhinella marina, Spea multiplicata, Leptobrachium leishanense, Xenopus laevis, and Xenopus tropicalis). In G. rugosa, we found an Mb-level large size of repeat sequences having a high identity with the W chromosome of the African bullfrog (P. adspersus). Our study concluded that G. rugosa has unique genome characteristics with a high CG frequency, and its genome is assumed to heterochromatinize a large size of genome via methylataion of CG.

A large new species of Rhinella (Anura: Bufonidae) from Cerrado of Brazil

Zootaxa ◽  
2007 ◽  
Vol 1627 (1) ◽  
pp. 23-39 ◽  
Author(s):  
NATAN M. MACIEL ◽  
REUBER A. BRANDÃO ◽  
LEANDRO A. CAMPOS ◽  
ANTONIO SEBBEN
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Morphological Characters ◽  
Morphological Features ◽  
Advertisement Call ◽  
Sexually Dimorphic ◽  
Rhinella Marina ◽  
Large Size ◽  
Morphometric Feature ◽  
Distrito Federal

A new toad, Rhinella cerradensis, is described, including its tadpole and the advertisement call. The new species occupies Cerrado habitats in the Brazilian states of Piauí, Bahia, Goiás, Minas Gerais, and Distrito Federal. The species is characterized by its large size; absence of tibial glands; well developed cranial crests; short hands; sexually dimorphic coloration; and by the absence of a spiracle tube of the tadpole. The new species is included in the Rhinella marina group by the presence of a jagged suture formed by the articulation between the pterygoid medial ramus and the parasphenoid alae, as well as other shared morphological features. Morphological characters and statistical analyses inferred by morphometric feature suggest the existence of two subgroups of species within R. marina group. However, taxonomic rearrangements are not made here and await phylogenetic analysis.

scholarly journals Halovirus HF2 Intergenic Repeat Sequences Carry Promoters

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2388
Author(s):  
Brendan Russ ◽  
Friedhelm Pfeiffer ◽  
Mike Dyall-Smith
Keyword(s):  
Comparative Genomics ◽  
Reverse Transcriptase ◽  
Experimental Evidence ◽  
Reporter Gene ◽  
Promoter Activity ◽  
Regulatory Role ◽  
Rt Pcr ◽  
Repeat Sequences ◽  
Pcr Method ◽  
Coding Potential

Halovirus HF2 was the first member of the Haloferacalesvirus genus to have its genome fully sequenced, which revealed two classes of intergenic repeat (IR) sequences: class I repeats of 58 bp in length, and class II repeats of 29 bp in length. Both classes of repeat contain AT-rich motifs that were conjectured to represent promoters. In the present study, nine IRs were cloned upstream of the bgaH reporter gene, and all displayed promoter activity, providing experimental evidence for the previous conjecture. Comparative genomics showed that IR sequences and their relative genomic positions were strongly conserved among other members of the same virus genus. The transcription of HF2 was also examined by the reverse-transcriptase-PCR (RT-PCR) method, which demonstrated very long transcripts were produced that together covered most of the genome, and from both strands. The presence of long counter transcripts suggests a regulatory role or possibly unrecognized coding potential.

Micro Humid Air Cycle: Part B — Thermoeconomic Analysis

2003 ◽  
Author(s):  
J. Parente ◽  
A. Traverso ◽  
A. F. Massardo
Keyword(s):  
Gas Turbines ◽  
Electrical Power ◽  
Specific Work ◽  
Operational Flexibility ◽  
Humid Air ◽  
Capital Costs ◽  
Large Size ◽  
Heat Demand ◽  
Short Period ◽  
Specific Capital

Part A of this paper demonstrated that the HAT cycle, when applied to small-size gas turbines, can significantly enhance the efficiency and specific work of simple and recuperated cycles without the drastic changes to plant layout necessary in medium- and large-size plants. In this part B a complete thermoeconomic analysis is performed for microturbines operating in a Humid Air cycle. The capital cost and internal rate of return for both new machines and existing microturbines working in an mHAT-optimised cycle are presented and analysed. Three different scenarios are considered. The first scenario reflects a distributed electrical power generation application where cogeneration is not taken into account. Instead, the other two scenarios deal with CHP civil applications for different heat demands. The thermoeconomic results of the integrated mHAT cycle, based on a preliminary design of the saturator, demonstrate that microturbine performance can be greatly enhanced, while specific capital costs, in some cases, can be reduced up to 14%, without significant increase in layout complexity. Moreover, thanks to its operational flexibility (able to operate in dry and wet cycles), the mHAT is financially attractive for distributed power and heat generation (micro-cogeneration), particularly when heat demand is commutated in short period.

scholarly journals Chromosomal Spreading of Microsatellites and (TTAGGG)n Sequences in the Characidium zebra and C. gomesi Genomes (Characiformes: Crenuchidae)

2016 ◽  
Vol 149 (3) ◽  
pp. 182-190 ◽  
Author(s):  
Marcela B. Pucci ◽  
Patricia Barbosa ◽  
Viviane Nogaroto ◽  
Mara C. Almeida ◽  
Roberto F. Artoni ◽  
...  
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Dna Sequences ◽  
Tandem Repeats ◽  
Additional Data ◽  
Sex Chromosome ◽  
Binding Motif ◽  
W Chromosome ◽  
Repeat Sequences ◽  
Heteromorphic Sex Chromosomes

Sex chromosome evolution involves the accumulation of repeat sequences such as multigenic families, noncoding repetitive DNA (satellite, minisatellite, and microsatellite), and mobile elements such as transposons and retrotransposons. Most species of Characidium exhibit heteromorphic ZZ/ZW sex chromosomes; the W is characterized by an intense accumulation of repetitive DNA including dispersed satellite DNA sequences and transposable elements. The aim of this study was to analyze the distribution pattern of 18 different tandem repeats, including (GATA)n and (TTAGGG)n, in the genomes of C. zebra and C. gomesi, especially in the C. gomesi W chromosome. In the C. gomesi W chromosome, weak signals were seen for (CAA)10, (CAC)10, (CAT)10, (CGG)10, (GAC)10, and (CA)15 probes. (GA)15 and (TA)15 hybridized to the autosomes but not to the W chromosome. The (GATA)n probe hybridized to the short arms of the W chromosome as well as the (CG)15 probe. The (GATA)n repeat is known to be a protein-binding motif. GATA-binding proteins are necessary for the decondensation of heterochromatic regions that hold coding genes, especially in some heteromorphic sex chromosomes that may keep genes related to oocyte development. The (TAA)10 repeat is accumulated in the entire W chromosome, and this microsatellite accumulation is probably involved in the sex chromosome differentiation process and crossover suppression in C. gomesi. These additional data on the W chromosome DNA composition help to explain the evolution of sex chromosomes in Characidium.

scholarly journals Phylogeny and Comparative Genomics Unveil Independent Diversification Trajectories ofqnrBand Genetic Platforms within Particular Citrobacter Species

2015 ◽  
Vol 59 (10) ◽  
pp. 5951-5958 ◽  
Author(s):  
Teresa G. Ribeiro ◽  
Ângela Novais ◽  
Raquel Branquinho ◽  
Elisabete Machado ◽  
Luísa Peixe
Keyword(s):  
Phylogenetic Analysis ◽  
Comparative Genomics ◽  
Pulsed Field Gel Electrophoresis ◽  
Divergent Evolution ◽  
High Identity ◽  
Content Type ◽  
Clonal Relatedness ◽  
Intergenic Regions ◽  
Genetic Sequences ◽  
Comparative Genomics Analysis

ABSTRACTTo gain insights into the diversification trajectories ofqnrBgenes, a phylogenetic and comparative genomics analysis of these genes and their surrounding genetic sequences was performed. For this purpose,Citrobactersp. isolates (n= 21) and genome or plasmid sequences (n= 56) available in public databases harboring complete or truncatedqnrBgenes were analyzed.Citrobacterspecies identification was performed by phylogenetic analysis of different genotypic markers. The clonal relatedness among isolates, the location ofqnrBgenes, and the genetic surroundings ofqnrBgenes were investigated by pulsed-field gel electrophoresis (PFGE), S1-/I-CeuI-PFGE and hybridization, and PCR mapping and sequencing, respectively. Identification ofCitrobacterisolates was achieved usingleuSandrecNgene sequences, and isolates characterized in this study were diverse and harbored chromosomalqnrBgenes. Phylogenetic analysis of all knownqnrBgenes revealed seven main clusters and two branches, with most of them included in two clusters. Specific platforms (comprisingpspFandsapAand varying in synteny and/or identity of other genes and intergenic regions) were associated with each one of theseqnrBclusters, and the reliable identification of allCitrobacterisolates revealed that each platform evolved in different recognizable (Citrobacter freundii,C. braakii,C. werkmanii, andC. pasteurii) and putatively new species. A high identity was observed between some of the platforms identified in the chromosome ofCitrobacterspp. and in different plasmids ofEnterobacteriaceae. Our data corroborateCitrobacteras the origin ofqnrBand further suggest divergent evolution of closely relatedqnrBgenes/platforms in particularCitrobacterspp., which were delineated using particular genotypic markers.

Habitat use of the introduced cane toad (Rhinella marina) and native frog species in tropical Australia

2015 ◽  
Vol 31 (6) ◽  
pp. 531-540 ◽  
Author(s):  
Martin Mayer ◽  
Gregory P. Brown ◽  
Barbara Zimmermann ◽  
Matthew J. Greenlees ◽  
Richard Shine
Keyword(s):  
Spatial Distribution ◽  
Habitat Selection ◽  
Habitat Use ◽  
Ecological Impacts ◽  
Northern Australia ◽  
Cane Toad ◽  
Rhinella Marina ◽  
Frog Species ◽  
Tropical Australia ◽  
Reducing Activity

Abstract:The ecological impacts of introduced species can reveal mechanisms underlying habitat selection and behaviour. We investigated the habitat use of native frog species and the invasive cane toads (Rhinella marina) in tropical northern Australia to measure overlap in habitat use, and to test if the presence of the cane toad influences frog behaviour. Native frog species and the cane toad both preferred habitats close to water and unvegetated holes. However, native frogs were found further from water (on average 19.4 m) than were toads (on average 12.6 m), and preferred areas with higher vegetation (8–50 cm) than did toads, which were more abundant in vegetation lower than 8 cm. For both types of anuran, the next neighbour was more often of the same type (89% in frogs, 52% in toads) than expected by chance (observed ratio: 75% frogs vs 25% toads), reflecting these differences in habitat use. Our counts of frog abundance increased on average 14.5% in areas from which we removed cane toads temporarily. This result suggests that cane toads inhibit the activity of native anurans either by inducing avoidance, or by reducing activity. By modifying the behaviour and spatial distribution of native taxa, invasive cane toads may curtail activities such as feeding and breeding.

scholarly journals Identification and inverse modeling of industrial systems using regional models

2021 ◽  
Author(s):  
Antonio Galeno Pereira Neto ◽  
Luis Gustavo Mota Souza ◽  
Francisco de Assis da Silva Mota
Keyword(s):  
System Identification ◽  
Industrial Processes ◽  
Self Organizing Map ◽  
Regional Models ◽  
Industrial Systems ◽  
Identification Process ◽  
Data Space ◽  
Short Period ◽  
The Subject ◽  
M Estimation

With the advancement of technology the speed of industrial processes has greatly increased resulting in the need of obtaining models and controllers in a faster and more interactive way. Fortunately, the speed and ability to obtain data have also shown great advances, allowing the use of techniques capable of modeling processes reliably and quickly using the System Identification process. For generate a model from the input and output data of the systems, the System Identification has been the subject of many studies, with several techniques being proposed capable of generating reliable models in a short period of time. Two of these techniques, presented in this article, are the techniques known as Regional Models and Robust Regional Models, which use Clustering techniques such as Self Organizing Map (SOM) and K-means to dividing the system’s data space into similar regions in order to produce more reliable models using supervised neural networks; the robust approach also performs the treatment of Outliers in the data using the M-Estimation technique. The techniques presented are applied in nonlinear industrial systems and evaluated based on their Normalized Mean Square Error (NMSE) and the residual autocorrelation.

scholarly journals PlantRep: a resource of plant repeats

2021 ◽  
Author(s):  
Yu Zhang ◽  
Xizhi Luo ◽  
Shiyu Chen
Keyword(s):  
Comparative Genomics ◽  
Taxonomic Group ◽  
Repeat Elements ◽  
Plant Genomes ◽  
Repeat Sequences ◽  
Free Resource ◽  
Genomics Research

Abstract We re-annotated repeats sequence of 459 plant genomes and release a new resource of plant repeats: PlantRep (http://www.plantrep.cn/). We compared the structural and evolutionary characteristics of repeat sequences in different plant taxonomic group. The contribution of repeat sequences to the genes was examined systematically. PlantRep sheds lights of evolution of plant repeats and provides a free-resource for deep annotation of genome and comparative genomics research of repeat elements in plants.

scholarly journals Using conventionalF-statistics to study unconventional sex-chromosome differentiation

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3207 ◽  
Author(s):  
Nicolas Rodrigues ◽  
Christophe Dufresnes
Keyword(s):  
Sex Chromosomes ◽  
Sex Chromosome ◽  
Rana Temporaria ◽  
Microsatellite Data ◽  
Homologous Chromosomes ◽  
Chromosome Differentiation ◽  
Population Analyses ◽  
Hyla Arborea ◽  
Frog Species ◽  
Heterogametic Sex

Species with undifferentiated sex chromosomes emerge as key organisms to understand the astonishing diversity of sex-determination systems. Whereas new genomic methods are widening opportunities to study these systems, the difficulty to separately characterize their X and Y homologous chromosomes poses limitations. Here we demonstrate that two simpleF-statistics calculated from sex-linked genotypes, namely the genetic distance (Fst) between sexes and the inbreeding coefficient (Fis) in the heterogametic sex, can be used as reliable proxies to compare sex-chromosome differentiation between populations. We correlated these metrics using published microsatellite data from two frog species (Hyla arboreaandRana temporaria), and show that they intimately relate to the overall amount of X–Y differentiation in populations. However, the fits for individual loci appear highly variable, suggesting that a dense genetic coverage will be needed for inferring fine-scale patterns of differentiation along sex-chromosomes. The applications of theseF-statistics, which implies little sampling requirement, significantly facilitate population analyses of sex-chromosomes.

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