scholarly journals Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

2019 ◽  
Author(s):  
P Natsidis ◽  
A Tsakogiannis ◽  
P Pavlidis ◽  
CS Tsigenopoulos ◽  
T Manousaki
Keyword(s):  
Phylogenetic Relationships ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
High Quality ◽  
Orthology Assignment ◽  
Gene Sets ◽  
The Family ◽  
Puffer Fish ◽  
Phylogenomic Analyses

ABSTRACTSparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a phylogenomic attempt to resolve the position of the family using five recently available Sparidae gene-sets and 26 available fish proteomes from species with a sequenced genome, to ensure higher quality of the predicted genes. A thorough phylogenomic analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used, a finding that contradicts our previous phylogenomic analysis that proposed the yellow croaker and the european seabass as closest taxa of sparids. By analytically comparing the methodologies applied in both cases, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

scholarly journals Phylogenomics investigation of sparids (Teleostei: Spariformes) using high-quality proteomes highlights the importance of taxon sampling

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Paschalis Natsidis ◽  
Alexandros Tsakogiannis ◽  
Pavlos Pavlidis ◽  
Costas S. Tsigenopoulos ◽  
Tereza Manousaki
Keyword(s):  
Phylogenetic Relationships ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
High Quality ◽  
Orthology Assignment ◽  
Gene Sets ◽  
Puffer Fish ◽  
Commercial Value ◽  
Phylogenomic Analyses ◽  
High Quality Genome

Abstract Sparidae (Teleostei: Spariformes) are a family of fish constituted by approximately 150 species with high popularity and commercial value, such as porgies and seabreams. Although the phylogeny of this family has been investigated multiple times, its position among other teleost groups remains ambiguous. Most studies have used a single or few genes to decipher the phylogenetic relationships of sparids. Here, we conducted a thorough phylogenomic analysis using five recently available Sparidae gene-sets and 26 high-quality, genome-predicted teleost proteomes. Our analysis suggested that Tetraodontiformes (puffer fish, sunfish) are the closest relatives to sparids than all other groups used. By analytically comparing this result to our own previous contradicting finding, we show that this discordance is not due to different orthology assignment algorithms; on the contrary, we prove that it is caused by the increased taxon sampling of the present study, outlining the great importance of this aspect in phylogenomic analyses in general.

scholarly journals Characterization and comparative analysis among plastome sequences of eight endemic Rubus (Rosaceae) species in Taiwan

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
JiYoung Yang ◽  
Yu-Chung Chiang ◽  
Tsai-Wen Hsu ◽  
Seon-Hee Kim ◽  
Jae-Hong Pak ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Gc Content ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Plastome Evolution ◽  
Rosaceae Species ◽  
The Family ◽  
Intergenic Regions

AbstractGenus Rubus represents the second largest genus of the family Rosaceae in Taiwan, with 41 currently recognized species across three subgenera (Chamaebatus, Idaoeobatus, and Malochobatus). Despite previous morphological and cytological studies, little is known regarding the overall phylogenetic relationships among the Rubus species in Taiwan, and their relationships to congeneric species in continental China. We characterized eight complete plastomes of Taiwan endemic Rubus species: subg. Idaeobatus (R. glandulosopunctatus, R. incanus, R. parviaraliifolius, R rubroangustifolius, R. taitoensis, and R. taiwanicolus) and subg. Malachobatus (R. kawakamii and R. laciniastostipulatus) to determine their phylogenetic relationships. The plastomes were highly conserved and the size of the complete plastome sequences ranged from 155,566 to 156,236 bp. The overall GC content ranged from 37.0 to 37.3%. The frequency of codon usage showed similar patterns among species, and 29 of the 73 common protein-coding genes were positively selected. The comparative phylogenomic analysis identified four highly variable intergenic regions (rps16/trnQ, petA/psbJ, rpl32/trnL-UAG, and trnT-UGU/trnL-UAA). Phylogenetic analysis of 31 representative complete plastomes within the family Rosaceae revealed three major lineages within Rubus in Taiwan. However, overall phylogenetic relationships among endemic species require broader taxon sampling to gain new insights into infrageneric relationships and their plastome evolution.

Child Diagnosis of Autism - How It Can Change the Family Life

2017 ◽  
Vol 5 (1) ◽  
pp. 498
Author(s):  
Maria Stănescu
Keyword(s):  
Early Intervention ◽  
Family Life ◽  
Social Life ◽  
Decisive Role ◽  
Autistic Children ◽  
Child Behaviors ◽  
High Quality ◽  
Child Diagnosis ◽  
The Family

The article is about the role of the family in the education and formation of children and, especially, in the life and development of autistic children. It describes the problems their family is facing and the need for counseling to parents with autistic children. The reaction to finding the diagnosis of autism varies from one family to another and may encounter a large variety: from disbelief, anger, guilt, helplessness, devastation, surprise, or even rejection of the child, to understanding and relief when finally the parents have an explanation for their child behaviors. Early intervention is important in psychological sustaining of the parent, as parent involvement in the recovery of the child with autism has a determinant role in his development and in ensuring a high quality of life of the child and the life of the hole family. The response to a child's autism diagnosis varies from one family to another. The family goes through a variety of disbelief, anger, guilt, helplessness, devastation, surprise, or even rejection of the child, to understanding and relief. Early intervention is very important in the psychological support of the parent. Because any change disturbs the family equilibrium. A diagnosis of autism changes not only the life of the diagnosed child, but also the life of family members. All the resources are focused on the need of the child. Although each parent is different, after diagnosing the child with autism, all parents are overwhelmed by confusion, shock and denial. Parents' feelings can be influenced by how their children's situation affects different aspects of life - it has an impact on service, on social life and all their personal life. If we look at the family as a system and when a disturbing factor appears, all parts of the system are affected. The involvement of parents in the recovery of the child with autism has a decisive role in its development and in ensuring a high quality of child's life and family life.

scholarly journals Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

2020 ◽  
Vol 70 (3) ◽  
pp. 1785-1792 ◽  
Author(s):  
Jae-Chan Lee ◽  
Kyung-Sook Whang
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
Diamino Acid ◽  
Phylogenomic Analyses ◽  
Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

scholarly journals Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3941 ◽  
Author(s):  
Alejandra Panzera ◽  
Adam D. Leaché ◽  
Guillermo D’Elía ◽  
Pedro F. Victoriano
Keyword(s):  
Incomplete Lineage Sorting ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Taxon Sampling ◽  
Phylogenomic Analysis ◽  
Molecular Systematic ◽  
Data Set ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

scholarly journals THE QUALITY OF CHILD TRAINING IN THE PRE-SCHOOL INSTITUTION: PARENTS‘ POINTS OF VIEW

2012 ◽  
Vol 45 (1) ◽  
pp. 40-50
Author(s):  
Daiva Malinauskienė ◽  
Roberta Pranaitytė
Keyword(s):  
School Education ◽  
Education Quality ◽  
Educational Institutions ◽  
High Quality ◽  
Social Success ◽  
The Family ◽  
The Status ◽  
Points Of View ◽  
Children Education

Lately, strategic documents prepared by Lithuanian and foreign educational institutions and recent discussions held by pedagogical societies and stakeholders have considered the issues of education quality. The question of ensuring quality has become one of the key priorities of educational policy assisting the system of education in Lithuania with integration into the space of European context. The status of the family can hardly guarantee the required conditions for self / educating children at home in all cases. Therefore, high-quality facilities should be a crucial aspect of training provided by the educational institutions since early childhood. Pre-school education in Lithuania, as one of the stages of a successive educational system, meets the basic needs of a child, including safety, activity and self-expression. Therefore, assessing a real situation in pre-school institutions seems to be an important point providing information on the needs for obtaining high quality self/education and training services, which is the way to implement one of the purposes of pre-school education – to help the family with fostering all qualities of a child (intellectual, emotional, volitional and physical) determining personal maturity and social success thus offering the programme of pre-school education and/or required educational help for the child or family. Empirical research has revealed parents’ points of view to the quality of education and quality evaluation and helped with identifying the factors that may have an impact on child self/education. Key words: children, education quality, institution of pre-school education.

scholarly journals Comparative Study of Growth Statistics of Two Species of Paulownia and Optimization of Rooting Methods

2019 ◽  
Vol 6 (1) ◽  
pp. 11-15
Author(s):  
Hari Krishna Saiju ◽  
Abhishesh Bajracharya ◽  
Brishav Rajbahak ◽  
Stuti Ghimire
Keyword(s):  
Growth Rate ◽  
Musical Instruments ◽  
Shoot Length ◽  
Ms Medium ◽  
High Quality ◽  
Paulownia Tomentosa ◽  
Fast Growing ◽  
The Family

Paulownia is a fast-growing woody tree, native to the forests of China. It belongs to the family Scrophulariaceae and is mainly used as a source of wood for furniture and musical instruments. Due to its fast-growing nature and high-quality of wood, there has been growing interest in cultivation and research of Paulownia in Nepal. Growth comparison was performed by measuring shoot length in in vitro condition. Among two species of Paulownia - Paulownia tomentosa (Thunb.) Steud and Paulownia fortuneii (Seem.) Hemsl., the growth rate of P. tomentosa was found to be 0.355 cm/week while that of P. fortuneii was found to be 0.637 cm/week in in-vitro conditions in MS medium supplemented with 0.1 mg/l NAA and 1mg/l BAP. Optimization of rooting methods was also performed, in which, sand rooting was found to be easier and more effective than in-vitro rooting. Dipping the plantlets in 1 mg/l of NAA was found to produce longer and denser roots than lower or higher concentrations during sand rooting.

scholarly journals Faktor-Faktor yang Mempengaruhi Kualitas Hidup Pasien Chronic Kidney Disease yang Menjalani Hemodialisa di Ruang Hemodialisa

2018 ◽  
Vol 1 (2) ◽  
pp. 32-46
Author(s):  
Handi Rustandi ◽  
Hengky Tranado ◽  
Tinalia Pransasti
Keyword(s):  
Quality Of Life ◽  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Family Support ◽  
Sampling Technique ◽  
High Quality ◽  
The Public ◽  
The Family ◽  
Provide Health Education

This study aimed to describe the factors that affect the quality of life of patients with CRF who undergo hemodialysis in dr. M. Yunushospital in Bengkulu 2016. The population of study is 205 people, the sampling technique used was an accidental sampling with a sample of 67 respondents.The results showed nearly all respondents aged smaller than 20 and greather than 35 years, more than the majority of respondents were female, more than the majority of respondents had pretty income or more, almost half of respondents had high levels of depression, more than the majority of respondents had either the family support, more than the majority of respondents had a high quality of life, there was a correlation between age, gender, producer, depression, and family support with quality of life, there was a relationship between sex with the quality of life for CRF patients undergoing hemodialysis in dr. M. Yunus Hospital in Bengkulu 2016.It is advisable for the public to provide health education for families of patients with CRF who undergo hemodialysis therapy on the importance of family support in improving the quality of life of family members. Keywords: Accidental Sampling, Chronic Kidney Disease, Hemodialysis, Quality of Life.    

scholarly journals Large-scale Phylogenomic Analysis Provides New Insights Into the Phylogeny of the Order Gadiformes and Evolution of Freshwater Gadiform Species Burbot (Lota lota)

2021 ◽  
Author(s):  
Zhiqiang Han ◽  
Chenyan Shou ◽  
Manhong Liu ◽  
Tianxiang Gao
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Amino Acid Sequences ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
Lota Lota ◽  
The Family ◽  
Tree Building

Our understanding of phylogenetic relationships among Gadiformes fish is obtained through the analysis of a small number of genes, but uncertainty remains around critical nodes. A series of phylogenetic controversial exists at the suborder, family, subfamily, and species levels. A total of 1105 orthologous exon sequences and translated amino acid sequences from 36 genomes and 12 transcriptomes covering 33 species were applied to investigate the phylogenetic relationships within Gadiformes and address these problems. Phylogenetic trees reconstructed with the amino acid data set using different tree-building methods (RAxML and MrBayes) showed consistent topology. The monophyly of Gadifromes was confirmed in our study. However, the three suborders Muraenolepidoidei, Macrouroidei, and Gadoidei were not well recovered by our phy-logenomic study, rejecting the validity of suborder Muraenolepidoidei. Four major lineages were revealed in this study. The family Bregmacerotidae forming clade I was the basal lineage of Gadiformes. The family Merluciidae formed clade II. Clade III contained families Melanonidae, Muraenolepididae, Macrouridae (with subfamilies Trachyrincinae, Macrourinae, and Bathygadinae), and Moridae. Clade IV contained at least three families of suborder Gadoidei, i.e., Gadidae, Phycidae, and Ranicipitidae. The subspecies of Lota lota from Amur River were confirmed, indicating that exon markers were a valid high-resolution method for delimiting subspecies or distinct lineages within species level. The PSMC analysis of different populations of L. lota suggests a continuous decline since 2 Myr.

scholarly journals Phylogenomic revision of the family Streptosporangiaceae, reclassification of Desertactinospora gelatinilytica as Spongiactinospora gelatinilytica comb. nov. and a taxonomic home for the genus Sinosporangium in the family Streptosporangiaceae

2020 ◽  
Vol 70 (4) ◽  
pp. 2569-2579 ◽  
Author(s):  
Hilal Ay ◽  
Hayrettin Saygin ◽  
Nevzat Sahin
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
Genome Data ◽  
The Family ◽  
Taxonomic Affiliation ◽  
Phylogenomic Analyses ◽  
Genome Comparisons

In recent years, the results of genome-based phylogenetic analyses have contributed to microbial systematics by increasing the availability of sequenced microbial genomes. Therefore, phylogenomic analysis within large taxa in the phylum Actinobacteria has appeared as a useful tool to clarify the taxonomic positions of ambiguous groups. In this study, we provide a revision of the actinobacterial family Streptosporangiaceae using a large collection of genome data and phylogenomics approaches. The phylogenomic analyses included the publicly available genome data of the members of the family Streptosporangiaceae and the state-of-the-art tools are used to infer the taxonomic affiliation of these species within the family. By comparing genome-based and 16S rRNA gene-based trees, as well as pairwise genome comparisons, the recently described genera Spongiactinospora and Desertactinospora are combined in the genus Spongiactinospora . In conclusion, a comprehensive phylogenomic revision of the family Streptosporangiaceae is proposed.

Sign in / Sign up

Export Citation Format

Share Document