scholarly journals Comparative Analysis and Phylogenetic Implications of Plastomes of Five Genera in Subfamily Amyridoideae (Rutaceae)

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 277
Author(s):  
Kuo Sun ◽  
Qiao-Yun Liu ◽  
Ao Wang ◽  
Yong-Wei Gao ◽  
Liang-Cheng Zhao ◽  
...  
Keyword(s):  
East Asian ◽  
Structural Variations ◽  
Phylogenetic Implications ◽  
Phylogenetic Hypotheses ◽  
Recent Classification ◽  
Toddalia Asiatica ◽  
Phylogenomic Analyses ◽  
Close Relatives ◽  
Varia Tions

In the most recent classification of Rutaceae, Amyridoideae is the largest and most diverse subfamily. In Amyridoideae, the genera Phellodendron, Tetradium, Toddalia and Zanthoxylum were proposed as “proto-Rutaceae”due to substantial phytochemical similarities. In this study, we investigated the plastome varia-tions in eight species representing these four genera and Melicope. All plastomes exhibited a typical quadripartite structure with four regions (LSC, SSC, IRa and IRb). The whole chloroplast genome size ranged from 158,383 bp to 159,014 bp and the gene number ranged from 115 to 116. By comparative analyses, we found that there were structural variations at the LSC/IR and SSC/IR borders of the plastomes in the five genera, especially in Melicope. Three most divergent regions (trnH-psbA, trnE-trnT and psaB) were found from the LSC region, which had great potential for developing effective genetic markers. In addition, we conducted a phylogenomic analyses of the “proto-Rutaceae”and related taxa with plastomes data from 36 species. Our results showed that (1) Phellodendron, Tetradium, Toddalia and Zanthoxylum were confirmed as close relatives and grouped together as the ‘proto-Rutaceae’, (2) Phellodendron was sister to Tetradium, and Toddalia was deeply nested within Zanthoxylum, and (3) Toddalia asiatica was closely related to the Southwest Pacific and East Asian species of Zanthoxylum, and Melicope pteleifolia was more closely related to Acronychia than it is to Tetradium. This study provided new insights into the plastome structural varia-tions in subfamily Amyridoideae, and demonstrated that the plastomes data were sufficiently robust to explore implications of the phylogeny for the previous phylogenetic hypotheses.

scholarly journals Insights into Phylogenetic Relationships and Genome Evolution of Subfamily Commelinoideae (Commelinaceae Mirb.) Inferred from Complete Chloroplast Genomes

2020 ◽  
Author(s):  
Joonhyung Jung ◽  
Changkyun Kim ◽  
Joo-Hwan Kim
Keyword(s):  
Chloroplast Genome ◽  
Structural Variations ◽  
Protein Coding ◽  
Morphological Variations ◽  
Genome Data ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Recent Classification ◽  
First Time

Abstract BackgroundCommelinaceae (Commelinales) comprise 41 genera and widely distributed in both the Old and New Worlds except Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Nowadays, many researchers are commonly using complete chloroplast genome data for inferring evolution of land plants. In this study, we completed 15 new chloroplast genome sequences of subfamily Commelinoideae using Mi-seq platform. We utilized genome data for the first time to reveal the structural variations and reconstruct the problematic positions of genera.Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15) and former two genes might be a synapomorphy within the Commelinales. Only four species in tribe Commelineae appear IR expansion which affected duplication of rpl22 gene. We identified inversions which range from approximately 3 to 15 kb from four taxa (Murdannia, Streptolirion, Amischotolype, and Belosynapsis). The phylogenetic analyse using 77 chloroplast protein coding genes with maximum parsimony, maximum likelihood, and the Bayesian inference suggest that Palisota connected with tribe Commelineae with high support values, differ from recent classification of Commelinaceae. Also, we resolved unclear position of Streptoliriinae and monophyly of Dichorisandrinae.Conclusions In this study, we provide detailed information of the 15 plastid genomes of Commelinaceae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used for inferring evolutionary history about this family. Also, we need a further research to revise position of Palisota in recent classification.

scholarly journals Plastome Characterization and Phylogenomics of East Asian Beeches with a Special Emphasis on Fagus multinervis on Ulleung Island, Korea

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1338
Author(s):  
JiYoung Yang ◽  
Koji Takayama ◽  
Jin-Suk Youn ◽  
Jae-Hong Pak ◽  
Seung-Chul Kim
Keyword(s):  
Sequence Similarity ◽  
East Asian ◽  
Geographic Origin ◽  
Gc Content ◽  
European Beech ◽  
Protein Coding ◽  
Ulleung Island ◽  
Usage Patterns ◽  
Phylogenomic Analyses ◽  
Close Relatives

Beech trees of the genus Fagus (Fagaceae) are monoecious and distributed in the Northern Hemisphere. They represent an important component of mixed broad-leaved evergreen–deciduous forests and are an economically important source of timber. Despite their ecological and economical importance, however, little is known regarding the overall plastome evolution among Fagus species in East Asia. In particular, the taxonomic position and status of F. multinervis, a beech species endemic to Ulleung Island of Korea, remains unclear even today. Therefore, in this study, we characterized four newly completed plastomes of East Asian Fagus species (one accession each of F. crenata and F. multinervis and two accessions of F. japonica). Moreover, we performed phylogenomic analyses comparing these four plastomes with F. sylvatica (European beech) plastome. The four plastomes were highly conserved, and their size ranged from 158,163 to 158,348 base pair (bp). The overall GC content was 37.1%, and the sequence similarity ranged from 99.8% to 99.99%. Codon usage patterns were similar among species, and 7 of 77 common protein-coding genes were under positive selection. Furthermore, we identified five highly variable hotspot regions of the Fagus plastomes (ccsA/ndhD, ndhD/psaC, ndhF/rpl32, trnS-GCU/trnG-UCC, and ycf1). Phylogenetic analysis revealed the monophyly of Fagus as well as early divergence of the subgenus Fagus and monophyletic Engleriana. Finally, phylogenetic results supported the taxonomic distinction of F. multinervis from its close relatives F. engleriana and F. japonica. However, the sister species and geographic origin of F. multinervis on Ulleung Island could not be determined.

scholarly journals Insights into phylogenetic relationships and genome evolution of subfamily Commelinoideae (Commelinaceae Mirb.) inferred from complete chloroplast genomes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joonhyung Jung ◽  
Changkyun Kim ◽  
Joo-Hwan Kim
Keyword(s):  
Nucleotide Diversity ◽  
Structural Variations ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Chloroplast Protein ◽  
Genome Data ◽  
Plastid Genomes ◽  
Chloroplast Genomes ◽  
Current Classification

Abstract Background Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. Results All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. Conclusions In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.

scholarly journals A57 THE USE AND INTERPRETATION OF HLA-DQ2/DQ8 GENOTYPING BY PEDIATRIC GASTROENTEROLOGISTS

2021 ◽  
Vol 4 (Supplement_1) ◽  
pp. 14-15
Author(s):  
B Moreau ◽  
E Robidoux
Keyword(s):  
Risk Groups ◽  
Risk Classification ◽  
Low Risk ◽  
Risk Alleles ◽  
Seronegative Patient ◽  
Espghan Guidelines ◽  
Recent Classification ◽  
American Society ◽  
Hla Dq2

Abstract Background A recent classification of high and low risk alleles associated with celiac disease (CD) shows that the presence of a single allele (DQA1*05 or DQB1*02; coding together for HLA-DQ2), without a positive genotype (HLA-DQ2 and or HLA-DQ8), represents a risk of developing the disease. Aims The aim of this study is to evaluate the use and interpretation of the HLA-DQ2/DQ8 genotyping by pediatric gastroenterologists, as there is no study on the matter and the latest guidelines do not address this risk classification. Methods A web-based survey was sent by email to all NASPGHAN (North American society of pediatric gastroenterolgy, hepatology and nutrition) members. Results Results 294 pediatric gastroenterologists sent a complete survey. 86,1% use the HLA-DQ2/DQ8 genotyping according mainly to the NASPGHAN and ESPGHAN guidelines. The main indications considered were to exclude CD in a patient on a gluten-free diet with a resolution of his symptoms and in a seronegative patient with equivocal biopsies. A minority would consider the genotyping for screening high risk groups or for making a diagnosis in children with high specific CD antibodies and strong clinical suspicion without performing biopsies, as suggested by the ESPGHAN guidelines. The alleles associated with CD are not well known, but 76,7% the participants are aware of the risk classification. While only 62,8% have access to the complete genotype, 47,8% consider it useful. Nevertheless, 82,6% would still want to know the presence of a low risk allele. Conclusions The risk classification of alleles related to CD warrants a modification of the genotyping result with access to the alleles and an adaptation of the guidelines. Funding Agencies None

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

scholarly journals Neuropathology of Temporal Lobe Epilepsy

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Fahd Al Sufiani ◽  
Lee Cyn Ang
Keyword(s):  
Temporal Lobe Epilepsy ◽  
Temporal Lobe ◽  
Focal Cortical Dysplasia ◽  
Cortical Dysplasia ◽  
Wide Range ◽  
Pathologic Findings ◽  
Pathologic Lesions ◽  
Recent Classification ◽  
Associated Tumors

Pathologic findings in surgical resections from patients with temporal lobe epilepsy include a wide range of diagnostic possibilities that can be categorized into different groups on the basis of etiology. This paper outlines the various pathologic entities described in temporal lobe epilepsy, including some newly recognized epilepsy-associated tumors, and briefly touch on the recent classification of focal cortical dysplasia. This classification takes into account coexistent pathologic lesions in focal cortical dysplasia.

A Global Phylogenomic Study of the Thelypteridaceae

2021 ◽  
Vol 46 (4) ◽  
pp. 891-915
Author(s):  
Susan Fawcett ◽  
Alan R. Smith ◽  
Michael Sundue ◽  
J. Gordon Burleigh ◽  
Emily B. Sessa ◽  
...  
Keyword(s):  
Morphological Characters ◽  
Morphological Evidence ◽  
Phylogenetic Studies ◽  
The Family ◽  
Likelihood Analysis ◽  
Single Genus ◽  
The Subject ◽  
Recent Classification ◽  
Phylogenomic Study

Abstract— The generic classification of the Thelypteridaceae has been the subject of much controversy. Proposed taxonomic systems have varied from recognizing the approximately 1200 species in the family within the single genus Thelypteris, to systems favoring upwards of 30 genera. Insights on intrafamilial relationships, especially for neotropical taxa, have been gained from recent phylogenetic studies; however, in the most recent classification, 10 of 30 recognized genera are either non-monophyletic or untested. We sequenced 407 nuclear loci for 621 samples, representing all recognized genera and approximately half the known species diversity. These were analyzed using both maximum likelihood analysis of a concatenated matrix and multi-species coalescent methods. Our phylogenomic results, informed by recently published morphological evidence, provide the foundation for a generic classification which recircumscribed 14 genera and recognized seven new genera. The 37 monophyletic genera sampled demonstrate greater geographic coherence than previous taxonomic concepts suggested. Additionally, our results demonstrate that certain morphological characters, such as frond division, are evolutionarily labile and are thus inadequate for defining genera.

Phylogenetic implications of mitogenome rearrangements in East Asian potamiscine freshwater crabs (Brachyura: Potamidae)

2020 ◽  
Vol 143 ◽  
pp. 106669 ◽  
Author(s):  
Zhan Zhang ◽  
Yuhui Xing ◽  
Jiajia Cheng ◽  
Da Pan ◽  
Linna Lv ◽  
...  
Keyword(s):  
East Asian ◽  
Freshwater Crabs ◽  
Phylogenetic Implications

SCALING THEORY AND THE CLASSIFICATION OF PHASE TRANSITIONS

1992 ◽  
Vol 06 (13) ◽  
pp. 773-784 ◽  
Author(s):  
R. HILFER
Keyword(s):  
Phase Transitions ◽  
Statistical Physics ◽  
Thermodynamic Description ◽  
Classification Theory ◽  
Nonequilibrium Phase Transitions ◽  
Critical Limit ◽  
Scaling Hypothesis ◽  
Recent Classification ◽  
Thermodynamics And Statistical Mechanics

The recent classification theory for phase transitions (R. Hilfer, Physica Scripta 44, 321 (1991)) and its relation with the foundations of statistical physics is reviewed. First it is outlined how Ehrenfests classification scheme can be generalized into a general thermodynamic classification theory for phase transitions. The classification theory implies scaling and multiscaling thereby eliminating the need to postulate the scaling hypothesis as a fourth law of thermodynamics. The new classification has also led to the discovery and distinction of nonequilibrium transitions within equilibrium statistical physics. Nonequilibrium phase transitions are distinguished from equilibrium transitions by orders less than unity and by the fact that equilibrium thermodynamics and statistical mechanics become inapplicable at the critical point. The latter fact requires a change in the Gibbs assumption underlying the canonical and grandcanonical ensembles in order to recover the thermodynamic description in the critical limit.

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