Taxonomía de los hongos: un rompecabezas al que le faltan muchas piezas

Los hongos son organismos polifacéticos presentes en casi todos los ecosistemas de la tierra, donde establecen diversos tipos de simbiosis con otros seres vivos. A pesar de ser reconocidos por los humanos desde la antigüedad -y de la cantidad de trabajos que han profundizado sobre su biología y ecología-, aún falta mucho por conocer sobre estos organismos. Algunos de los criterios que clásicamente se han utilizado para su estudio, hoy resultan limitados y hasta cierto punto permiten un agrupamiento de los aislamientos según algunas características, pero generan confusión en su clasificación y, más aún, cuando se pretende comprender sus relaciones genealógicas. Los caracteres fenotípicos no son suficientes para identificar una especie de hongos y, menos aún, para construir una filogenia amplia o de un grupo particular. Hay grandes vacíos que hacen que los árboles generados sean inestables y fácilmente debatidos. Para los profesionales de la salud, parece que la identificación de los hongos hasta niveles inferiores como género y especie es suficiente para elegir el tratamiento más adecuado para su control, comprender la epidemiología de los cuadros clínicos asociados y reconocer los brotes y los factores determinantes de la resistencia a los antimicrobianos. No obstante, la ubicación taxonómica dentro del reino permitiría establecer relaciones filogenéticas entre los taxones fúngicos, facilitando la comprensión de su biología, su distribución en la naturaleza y la evolución de su potencial patogénico. Los avances de las técnicas de biología molecular y las ciencias de la computación en los últimos 30 años han permitido cambios importantes dirigidos a establecer los criterios para definir una especie fúngica y alcanzar una construcción filogenética más o menos estable. Sin embargo, el camino por recorrer aún es largo, y supone un trabajo mancomunado de la comunidad científica a nivel global y el apoyo a la investigación básica.

Fungi are multifaceted organisms found in almost all ecosystems on Earth, where they establish various types of symbiosis with other living beings. Despite being recognized by humans since ancient times, and the high number of works delving into their biology and ecology, much is still unknown about these organisms. Some criteria classically used for their study are nowadays limited, generating confusion in categorizing them, and even more, when trying to understand their genealogical relationships. To identify species within Fungi, phenotypic characters to date are not sufficient, and to construct a broad phylogeny or a phylogeny of a particular group, there are still gaps affecting the generated trees, making them unstable and easily debated. For health professionals, fungal identification at lower levels such as genus and species, is enough to select the most appropriate therapy for their control, understand the epidemiology of clinical pictures associated, and recognize outbreaks and antimicrobial resistance. However, the taxonomic location within the kingdom, information with apparently little relevance, can allow phylogenetic relationships to be established between fungal taxa, facilitating the understanding of their biology, distribution in nature, and pathogenic potential evolution. Advances in molecular biology and computer science techniques from the last 30 years have led to crucial changes aiming to establish the criteria to define a fungal species, allowing us to reach a kind of stable phylogenetic construction. However, there is still a long way to go, and it requires the joint work of the scientific community at a global level and support for basic research.

Genomic constellations of RVA detected in Brazil from 1986 to 2016: a temporal and geographical distribution and occurrence of reassortments / Constelações genômicas de RVA detectadas no Brasil de 1986 a 2016: uma distribuição temporal e geográfica e ocorrência de rearranjos

INTRODUCTION: Species A rotavirus (RVA) infections are a major cause of severe gastroenteritis in children of <5 years worldwide. In Brazil, before vaccination, RVA was associated with 3.5 million episodes of acute diarrheal disease per year. Due to the segmented nature of their genomes, rotaviruses can exchange genes during co-infections, and generate new virus strains and new reinfections. OBJECTIVE: To evaluate the genomic diversity of RVA isolated in Brazil in 30 years, between 1986 to 2016, to investigate possible changes in the frequency of genotype constellations before and after the implementation of the vaccine. METHODS: In total, 4,474 nucleotide sequences were obtained from the Virus Variation Database. Genomic constellation was compared, and the proportion of rotavirus genotypes was analyzed by time and geographic region. RESULTS: Our results showed that major known genotypes were circulating in the country during the period under analysis, with a prevalence of the G1P[8] Wa-like genotype, decreasing only in the period immediately after the introduction of the vaccine. Regarding the geographical distribution, most of our constellations, 62 (39.2%), and 50 (31.6%) were concentrated in the North and Northeast regions. Our analysis also showed the circulation of multiple strains during the periods when the DS-1-like and AU-1-like genotypes were co-circulating with the Wa-like genotype. CONCLUSION: Therefore, it is likely that inter-genogroup reassortments are still occurring in Brazil and so it is important to establish an efficient surveillance system to follow the emergence of novel reassorted strains that might not be targeted by the vaccine.

INTRODUÇÃO: As infecções por rotavírus A (RVA) são uma das principais causas de gastroenterite grave em crianças <5 anos em todo o mundo. No Brasil, antes da vacinação, o RVA estava associado a 3,5 milhões de episódios de diarreia aguda por ano. Devido à natureza segmentada de seus genomas, os rotavírus podem trocar genes durante as coinfecções, gerar novas cepas de vírus e novas reinfecções. OBJETIVO: Avaliar a diversidade genômica de RVA isolados no Brasil entre 1986 a 2016 para investigar possíveis alterações na frequência das constelações de genótipos antes e após a implantação da vacina. MÉTODOS: No total, 4.474 sequências de nucleotídeos foram obtidas do Banco de Dados de Variação de Vírus. A constelação genômica foi comparada e a proporção dos genótipos de rotavírus foi analisada por tempo e região geográfica. RESULTADOS: Nossos resultados mostraram que os principais genótipos conhecidos circulavam no país no período em análise, com prevalência do genótipo G1P[8] Wa-like, diminuindo apenas no período imediatamente após a introdução da vacina. Em relação à distribuição geográfica, a maioria das nossas constelações, 62 (39,2%) e 50 (31,6%), concentrava-se nas regiões Norte e Nordeste. Nossa análise também mostrou a circulação de cepas múltiplas durante os períodos em que os genótipos DS-1-like e AU-1-like estavam co-circulando com o genótipo Wa-like. CONCLUSÃO: Portanto, é provável que rearranjos inter-genogrupos ainda estejam ocorrendo no Brasil e por isso é importante estabelecer um sistema de vigilância eficiente para acompanhar o surgimento de novas cepas rearranjadas que podem não ser protegidas pela vacina.

Molecular Identification and phylogenetic analysis of mosquito vectors from Mananthavady Taluk, Wayanad, Kerala, India

Background & objectives: Every year more than one billion people are infected and about one million people die from vector-borne diseases; of which mosquito-borne diseases remain as the world’s most severe insect-borne diseases with excessive rates of morbidity and mortality. This study aimed to examine the mosquito vectors and the possible diseases transmitted by them in the Mananthavady Taluk of Wayanad, Kerala. Methods: The area selected for the present study was Mananthavady Taluk of Wayanad district, Kerala, during 2019–2021. The collected specimen were subjected for morphological identification using taxonomic keys and were confirmed by DNA barcoding. Molecular phylogeny assessment was done for the collected species of vector mosquitoes. Results: A total of 17 mosquito species belonging to 5 genera, Anopheles, Aedes, Culex, Mansonia and Armigeres were identified. The mitochondrial COI gene sequences generated for molecular identification of these species were submitted to NCBI GenBank. Interpretation & conclusion: Overall, this study extends our understanding of the molecular evolution of mosquito vectors of medical and veterinary concern, which could aid in developing biotechnological approaches used in Culicidae control programs.

Characteristics of the chloroplast genome of Dracaena marginata and phylogenetic analysis / 生物工程学报

Dracaena marginata is a widely cultivated horticultural plant in the world, which has high ornamental and medicinal value. In this study, the whole genome of leaves from D. marginata was sequenced by Illumina HiSeq 4000 platform. The chloroplast genome were assembled for functional annotation, sequence characteristics and phylogenetic analysis. The results showed that the chloroplast genome of D. marginata composed of four regions with a size of 154 926 bp, which was the smallest chloroplast genome reported for Dracaena species to date. A total of 132 genes were identified, including 86 coding genes, 38 tRNA genes and 8 rRNA genes. Codon bias analysis found that the codon usage bias was weak and there was a bias for using A/U base endings. 46 simple sequence repeat and 54 repeats loci were detected in the chloroplast genome, with the maximum detection rate in the large single copy region and inverted repeat region, respectively. The inverted repeats boundaries of D. marginata and Dracaena were highly conserved, whereas gene location differences occurred. Phylogenetic analysis revealed that D. serrulata and D. cinnabari form a monophyletic clade, which was the closest relationship and conformed to the morphological classification characteristics. The analysis of the chloroplast genome of D. marginata provides important data basis for species identification, genetic diversity and chloroplast genome engineering of Dracaena.

Chloroplast genomic characterization and phylogenetic analysis of Pellionia scabra / 生物工程学报

Pellionia scabra belongs to the genus Pellionia in the family of Urticaceae, and is a high-quality wild vegetables with high nutritional value. In this study, high-throughput techniques were used to sequence, assemble and annotate the chloroplast genome. We also analyzed its structure, and construct the phylogenetic trees from the P. scabra to further study the chloroplast genome characteristics. The results showed that the chloroplast genome size was 153 220 bp, and the GC content was 36.4%, which belonged to the typical tetrad structure in P. scabra. The chloroplast genome encodes 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes in P. scabra. Among them, 15 genes contained 1 intron, 2 genes contained 2 introns, and rps12 had trans-splicing, respectively. In P. scabra, chloroplast genomes could be divided into four categories, including 43 photosynthesis, 64 self-replication, other 7 coding proteins, and 4 unknown functions. A total of 51 073 codons were detected in the chloroplast genome, among which the codon encoding leucine (Leu) accounted for the largest proportion, and the codon preferred to use A and U bases. There were 72 simple sequence repeats (SSRs) in the chloroplast genome of P. scabra, containing 58 single nucleotides, 12 dinucleotides, 1 trinucleotide, and 1 tetranucleotide. The ycf1 gene expansion was present at the IRb/SSC boundary. The phylogenetic trees showed that P. scabra (OL800583) was most closely related to Elatostema stewardii (MZ292972), Elatostema dissectum (MK227819) and Elatostema laevissimum var. laevissimum (MN189961). Taken together, our results provide worthwhile information for understanding the identification, genetic evolution, and genomics research of P. scabra species.

The molecular investigations on the subgenus Artemisia Less. of the genus Artemisia L. (Asteraceae) in Turkey / Investigações moleculares sobre o subgênero Artemisia Less. do gênero Artemisia L. (Asteraceae) na Turquia

Abstract The genus Artemisia L. of the family Asteraceae is systematically very complex. The aim of this study was to evaluate taxonomic positions of taxa of the subgenus Artemisia belonging to the genus Artemisia in Turkey using some molecular techniques. In this molecular study, 44 individuals belong to 14 species of the subgenus Artemisia were examined. Analyses were performed on the combined dataset using maximum parsimony, maximum likelihood and Bayesian inference and Molecular parameters obtained from co-evaluations of sequences of the psbA-trnH, ITS and ETS regions of examined individuals were used in the phylogenetic tree drawing. According to the results of this study, two molecular groups have been formed based on the DNA sequence similarity of the species, but there are no obvious morphological characters corresponding to two molecular groups. There is no also agreement between the two molecular groups and the two morphological groups formed according to the hairiness condition of the receptacle of species. Due to the lack of molecular significance of their receptacles with or without hair, dividing of the subgenus Artemisia species into new subgenera or sections was not considered appropriate. Likewise, it has been found that with or without hair on the corolla lobes of the central hermaphrodite disc flowers have no molecular significance. It was found that there were no gene flow and hybridization between the 14 species of the subgenus Artemisia and these 14 species were found completed their speciation. This study is important as it is the first molecular based study relating with belong to subgenus Artemisia species growing naturally in Turkey. In addition, new haplotypes related to the populations of Turkey belonging to the subgenus Artemisia taxa were reported by us for the first time and added to the GenBank database.

Resumo O gênero Artemisia L. da família Asteraceae é sistematicamente muito complexo. O objetivo deste estudo foi avaliar as posições taxonômicas de táxons do subgênero Artemisia pertencentes ao gênero Artemisia na Turquia usando algumas técnicas moleculares. Neste estudo molecular, 44 indivíduos pertencentes a 14 espécies do subgênero Artemisia foram examinados. As análises foram realizadas no conjunto de dados combinado usando máxima parcimônia, máxima verossimilhança e inferência bayesiana e parâmetros moleculares obtidos a partir de coavaliações de sequências das regiões psbA-trnH, ITS e ETS de indivíduos examinados foram usados ​​no desenho da árvore filogenética. De acordo com os resultados deste estudo, dois grupos moleculares foram formados com base na similaridade da sequência de DNA das espécies, mas não há caracteres morfológicos óbvios correspondentes a dois grupos moleculares. Também não há concordância entre os dois grupos moleculares e os dois grupos morfológicos formados de acordo com a condição de pilosidade do receptáculo da espécie. Devido à falta de significado molecular de seus receptáculos com ou sem cabelo, a divisão das espécies do subgênero Artemisia em novos subgêneros ou seções não foi considerada apropriada. Da mesma forma, verificou-se que com ou sem cabelo nos lobos da corola das flores do disco hermafrodita central não tem significado molecular. Constatou-se que não houve fluxo gênico e hibridização entre as 14 espécies do subgênero Artemisia e essas 14 espécies concluíram sua especiação. Este estudo é importante porque é o primeiro estudo de base molecular relacionado com espécies pertencentes ao subgênero Artemisia crescendo naturalmente na Turquia. Além disso, novos haplótipos relacionados às populações da Turquia pertencentes ao subgênero Artemisia taxa foram relatados por nós pela primeira vez e adicionados ao banco de dados do GenBank.

Characterization of the complete chloroplast genome of Polygonatum franchetii Hua, a Chinese endemic medicinal species, and phylogenetic relationships of Polygonatum / 药学学报

italic>Polygonatum franchetii Hua is a medicinal plant endemic to China from Polygonatum Mill. The chloroplast genomes of two P. franchetii individuals sampled from two different habitats were sequenced by using the DNBSEQ-T7 high-throughput sequencing platform. After assembly and annotation, the two complete chloroplast genomes were characterized, and then comparative and phylogenetic analyses were performed with other published chloroplast genome sequences from Polygonatum. The whole chloroplast genomes of the two P. franchetii individuals were 155 942 and 155 962 bp in length, with a large single copy region (LSC, 84 670 and 84 722 bp), a small single copy region (SSC, 18 564 and 18 566 bp) and a pair of reverse repeats (IRa/IRb, 26 354 and 26 337 bp), respectively. Both of them contained 113 genes, including 79 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Comparative analyses showed that the genome length, the guanine and cytosine (GC) content, genes content and order were highly conserved between the two P. franchetii individuals and among different Polygonatum species. The detected repeat sequences, including dispersed repeats, tandem repeats and simple sequence repeats (SSRs), were also relatively similar in types and positions, though showing a slightly difference in number. No significant expansion or contraction of the inverted repeat regions was found. Sequences variation between the two P. franchetii individuals was lower than that among different Polygonatum species. Besides, coding sequences (CDS) showed less divergence than noncoding sequences, and sequence divergence of IRs regions was lower than that of the LSC and SSC regions, both intraspecifically and interspecifically. Eight sequences with high nucleotide diversity among different species were screened, all of which were found located in the LSC and SSC regions. Phylogenetic inference showed that all Polygonatum species clustered into a monophyletic clade with a 100% bootstrap value, within which, species in section Verticillata formed a distinct group, section Sibirica and section Polygonatum were sister groups. The two P. franchetii individuals grouped together and showed the closest phylogenetic affinity to P. stenophyllum Maxim., belonging to the section Verticillata. The chloroplast genome of P. franchetii and its phylogenetic position in Polygonatum were comprehensively investigated and clearly elucidated in this study, the results may lay a foundation for the resource development and utilization of P. franchetii, as well as further molecular identification and phylogenetic studies of medicinal Polygonatum species.

Phylogenetic analysis of chloroplast genome of Tussilago farfara L / 药学学报

italic>Tussilago farfara L. is a perennial herb of Tussilago genus in the Compositae family. Its dried buds and leaves have good biological activities and have a long history of medicinal use in China and Europe. In this paper, we investigated the whole chloroplast genome characteristics, sequence duplication, structural variation and phylogeny of the Tussilago farfara L. After sequencing the Tussilago farfara L. chloroplast genome using Illumination technology, the complete Tussilago farfara L. chloroplast genome was further obtained by assembly and annotation, followed by a series of inverted repeat-large single copy/small single copy region contraction and expansion analysis, genome sequence variation, etc. The sequences of 13 homologous plants downloaded from NCBI were used to construct a neighbor-joining phylogenetic tree. The results showed that the total GC content of the chloroplast genome was 37.4% and the length was 150 300 bp; 125 genes were annotated, including 82 protein-coding genes, 35 tRNAs and 8 rRNAs; 148 (simple sequence repeats, SSR) loci were detected, and the relative synonymous codon usage showed that 31 codons out of 64 codons had a usage of >1. In the phylogenetic analysis, the chloroplast genomes of the seven species of Asteraceae, including the Yulin Tussilago farfara L., were highly conserved, and the sequence variation of the (large single-copy, LSC) and (small single-copy, SSC) regions was higher than that of the (inverted repeat, IR) region. This is in general agreement with the reported phylogeny of Yulin Tussilago farfara L. In this study, we obtained a high quality chloroplast genome and analyzed its genome characteristics, codon preference, SSR characteristics, SC/IR boundary, sequence variation and phylogeny, which can provide a basis for species identification, genetic diversity analysis and resource development of this medicinal plant.

Phylogeny and virulence gene profile of Francisella salimarina / 中华微生物学和免疫学杂志

Objective:To study the molecular phylogeny and virulence gene profile of Francisella salimarina. Methods:Phylogenetic analysis of Francisella salimarina was performed based on the global genome data of related Francisella species on GenBank database. The consistency in phylogenetic analysis based on single marker genes (such as 16S rRNA gene, rpoB gene and mdh gene) and the core genome as compared. Virulence genes and antibiotic resistance genes were annotated using the virulence factor database (VFDB) and the Comprehensive Antibiotic Resistance Database (CARD), respectively. The virulence of Francisella salimarina was analyzed with a Galleria mellonella (greater wax moth) infection model using Francisella philomiragia ATCC 25015 T as reference strain. Results:The phylogenetic analysis revealed that Francisella salimarina was closely related to Francisella philomiragia. The phylogenetic tree based on mdh gene was highly similar to that based on the core genome. Francisella salimarina could be differentiated from other related species by 16S rRNA gene or mdh gene, with the latter being more accurate. Eight Francisella salimarina strains carried multiple virulence genes, mainly involved in secretion, adhesion, immune regulation, motility and stress survival. Moreover, beta-lactam resistance gene blaFPH was identified in all eight strains. Francisella salimarina showed high lethality in the Galleria mellonella infection model, which was similar to Francisella philomiragia ATCC 25015 T. Conclusions:Francisella salimarina was a rare pathogen with similar pathogenicity to Francisella philomiragia. The mdh gene could be used as a molecular target for rapid identification of Francisella salimarina.

The molecular investigations on the subgenus Artemisia Less. of the genus Artemisia L. (Asteraceae) in Turkey / Investigações moleculares sobre o subgênero Artemisia Less. do gênero Artemisia L. (Asteraceae) na Turquia

The genus Artemisia L. of the family Asteraceae is systematically very complex. The aim of this study was to evaluate taxonomic positions of taxa of the subgenus Artemisia belonging to the genus Artemisia in Turkey using some molecular techniques. In this molecular study, 44 individuals belong to 14 species of the subgenus Artemisia were examined. Analyses were performed on the combined dataset using maximum parsimony, maximum likelihood and Bayesian inference and Molecular parameters obtained from co-evaluations of sequences of the psbA-trnH, ITS and ETS regions of examined individuals were used in the phylogenetic tree drawing. According to the results of this study, two molecular groups have been formed based on the DNA sequence similarity of the species, but there are no obvious morphological characters corresponding to two molecular groups. There is no also agreement between the two molecular groups and the two morphological groups formed according to the hairiness condition of the receptacle of species. Due to the lack of molecular significance of their receptacles with or without hair, dividing of the subgenus Artemisia species into new subgenera or sections was not considered appropriate. Likewise, it has been found that with or without hair on the corolla lobes of the central hermaphrodite disc flowers have no molecular significance. It was found that there were no gene flow and hybridization between the 14 species of the subgenus Artemisia and these 14 species were found completed their speciation. This study is important as it is the first molecular based study relating with belong to subgenus Artemisia species growing naturally in Turkey. In addition, new haplotypes related to the populations of Turkey belonging to the subgenus Artemisia taxa were reported by us for the first time and added to the GenBank database.

O gênero Artemisia L. da família Asteraceae é sistematicamente muito complexo. O objetivo deste estudo foi avaliar as posições taxonômicas de táxons do subgênero Artemisia pertencentes ao gênero Artemisia na Turquia usando algumas técnicas moleculares. Neste estudo molecular, 44 indivíduos pertencentes a 14 espécies do subgênero Artemisia foram examinados. As análises foram realizadas no conjunto de dados combinado usando máxima parcimônia, máxima verossimilhança e inferência bayesiana e parâmetros moleculares obtidos a partir de coavaliações de sequências das regiões psbA-trnH, ITS e ETS de indivíduos examinados foram usados no desenho da árvore filogenética. De acordo com os resultados deste estudo, dois grupos moleculares foram formados com base na similaridade da sequência de DNA das espécies, mas não há caracteres morfológicos óbvios correspondentes a dois grupos moleculares. Também não há concordância entre os dois grupos moleculares e os dois grupos morfológicos formados de acordo com a condição de pilosidade do receptáculo da espécie. Devido à falta de significado molecular de seus receptáculos com ou sem cabelo, a divisão das espécies do subgênero Artemisia em novos subgêneros ou seções não foi considerada apropriada. Da mesma forma, verificou-se que com ou sem cabelo nos lobos da corola das flores do disco hermafrodita central não tem significado molecular. Constatou-se que não houve fluxo gênico e hibridização entre as 14 espécies do subgênero Artemisia e essas 14 espécies concluíram sua especiação. Este estudo é importante porque é o primeiro estudo de base molecular relacionado com espécies pertencentes ao subgênero Artemisia crescendo naturalmente na Turquia. Além disso, novos haplótipos relacionados às populações da Turquia pertencentes ao subgênero Artemisia taxa foram relatados por nós pela primeira vez e adicionados ao banco de dados do GenBank.

The molecular investigations on the subgenus Artemisia Less. of the genus Artemisia L. (Asteraceae) in Turkey

Abstract The genus Artemisia L. of the family Asteraceae is systematically very complex. The aim of this study was to evaluate taxonomic positions of taxa of the subgenus Artemisia belonging to the genus Artemisia in Turkey using some molecular techniques. In this molecular study, 44 individuals belong to 14 species of the subgenus Artemisia were examined. Analyses were performed on the combined dataset using maximum parsimony, maximum likelihood and Bayesian inference and Molecular parameters obtained from co-evaluations of sequences of the psbA-trnH, ITS and ETS regions of examined individuals were used in the phylogenetic tree drawing. According to the results of this study, two molecular groups have been formed based on the DNA sequence similarity of the species, but there are no obvious morphological characters corresponding to two molecular groups. There is no also agreement between the two molecular groups and the two morphological groups formed according to the hairiness condition of the receptacle of species. Due to the lack of molecular significance of their receptacles with or without hair, dividing of the subgenus Artemisia species into new subgenera or sections was not considered appropriate. Likewise, it has been found that with or without hair on the corolla lobes of the central hermaphrodite disc flowers have no molecular significance. It was found that there were no gene flow and hybridization between the 14 species of the subgenus Artemisia and these 14 species were found completed their speciation. This study is important as it is the first molecular based study relating with belong to subgenus Artemisia species growing naturally in Turkey. In addition, new haplotypes related to the populations of Turkey belonging to the subgenus Artemisia taxa were reported by us for the first time and added to the GenBank database.

Resumo O gênero Artemisia L. da família Asteraceae é sistematicamente muito complexo. O objetivo deste estudo foi avaliar as posições taxonômicas de táxons do subgênero Artemisia pertencentes ao gênero Artemisia na Turquia usando algumas técnicas moleculares. Neste estudo molecular, 44 indivíduos pertencentes a 14 espécies do subgênero Artemisia foram examinados. As análises foram realizadas no conjunto de dados combinado usando máxima parcimônia, máxima verossimilhança e inferência bayesiana e parâmetros moleculares obtidos a partir de coavaliações de sequências das regiões psbA-trnH, ITS e ETS de indivíduos examinados foram usados no desenho da árvore filogenética. De acordo com os resultados deste estudo, dois grupos moleculares foram formados com base na similaridade da sequência de DNA das espécies, mas não há caracteres morfológicos óbvios correspondentes a dois grupos moleculares. Também não há concordância entre os dois grupos moleculares e os dois grupos morfológicos formados de acordo com a condição de pilosidade do receptáculo da espécie. Devido à falta de significado molecular de seus receptáculos com ou sem cabelo, a divisão das espécies do subgênero Artemisia em novos subgêneros ou seções não foi considerada apropriada. Da mesma forma, verificou-se que com ou sem cabelo nos lobos da corola das flores do disco hermafrodita central não tem significado molecular. Constatou-se que não houve fluxo gênico e hibridização entre as 14 espécies do subgênero Artemisia e essas 14 espécies concluíram sua especiação. Este estudo é importante porque é o primeiro estudo de base molecular relacionado com espécies pertencentes ao subgênero Artemisia crescendo naturalmente na Turquia. Além disso, novos haplótipos relacionados às populações da Turquia pertencentes ao subgênero Artemisia taxa foram relatados por nós pela primeira vez e adicionados ao banco de dados do GenBank.

Chloroplast Genome Structure of Stemona tuberosa and Phylogenetic Analysis Based on PacBio Sequencing / 中国实验方剂学杂志

ObjectiveTo obtain high-quality chloroplast genome information on Stemona tuberosa and clarify its structure， sequence features， and phylogenetic status. MethodThe Illumina NovaSeq 6000 and PacBio RS Ⅱ platforms were used for library construction and sequencing of S. tuberosa， respectively. The data from both sequencing platforms were combined and subjected to bioinformatics analysis for genome assembly and base correction， resulting in a high-quality chloroplast genome. Subsequently， sequence features， repetitive sequences， gene diversity， and phylogeny were analyzed. ResultThe chloroplast genome size of S. tuberosa was determined to be 154 379 bp. The structure of the chloroplast genome followed the typical quadripartite circular form， consisting of a pair of inverted repeat regions （IRs） with a length of 27 074 bp， a small single-copy region （SSC） of 17 924 bp， and a large single-copy region （LSC） of 82 307 bp. The average GC content was 37.86%. A total of 121 genes were annotated， including 30 tRNA genes， four rRNA genes， and 87 protein-coding genes. Among them， six tRNA genes and 12 protein-coding genes contained introns. In the chloroplast genome of S. tuberosa， 49 long repetitive sequences and 59 single-nucleotide simple sequence repeats （SSRs） were identified. Comparative analysis of chloroplast genomes among four Stemona species revealed high diversity in the ycf1 and ndhF genes. The phylogenetic tree constructed based on the chloroplast genome showed consistent classification with the current taxonomic status of S. tuberosa. ConclusionThe high-quality chloroplast genome of S. tuberosa was successfully assembled， providing valuable information on the structure and sequence features of chloroplast genomes in four Stemona species， including S. tuberosa. These findings lay a foundation for the identification， evolution， and phylogenetic studies of medicinal plants in the genus Stemona.

Chloroplast genome resolution and phylogenetic analysis of Ardisia crispa var. amplifolia and Ardisia crispa var. dielsii / 药学学报

italic>Ardisia crispa (Thunb.) A. DC. is a traditional Miao medicinal herb with significant therapeutic effects in the treatment of sore throat, tonsillitis, edema of nephritis and bruising and rheumatism, etc. Ardisia crispa var. amplifolia and Ardisia crispa var. dielsii are varieties of A. crispa. A. crispa var. amplifolia and A. crispa var. dielsii are controversial in terms of species evolutionary relationships and taxonomic identification. In this study, we sequenced the whole genome sequences of A. crispa var. amplifolia and A. crispa var. dielsii chloroplasts using Illumina platform, assembled, annotated and characterized them, compared the structural features and degree of variation among chloroplast genomes using bioinformatics methods, and also downloaded constructing phylogenetic trees to analyze the phylogenetic relationships of chloroplasts in Primulaceae and Myrsinaceae using whole genome sequence information. The results showed that the complete chloroplast genome sequences of A. crispa var. amplifolia and A. crispa var. dielsii were 156 749 bp and 156 748 bp in length, with 132 genes annotated, including 87 protein-coding genes; the codon preference of A/U was greater than that of G/C; The differences in the coding regions of rps15 and rpoB genes in the comparative genome analysis can be used as loci for molecular identification of the two species; the differences in the coding regions of ycf1, ycf2, rpoC1, ycf3, petD and rpl16 genes in the chloroplast genome compared with those of the same genus can be used as loci for identification of the genus. In the phylogenetic results, A. crispa var. amplifolia and A. crispa var. dielsii were clustered together with 100% support, indicating that they are closely related. In this research, we analyzed the chloroplast genome structure and phylogenetic relationships of A. crispa var. amplifolia and A. crispa var. dielsii, providing an important theoretical basis for their molecular identification, genetic variation, breeding and phylogenetic analysis.

Chloroplast genomic characterization and phylogenetic analysis of Castanopsis hystrix / 生物工程学报

The structure and size of the chloroplast genome of Castanopsis hystrix was determined by Illumina HiSeq 2500 sequencing platform to understand the difference between C. hystrix and the chloroplast genome of the same genus, and the evolutionary position of C. hystrix in the genus, so as to facilitate species identification, genetic diversity analysis and resource conservation of the genus. Bioinformatics analysis was used to perform sequence assembly, annotation and characteristic analysis. R, Python, MISA, CodonW and MEGA 6 bioinformatics software were used to analyze the genome structure and number, codon bias, sequence repeats, simple sequence repeat (SSR) loci and phylogeny. The genome size of C. hystrix chloroplast was 153 754 bp, showing tetrad structure. A total of 130 genes were identified, including 85 coding genes, 37 tRNA genes and 8 rRNA genes. According to codon bias analysis, the average number of effective codons was 55.5, indicating that the codons were highly random and low in bias. Forty-five repeats and 111 SSR loci were detected by SSR and long repeat fragment analysis. Compared with the related species, chloroplast genome sequences were highly conserved, especially the protein coding sequences. Phylogenetic analysis showed that C. hystrix is closely related to the Hainanese cone. In summary, we obtained the basic information and phylogenetic position of the chloroplast genome of red cone, which will provide a preliminary basis for species identification, genetic diversity of natural populations and functional genomics research of C. hystrix.

Chloroplast DNA reveals genetic population structure in Sinomenium acutum in subtropical China / 中草药·英文版

OBJECTIVE@#The population density and diversity of Sinomenium acutum (Menispermaceae) have been greatly reduced recently by overharvesting for medicinal purposes in China. Therefore, it is urgent that the remaining populations are investigated, and that strategies for the utilization and conservation of this species are developed. This study aimed to find the possible glacial refugia and define the genetic diversity of S. acutum for its proper utilization and conservation.@*METHODS@#A total of 77 S. acutum samples were collected from four locations, Qinling Mountains, Daba Mountains, Dalou Mountains, and Xuefeng Mountains, in subtropical China. Genetic diversity among and between these populations were phylogenetically analyzed using four chloroplast DNA molecular markers (atpI-atpH, trnQ-5'rps16, trnH-psbA and trnL-trnF).@*RESULTS@#A total of 14 haplotypes (C1 to C14) were found in collected samples. Haplotypes C1 and C3 were shared among all populations, with C3 as the ancestral haplotype. Haplotypes C11 and C12 diverged the most from C3 and other haplotypes. No obvious phylogeographic structure was found in four locations using the GST/NST test. There is no evidence of rapid demographic expansion in S. acutum based on the mismatch distribution, and the results of Tajima's D test, and Fu's FS test. Our analyses of molecular variance revealed a high level of genetic variation within populations. In contrast, the genetic differentiation among S. acutum populations was low, indicating frequent gene flow.@*CONCLUSION@#Xuefeng, Dalou, and Daba Mountains were possible glacial refugia for the populations of S. acutum. C1, C3, C11 and C12 haplotypes of S. acutum should be carefully preserved and managed for their genetic value.

Lineage and phylogenetic analysis of HPV-16, -18 in saliva of HNSCC patients

Aim: Head and Neck Squamous Cell Carcinoma (HNSCC) is a global health problem whose incidence varies by geographic region and race according to risk factors. Human papillomavirus (HPV) infection is a significant risk factor for HNSCC. HPV-16 and HPV-18 are two forms of HPV that are carcinogenic. HNSCCs that are HPV positive have a better prognosis rather than HPV negative. The purpose of this research was to characterize HPV-16, -18 variations in the saliva of HNSCC patients by examining the genetic diversity of HPV-16, -18 utilizing the full E6, E7, and L1 genes. Methods:The case-control research included 15 patients with HNSCC and 15 healthy volunteers. Unstimulated entire saliva samples were obtained from the case and control groups by spitting method. Genomic DNA was isolated from all saliva samples. A PCR reaction was used to determine the presence of HPV in saliva. HPV-positive samples were genotyped and data were analyzed. We conducted a variant study on the HPV-16, -18 E6, and E7 genes. Results: Three patients with HNSCC were HPV-positive for two HPV genotypes out of 30 people diagnosed with HPV-DNA. HPV-16 and -18 were the most common genotypes. The HPV-16, -18 E6, and E7 genes were sequenced and compared to the HPV-16, -18 (E6, E7) prototype sequence. In all, HPV-16 lineages A1 and HPV-18 lineages A3 were discovered. Conclusion: Regarding the variation of HPV found in Iranian HNSCC patients, the need for further studies in HPV genotyping was seen. Sequencing HPV genes in HNSCC may help answer questions about HPV genotyping in the Iranian population. HPV genotype analysis aids in the development of vaccinations against HNSCC, halting disease progression and preventing HPV-associated HNSCC

Seasonal droughts during the Miocene drove the evolution of Capparaceae towards Neotropical seasonally dry forests / Las sequías estacionales del Mioceno impulsaron la evolución de Capparaceae hacia los bosques neotropicales estacionalmente secos

Abstract Introduction: Neotropical seasonally dry forest (NSDF) climatic constraints increased endemism, and phylogenetic niche conservatism in species that are restricted to this biome. NSDF have a large number of endemic Capparaceae taxa, but it is unknown if phylogenetic niche conservatism has played a role in this pattern. Objective: We carried out an evolutionary analysis of the climatic niche of neotropical species of Capparaceae to identify whether the climatic constraints of NSDF have played a major role throughout the family's evolutionary history. Methods: Using three chloroplastic (ndhF, matK, rbcL) and one ribosomal (rsp3) DNA sequences, we proposed a date phylogeny to reconstruct the evolutionary climatic niche dynamics of 24 Neotropical species of Capparaceae. We tested the relationship between niche dissimilarity and phylogenetic distance between species using the Mantel test. Likewise, we used a set of phylogenetic comparative methods (PGLS) on the phylogeny of Capparaceae to reconstruct the main evolutionary historic events in their niche. Results: Capparaceae originated in humid regions and subsequently, convergent evolution occurred towards humid and dry forest during the aridification phases of the Middle Miocene (16-11 Mya). However, adaptation towards drought stress was reflected only during the precipitation of the coldest quarter, where we found phylogenetic signal (Pagel λ) for gradual evolution and, therefore, evidence of phylogenetic niche conservatism. We found convergent species-specific adaptations to both drought stress and rainfall during the Miocene, suggesting a non-phylogenetic structure in most climatic variables. Conclusions: Our study shows how the Miocene climate may have influenced the Capparaceae speciation toward driest environments. Further, highlights the complexity of climatic niche dynamics in this family, and therefore more detailed analyses are necessary in order to better understand the NSDF climatic constrictions affected the evolution of Capparaceae.

Resumen Introducción: Las limitaciones climáticas del bosque neotropical estacionalmente seco (NSDF) produjeron endemismo y conservadurismo filogenético del nicho en especies restringidas a este bosque. En las Caparáceas neotropicales se ha encontrado endemismo en los NSDF, pero se desconoce si el conservadurismo de nicho filogenético ha influido en su evolución. Objetivos: Se llevó a cabo un análisis evolutivo del nicho climático de las especies neotropicales de Capparaceae para evaluar si las limitaciones climáticas del bosque neotropical estacionalmente seco (NSDF) han jugado un papel importante a lo largo de la historia evolutiva de la familia. Métodos: Usando tres secuencias de ADN cloroplastico (ndhF, matK, rbcL) y una ribosomal (rsp3) se propuso una filogenia datada para reconstruir la dinámica evolutiva del nicho climático de 24 especies Neotropicales de Capparaceae. Utilizando la prueba de Mantel, se realizaron análisis para establecer si hay diferencia de nicho y la distancia filogenética entre especies. Asimismo, se emplearon un conjunto de métodos comparativos filogenéticos sobre la filogenia de la familia para reconstruir los principales eventos históricos evolutivos en su nicho. Resultados: Capparaceae se originó en regiones húmedas y posteriormente se dio una evolución convergente hacia bosque húmedo y seco durante las fases de aridificación del Mioceno Medio (16-11 Ma). Sin embargo, la adaptación al estrés por sequía se reflejó solo en la precipitación del cuarto más frío del año, donde se evidencio señal filogenética, evolución gradual y, por lo tanto, evidencia de conservadurismo de nicho filogenético. También se hallaron especies con adaptaciones convergentes específicas tanto al estrés por sequía como a las lluvias durante el Mioceno, sugiriendo la carencia de estructura filogenética en la mayoría de las variables climáticas. Conclusiones: Este estudio muestra cómo el clima del Mioceno pudo haber influenciado la especiación de Capparaceae hacia ambientes mas secos. Además, la compleja dinámica del nicho climático en esta familia y, por lo tanto, la necesidad de realizar análisis más detallados para comprender mejor como las constricciones climáticas del NSDF afectaron la evolución de Capparaceae.

Filogenia y resistencia de cepas de Escherichia coli productoras de betalactamasas de espectro extendido a los antibióticos en pacientes con cáncer hospitalizados en Perú / Phylogeny and antimicrobial resistance of extended-spectrum beta-lactamase- producing Escherichia coli from hospitalized oncology patients in Perú

Introducción. Las infecciones asociadas con la atención en salud constituyen un problema de salud pública porque aumentan la morbimortalidad de los pacientes, sobre todo de aquellos con factores de riesgo, como la inmunosupresión debida a enfermedades oncológicas. Es importante conocer la diversidad genética de los principales microorganimos causantes de infecciones hospitalarias mediante la vigilancia epidemiológica tradicional y la epidemiología molecular, para hacer un mejor seguimiento y detectar brotes tempranamente. Objetivo. Determinar el grupo filogenético y la resistencia a antibióticos de las cepas de Escherichia coli aisladas de pacientes con cáncer hospitalizados. Materiales y métodos. Se hizo un estudio de tipo transversal que incluyó 67 cepas de Escherichia coli productoras de betalactamasas de espectro extendido (BLEE). Se determinó el grupo filogenético, el perfil de resistencia a los antibióticos, los genes de resistencia a betalactámicos, el tipo de las muestras y los servicios de hospitalización de donde fueron recuperadas. Resultados. El grupo filogenético más frecuente fue el B2 (36 %). El 57 % de las cepas B2 fueron aisladas de muestras de orina y el 33 % provenía del servicio de urología. La resistencia a ciprofloxacino y gentamicina fue de 91 y 53 %, respectivamente, y el 79 % de las cepas tenía el gen blaCTX-M. Se encontró una relación significativa (p<0,05) entre los grupos filogenéticos y la resistencia a ciprofloxacina, así como a la edad del paciente. Conclusión. El filogrupo de E. coli predominante fue el B2. Se evidenció una gran resistencia a ciprofloxacina y gentamicina, una proporción elevada de cepas BLEE con el blaCTX-M, y una relación entre el grupo filogenético y la resistencia a ciprofloxacino.

Introduction: Healthcare-associated infections are a public health problem due to the increased morbimortality of patients, especially those with risk factors such as immunosuppression due to oncological diseases. It is essential to determine the genetic diversity of the main microorganisms causing healthcare infections by combining traditional epidemiological surveillance and molecular epidemiology for better outbreak follow-up and early detection. Objective: To determine the phylogenetic group and antibiotic resistance of Escherichia coliisolated from hospitalized oncologic patients. Materials and methods: We conducted a cross-sectional study of 67 strains of ESBL-producing Escherichia coli to determine their phylogenetic group and described their antibiotic resistance profile, beta-lactam resistance genes, as well as the type of sample and the hospitalization areas from which they were recovered. Results: The most frequent phylogenetic group was B2 (36%); 57% of B2 strains were isolated from urine and 33% came from the urology department. Resistance to ciprofloxacin and gentamicin was 92% and 53%, respectively, and 79% of the strains had the blaCTX-Mgene. A significant association (p<0.05) was found between the phylogenetic groups, ciprofloxacin resistance, and the age of the patients. Conclusion: The predominant E. coli phylogroup was B2. We evidenced high resistance to ciprofloxacin and gentamicin, a high proportion of ESBL strains with the blaCTX-M gene, and a significant association between the phylogenetic group and the resistance to ciprofloxacin.

Monkeypox virus genome sequence from an imported human case in Colombia / Secuencia genómica del virus de la viruela símica de un caso importado en Colombia

Introduction: Monkeypox virus (MPXV) is an enveloped double-stranded DNA virus with a genome of approximately 197.209 bp. The current classification divides MPXV into three clades: Clade I (Central African or Congo Basin clade) and clades IIa and IIb (West African clades). Objective: To report the complete genome and phylogenetic analysis of a human monkeypox case detected in Colombia. Materials and methods: Exudate from vesicular lesions was obtained from a male patient with recent travel history to Spain. A direct genomic approach was implemented in which total DNA from the sample was purified through a column-based method, followed by sequencing on the Nanopore GridION. Reads were aligned against the MPXV reference genome using minimap2 v.2.24 and phylogenetic inference was performed using maximum likelihood estimation. Results: A total of 11.951 reads mapped directly to a reference genome with 96.8% of coverage (190.898 bp). Conclusion: Phylogenetic analysis of the MPXV circulating in Colombia demonstrated its close relationship to clade IIb responsible for the multi-country outbreak in 2022.

Introducción. El virus de la viruela del mono (MPXV) está compuesto por un genoma de ADN bicatenario, aproximadamente, de 197.209 pb. La clasificación actual agrupa el MPXV en tres clados: clado I (de la cuenca del Congo en África central), y clados IIa y IIb (de África occidental). Objetivo. Reportar el genoma completo y el análisis filogenético de un caso humano de viruela símica detectado en Colombia. Materiales y métodos. Se obtuvo exudado de lesiones vesiculares de un paciente varón con el antecedente de un viaje reciente a España. Se implementó un enfoque directo, en el cual se purificó el ADN total de la muestra mediante un método basado en columnas, seguido de la secuenciación directa en la plataforma Nanopore GridION. Las lecturas se alinearon con el genoma de referencia del MPXV, utilizando minimap2, v.2.24, y la inferencia filogenética fue realizada mediante la estimación por máxima verosimilitud. Resultados. Un total de 11.951 lecturas se alinearon directamente con el genoma de referencia con una cobertura del 96,8 % (190.898 pb). Conclusión. El análisis filogenético del MPXV circulante en Colombia demostró su estrecha relación con el clado de África occidental (clado IIb) responsable del brote en múltiples países en el 2022.

Andrographis Echioides Molecular Characterization and Phylogenetic Study Using DNA Barcoding Technique

With the advancement in various molecular diagnostic tools, DNA Barcoding has emerged as a gold standard molecular diagnostic tool across the globe. Since ancient times, medicinal plants have been widely used in Indian Ayurvedic medicine for treating a variety of ailments. Plants of the genus Andrographis have been extensively used for treating different types of ailments. In this study, rarely studied medicinal plant species were isolated, sequenced at the genetic level and studied for their evolutionary characteristics using phylogenetic analysis. In the present study, the identity of A. echioides was confirmed by targeting different barcoding genes such as ribulose-bisphosphate carboxylase, internal transcribed spacer, RNA polymerase-beta subunit, maturase K, and photosystem II protein D1 genes using a phylogenetic approach. After successful isolation and amplification of genomic DNA, specific primers were utilised for sequencing of each barcoding gene, followed by nucleotide BLAST analysis to determine the sequence percent identity of each gene with that from other plant species. The best homologs were then utilised for conducting phylogenetic analysis which confirmed the identity of the plant as Andrographis echioides.