Genetics and Molecular Biology, Volume: 45, Issue: 1, Published: 2022
  • Frequency of CFTR variants in southern Brazil and indication for modulators therapy in patients with cystic fibrosis Human And Medical Genetics

    Lima, Eliandra da Silveira; Pezzin, Luíse Sgarabotto; Fensterseifer, Ana Carolina; Pinto, Leonardo Araújo

    Abstract in English:

    Abstract This is a descriptive cross-sectional study that aims to determine the distribution of the CFTR causing variant in a group of patients at a cystic fibrosis (CF) center in southern Brazil, as well as to describe causing variants that are treatable with mutation-specific drugs. Ninety-two patients from a CF reference center were assessed in this research, all of them with a clinical diagnosis of CF and both alleles identified with pathogenic variants. The most prevalent causing variants were F508del, R1162X, G542X, and N1303K. As for patients with a mutation-specific drug indication, 69.6 % were candidates for the use of Elexacaftor/Tezacaftor/Ivacaftor (Trikafta®), 44.6 % for the use of Tezacaftor/Ivacaftor (Symdeko®), and 35.9 % for the use of Lumacaftor/Ivacaftor (Orkambi®). For the use of Ivacaftor (Kalydeco®), only two patients (2.2 %) were candidates following the Brazilian agency approval. According to the FDA, 10 patients would be candidates for Ivacaftor (10.9 %). Causing variants of classes I and II, which are related to a major severity of the illness, were identified in 135 of 184 alleles (73.3 %). In this study, more than 2/3 of the patients were candidates for the use of CFTR modulators therapy.
  • The expression of LRRN4 was correlated with the progression and prognosis of colon adenocarcinoma (COAD) patients Human And Medical Genetics

    Zhang, Yuxian; Xie, Jianlan; Liu, Diangang; Zhu, Shengtao; Zhang, Shutian

    Abstract in English:

    Abstract Our present study aims to investigate the value of LRRN4 in the progression and prognosis of COAD patients. All COAD and adjacent sample data was downloaded from TCGA database. Survival analysis was performed according to Kaplan-Meier method. The real-time quantitative PCR and immunohistochemistry analysis were conducted for validation in cell lines and tissues. The GSEA was conducted to find functional KEGG pathways. Multivariate Cox regression proportional hazard mode was used to determine whether LRRN4 expression was an independent prognostic factor. The LRRN4 expression in COAD samples were significantly higher than that in adjacent samples, which was consistent with our experiments in cell lines and tissues. Along with the increase of TNM Stage, LRRN4 expression had an increasing tendency. The COAD patients with high LRRN4 expression showed undesirable prognoses. Additionally, the TGF-β signaling pathway, WNT signaling pathway and other 25 pathways were significantly activated in the high LRRN4 expression group. In conclusion, high LRRN4 expression was closely related to the onset of COAD and it was a poor prognostic factor for COAD patients.
  • COVID-19 impact on the diagnosis of Inborn Errors of Metabolism: Data from a reference center in Brazil Human And Medical Genetics

    Sebastião, Fernanda Medeiros; Michelin-Tirelli, Kristiane; Bender, Fernanda; Lopes, Franciele Fátima; Moraes, Inamara; Kubaski, Francyne; Giugliani, Roberto; Burin, Maira

    Abstract in English:

    Abstract The COVID-19 pandemic led to the reorganization of health care in several countries, including Brazil. Inborn Errors of Metabolism (IEM) are a group of rare and difficult to diagnose genetic diseases caused by pathogenic variants in genes that code for enzymes, cofactors, or structural proteins affecting different metabolic pathways. The aim of this study was to evaluate how COVID-19 affected the diagnosis of patients with IEM during the first year of the pandemic in Brazil comparing two distinct periods: from March 1st, 2019 to February 29th, 2020 (TIME A) and from March 1st, 2020 to February 28th, 2021 (TIME B), by the analysis of the number of tests and diagnoses performed in a Reference Center in South of Brazil. In the comparison TIME A with TIME B, we observe a reduction in the total number of tests performed (46%) and in the number of diagnoses (34%). In both periods analyzed, mucopolysaccharidoses (all subtypes combined) was the most frequent LD suspected and/or confirmed. Our data indicates a large reduction in the number of tests requested for the investigation of IEM and consequently a large reduction in the number of diagnoses caused by the COVID-19 pandemic leading to a significant underdiagnosis of IEM.
  • Haplotypes of single cancer driver genes and their local ancestry in a highly admixed long-lived population of Northeast Brazil Human And Medical Genetics

    Galisa, Steffany Larissa Galdino; Jacob, Priscila Lima; Farias, Allysson Allan de; Lemes, Renan Barbosa; Alves, Leandro Ucela; Nóbrega, Júlia Cristina Leite; Zatz, Mayana; Santos, Silvana; Weller, Mathias

    Abstract in English:

    Abstract Admixed populations have not been examined in detail in cancer genetic studies. Here, we inferred the local ancestry of cancer-associated single nucleotide polymorphisms (SNPs) and haplotypes of a highly admixed Brazilian population. SNP array was used to genotype 73 unrelated individuals aged 80-102 years. Local ancestry inference was performed by merging genotyped regions with phase three data from the 1000 Genomes Project Consortium using RFmix. The average ancestry tract length was 9.12-81.71 megabases. Strong linkage disequilibrium was detected in 48 haplotypes containing 35 SNPs in 10 cancer driver genes. All together, 19 risk and eight protective alleles were identified in 23 out of 48 haplotypes. Homozygous individuals were mainly of European ancestry, whereas heterozygotes had at least one Native American and one African ancestry tract. Native-American ancestry for homozygous individuals with risk alleles for HNF1B, CDH1, and BRCA1 was inferred for the first time. Results indicated that analysis of SNP polymorphism in the present admixed population has a high potential to identify new ancestry-associated alleles and haplotypes that modify cancer susceptibility differentially in distinct human populations. Future case-control studies with populations with a complex history of admixture could help elucidate ancestry-associated biological differences in cancer incidence and therapeutic outcomes.
  • Characterization of the 3'UTR of the BTD gene and identification of regulatory elements and microRNAs Human And Medical Genetics

    Silva, Gerda Cristal Villalba; Borsatto, Taciane; Schwartz, Ida Vanessa Doederlein; Sperb-Ludwig, Fernanda

    Abstract in English:

    Abstract Reduced biotinidase activity is associated with a spectrum of deficiency ranging from total deficiency to heterozygous levels, a finding that is not always explained by the pathogenic variants observed in the BTD gene. The investigation of miRNAs, regulatory elements and variants in the 3’UTR region may present relevance in understanding the genotype-phenotype association. The aims of the study were to characterize the regulatory elements of the 3’UTR of the BTD gene and identify variants and miRNAs which may explain the discrepancies observed between genotype and biochemical phenotype. We evaluated 92 individuals with reduced biotinidase activity (level of heterozygotes = 33, borderline = 35, partial DB = 20 or total DB= 4) with previously determined BTD genotype. The 3’UTR of the BTD gene was Sanger sequenced. In silico analysis was performed to identify miRNAs and regulatory elements. No variants were found in the 3’UTR. We found 97 possible miRNAs associated with the BTD gene, 49 predicted miRNAs involved in the alanine, biotin, citrate and pyruvate metabolic pathways and 5 genes involved in biotin metabolism. Six AU-rich elements were found. Our data suggest variants in the 3'UTR of BTD do not explain the genotype-phenotype discrepancies found in Brazilian individuals with reduced biotinidase.
  • APOE and KLF14 genetic variants are sex-specific for low high-density lipoprotein cholesterol identified by a genome-wide association study Human And Medical Genetics

    Lee, Ying-Hui; Chang, Ya-Sian; Hsieh, Chih-Chang; Wang, Rong-Tsorng; Chang, Jan-Gowth; Chen, Chung-Jen; Chang, Shun-Jen

    Abstract in English:

    Abstract To demonstrate the loci that relate to high-density lipoprotein cholesterol (HDL-C) levels and genetic sex heterogeneity, we enrolled 41,526 participants aged between 30 and 70 years old from the Taiwan Biobank in a genome-wide association study. We applied the Manhattan plot to display the p-values estimated for the relationships between loci and low HDL-C. A total of 160 variants were significantly associated with low HDL-C. The genotype TT of rs1364422 located in the KLF14 gene has 1.30 (95% CI=1.20 - 1.42) times the risk for low-HDL compared to genotype CC in females (log(-p) =8.98). Moreover, the genes APOC1, APOE, PVRL2, and TOMM40 were associated significantly with low-HDL-C in males only. Excluding the variants with high linkage disequilibrium, we revealed the rs429358 located in APOE as the major genetic variant for lowering HDL-C, in which genotype CT has 1.24 (95% CI= 1.16 - 1.32) times the risk. In addition, we also examine 12 genes related to HDL-C in both sexes, including LPL, ABCA1, APOA5, BUD13, ZPR1, ALDH1A2, LIPC, CETP, HERPUD1, LIPG, ANGPTL8, and DOCK6. In conclusion, low-HDL-C is a genetic and sex-specific phenotype, and we discovered that the APOE and KLF14 are specific to low-HDL-C for men and women, respectively.
  • Increased runs of homozygosity in the autosomal genome of Brazilian individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies investigated by chromosomal microarray analysis Human And Medical Genetics

    Correia-Costa, Gabriela Roldão; Sgardioli, Ilária Cristina; Santos, Ana Paula dos; Araujo, Tânia Kawasaki de; Secolin, Rodrigo; Lopes-Cendes, Iscia; Gil-da-Silva-Lopes, Vera Lúcia; Vieira, Társis Paiva

    Abstract in English:

    Abstract Runs of homozygosity (ROH) in the human genome may be clinically relevant. The aim of this study was to report the frequency of increased ROH of the autosomal genome in individuals with neurodevelopmental delay/intellectual disability and/or multiple congenital anomalies, and to compare these data with a control group. Data consisted of calls of homozygosity from 265 patients and 289 controls. In total, 7.2% (19/265) of the patients showed multiple ROH exceeding 1% of autosomal genome, compared to 1.4% (4/289) in the control group (p=0.0006). Homozygosity ranged from 1.38% to 22.12% among patients, and from 1.53 to 2.40% in the control group. In turn, 1.9% (5/265) of patients presented ROH ≥10Mb in a single chromosome, compared to 0.3% (1/289) of individuals from the control group (p=0.0801). By excluding cases with reported consanguineous parents (15/24), the frequency of increased ROH was 3.4% (9/250) among patients and 1.7% (5/289) in the control group, considering multiple ROH exceeding 1% of the autosome genome and ROH ≥10Mb in a single chromosome together, although not statistically significant (p=0.1873). These results reinforce the importance of investigating ROH, which with complementary diagnostic tests can improve the diagnostic yield for patients with such conditions.
  • Evolutionary history of the SARS-CoV-2 Gamma variant of concern (P.1): a perfect storm Human And Medical Genetics

    Yépez, Yuri; Marcano-Ruiz, Mariana; Bezerra, Rafael S; Fam, Bibiana; Ximenez, João PB; Silva Jr, Wilson A; Bortolini, Maria Cátira

    Abstract in English:

    Abstract Our goal was to describe in more detail the evolutionary history of Gamma and two derived lineages (P.1.1 and P.1.2), which are part of the arms race that SARS-CoV-2 wages with its host. A total of 4,977 sequences of the Gamma strain of SARS-CoV-2 from Brazil were analyzed. We detected 194 sites under positive selection in 12 genes/ORFs: Spike, N, M, E, ORF1a, ORF1b, ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF10. Some diagnostic sites for Gamma lacked a signature of positive selection in our study, but these were not fixed, apparently escaping the action of purifying selection. Our network analyses revealed branches leading to expanding haplotypes with sites under selection only detected when P.1.1 and P.1.2 were considered. The P.1.2 exclusive haplotype H_5 originated from a non-synonymous mutational step (H3509Y) in H_1 of ORF1a. The selected allele, 3509Y, represents an adaptive novelty involving ORF1a of P.1. Finally, we discuss how phenomena such as epistasis and antagonistic pleiotropy could limit the emergence of new alleles (and combinations thereof) in SARS-COV-2 lineages, maintaining infectivity in humans, while providing rapid response capabilities to face the arms race triggered by host immuneresponses.
  • Cytochrome b sequence of the Mazama americana jucunda Thomas, 1913 holotype reveals Mazama bororo Duarte, 1996 as its junior synonym Animal Genetics

    Mantellatto, Aline Meira Bonfim; González, Susana; Duarte, José Maurício Barbanti

    Abstract in English:

    Abstract The small red brocket deer, Mazama bororo Duarte, 1996 was described based on karyotypical and morphological characters. However, the original description of Mazama americana jucunda suggested that this subspecies could represent the same taxon as Mazama bororo. This assumption was based on the type locality of Mazama americana jucunda and on morphological similarities between Mazama americana jucunda and Mazama bororo. To solve this question, we obtained DNA sequences of the holotype of Mazama americana jucunda and compared it with other species of Mazama, including the holotype of M. bororo. A phylogenetic tree was obtained to verify the relationships among these taxa. The results clearly showed that M. americana jucunda and M. bororo represent the same biological entity. Therefore, the oldest name available for the small red brocket occurring in the Atlantic Forest of southern Brazil should be Mazama jucunda, remaining M. bororo as a junior synonym. We emphasise the importance of using DNA from museum specimens, especially from holotypes, in order to obtain a more accurate taxonomic identification. We also highlight the importance of application of valid names for labelling all aspects of biodiversity research, as well as for monitoring and conservation efforts.
  • Chromosomal diversity in three species of Lycosa Latreille, 1804 (Araneae, Lycosidae): Inferences on diversification of diploid number and sexual chromosome systems in Lycosinae Animal Genetics

    Cavenagh, Analiza Fernanda; Rincão, Matheus Pires; Dias, Felipe Cordeiro; Brescovit, Antonio Domingos; Dias, Ana Lúcia

    Abstract in English:

    Abstract Lycosa is one of the most speciose genera in Lycosidae, including species with different sexual chromosome systems (SCS). We carried out cytogenetic analyses in three species of Lycosa, revealing that L. erythrognatha and L. sericovittata share 2n ♂ = 22 and SCS X1X20 while L. gr. nordenskjoldi presents 2n ♂ = 19 and SCS XO, composed only of acrocentric chromosomes. All species shared pericentromeric heterochromatin. Nonetheless, one specimen of L. sericovittata carried two chromosomes with terminal heterochromatin and L. gr. nordenskjoldi showed four chromosomes with interstitial heterochromatin plus another chromosome with terminal C-bands. The pericentromeric heterochromatin of all species as well as the terminal heterochromatic blocks in L. sericovittata were CMA3+. The 18S rDNA sites varied in number and type of bearing chromosomes both at inter and intrapopulational levels, with the highest variation in L. gr. nordenskjoldi. These differences may be related to gene dispersal due to the influence of transposition elements and translocation events. Despite these variations, all species shared ribosomal sites in pair 5. This study demonstrated intra and interspecific chromosomal variability of Lycosa, suggesting that chromosomal rearrangements are related to the diversification of diploid number and SCS in this group of spiders.
  • Molecular data reveal a complex population genetic structure for Psalidodon scabripinnis (Teleostei: Characidae) in the Atlantic Rainforest, Brazil Animal Genetics

    Limeira, Daniel Meneguello; Santos, Mateus Henrique; Mateus, Rogério Pincela; Ruas, Claudete de Fátima; Almeida, Mara Cristina de; Moreira Filho, Orlando; Artoni, Roberto Ferreira

    Abstract in English:

    Abstract Recently renamed, Psalidodon scabripinnis populations of Serra da Mantiqueira, previously known as Astyanax scabripinnis have been deeply studied in the last years. These populations are small and isolated and occur very close to the watershed between Paraíba do Sul River basin and Upper Paraná River basin, in Serra da Mantiqueira region in the Atlantic Rainforest. These conditions arouse the interest in knowing theor genetic conservation status and how they responded to the separation between the two rivers basins. Therefore, we accessed the genetic diversity of five P. scabripinnis populations of this region with microsatellites and mitochondrial data. The results showed a complex structure pattern that doesn’t match the simple basin separation and a reasonably conservation status when compared with other populations of the same family or with similar natural history.
  • Fire ants: What do rural and urban areas show us about occurrence, diversity, and ancestral state reconstruction? Animal Genetics

    Ramalho, Manuela de O.; Menino, Leonardo; Souza, Rodrigo F.; Kayano, Débora Y.; Alves, Juliana M. C.; Harakava, Ricardo; Nagatani, Victor H.; Silva, Otávio G. M.; Bueno, Odair C.; Morini, Maria S. C.

    Abstract in English:

    Abstract In South America, Solenopsis saevissima and S. invicta are the most common fire ants. Nests are founded in areas under anthropic interference like urban or rural areas, but S. invicta is found preferentially in those with the greatest anthropic interference. However, we do not know the rates at which they exist in anthropized areas next to high density of native vegetation. Areas with 60 to 90% of native Atlantic Forest were selected to verify the occurrence of both species in rural and urban areas. We investigated the molecular diversity and applied the reconstruction of the ancestral state analysis for each species. A total of 186 nests were analyzed and we found that the two species had the same proportion in the urban area. However, S. saevissima had a higher rate of prevalence in the rural area, in addition to having a greater number of haplotypes and ancestry associated with this type of habitat for the region. S. invicta had the same number of haplotypes in both rural and urban regions, and less haplotypic diversity. We conclude that S. saevissima is a species typically associated with rural areas and S. invicta, although present, is not dominant in urban areas.
  • DNA barcode reveals candidate species of Scinax and Ololygon (Anura: Hylidae) in Atlantic Forest Animal Genetics

    Nogueira, Lídia; Rodrigues Filho, Luís Fernando da Silva; Solé, Mirco; Affonso, Paulo Roberto Antunes de Mello; Siqueira, Sergio; Sampaio, Iracilda

    Abstract in English:

    Abstract Molecular species delimitation methods are efficient tools to identify species, including the discovery of new taxa and cryptic organisms, thus being useful to biodiversity studies. In the present work, 16S mitochondrial sequences and cytochrome oxidase I (COI) were used to evaluate the richness of species in the genus Scinax and Ololygon from a biodiversity hotspot in Atlantic Forest. A total of 109 specimens formally belonging to eight species of Scinax and three species of Ololygon were collected in 13 localities along the state of Bahia (northeastern Brazil) and one site in Espírito Santo (southeastern Brazil). Of the Scinax species collected in this study, three were morphologically differentiated from other described species and identified as putative new species (Scinax sp.1, Scinax sp.2 and Scinax sp.3). The species delimitations were inferred using three different methods: ABGD, PTP and mPTP which allowed recognizing 11 Scinax species and five Ololygon species. Scinax sp. 1, Scinax sp. 2 and Scinax sp. 3, have been confirmed as new putative species and Ololygon argyreornata possibly contains cryptic species. We suggest additional studies, including morphological and bioacoustic data to validate these new putative species.
  • Genetic structure and diversity of the Chilean flat oyster Ostrea chilensis (Bivalvia: Ostreidae) along its natural distribution from natural beds subject to different fishing histories Animal Genetics

    Toro, Jorge E.; Oyarzún, Pablo A.; Toledo, Felipe E.; Navarro, Jorge M.; Illesca, Alex F.; Gardner, Jonathan P.A.

    Abstract in English:

    Abstract Ostrea chilensis (Küster, 1844), the flat oyster, is native to Chile and New Zealand. In Chile, it occurs in a few natural beds, from the northern part of Chiloé Island (41 ºS) to the Guaitecas Archipelago (45 ºS). This bivalve is slow growing, broods its young, and has very limited dispersal potential. The Ostrea chilensis fishery has been over-exploited for a number of decades such that in some locations oysters no longer exist. The aim of this study was to study the genetic diversity of the Chilean flat oyster along its natural distribution to quantify the possible impact of the dredge fishery on wild populations. The genetic structure and diversity of Ostrea chilensis from six natural beds with different histories of fishing activity were estimated. Based on mitochondrial (Cytb) and nuclear (ITS1) DNA sequence variation, our results provide evidence that genetic diversity is different among populations with recent history of wild dredge fishery efforts. We discuss the possible causes of these results. Ultimately, such new information may be used to develop and apply new management measures to promote the sustainable use of this valuable marine resource.
  • Flowering process in soybean under water deficit conditions: A review on genetic aspects Plant Genetics

    Molinari, Mayla Daiane Correa; Fuganti-Pagliarini, Renata; Barbosa, Daniel de Amorim; Marin, Silvana Regina Rockenbach; Marin, Daniel Rockenbach; Rech, Elíbio Leopoldo; Mertz-Henning, Liliane Marcia; Nepomuceno, Alexandre Lima

    Abstract in English:

    Abstract Soybean is a key crop in many countries, being used from human food to the animal industry due to its nutritional properties. Financially, the grain chain moves large sums of money into the economy of producing countries. However, like other agricultural commodities around the world, it can have its final yield seriously compromised by abiotic environmental stressors, like drought. As flowers imply in pods and in grains inside it to minimize damages caused by water restriction, researchers have focused on understanding flowering-process related genes and their interactions. Here a review dedicated to the soybean flowering process and gene network involved in it is presented, describing gene interactions and how genes act in this complex mechanism, also ruled by environmental triggers such as day-light and circadian cycle. The objective was to gather information and insights on the soybean flowering process, aiming to provide knowledge useful to assist in the development of drought-tolerant soybean lines, minimizing losses due to delays or anticipation of flowering and, consequently, restraining financial and productivity losses.
  • The first complete plastome of Mimusops coriacea (A. DC.) Miq. (Sapotaceae) Plant Genetics

    Trad, Rafaela Jorge; Silva, Saura Rodrigues da; Amaral, Maria do Carmo Estanislau do

    Abstract in English:

    Abstract Mimusops coriacea (A. DC.) Miq. (Sapotoideae, Sapotaceae, Ericales) is native to Madagascar and the Comoro Islands. This species is cultivated in many countries around the world and grows on sand in coastal vegetation. Here we sequenced, assembled, and annotated the first complete chloroplast genome of M. coriacea. The newly assembled chloroplast was analyzed with other available chloroplasts of Sapotaceae. Our results found a general conserved structure. The complete chloroplast genome has 159,689 bp, including 133 genes distributed in four regions: a large single-copy region of 88,887 bp, a small single-copy region of 18,618 bp, and two inverted repeats of 26,092 bp each. Our maximum likelihood phylogenetic tree was generated with 80 protein-coding genes and recovered a monophyletic Sapotaceae sister to a clade formed by Ebenaceae + Primulaceae. In our analysis, Mimusops coriacea clustered with the other eight species of Sapotaceae included in the study.
  • Identification of bZIP transcription factors and their responses to brown spot in pear Plant Genetics

    Liu, Li; Zhang, Yuxin; Wang, Qi; Tao, Xingyu; Fang, Jing; Zheng, Wenjuan; Zhu, Liwu; Jia, Bing; Heng, Wei; Li, Shaowen

    Abstract in English:

    Abstract Basic leucine zipper (bZIP) is a conserved transcription factor (TF) widely present in eukaryotes, and it plays an important role in regulating plant growth and stress responses. To better understand the white pear bZIP gene family, comprehensive bioinformatics analysis of the pear genome was performed. A total of 84 PbbZIP genes were identified, which were divided into 13 subfamilies by phylogenetic analysis. The 84 PbbZIP genes were all located in the nucleus, and 77 of those genes were unevenly distributed across the 17 chromosomes of white pear. The other 7 PbbZIP genes were located on the scaffold. Subsequent expression profile analysis showed that PbbZIP genes in exocarp were significantly upregulated or downregulated in ‘Huangguan’ pear with brown spot (BS) compared with healthy pear and in response to hormonal treatment with gibberellin A3 (GA3). These results provide helpful insights into the characteristics of PbbZIP genes and their responses to BS in ‘Huangguan’ pear.
  • Structural and evolutive features of the Plinia phitrantha and P. cauliflora plastid genomes and evolutionary relationships within tribe Myrteae (Myrtaceae) Plant Genetics

    Machado, Lilian de Oliveira; Stefenon, Valdir Marcos; Vieira, Leila do Nascimento; Nodari, Rubens Onofre

    Abstract in English:

    Abstract Plinia phitrantha and P. cauliflora are Myrtaceae species with recognized horticultural and pharmacological potential. Nevertheless, studies on molecular genetics and the evolution of these species are absent in the literature. In this study, we report the complete plastid genome sequence of these species and an analysis of structural and evolutive features of the plastid genome within the tribe Myrteae. The two plastid genomes present the conserved quadripartite structure and are similar to already reported plastid genomes of Myrteae species concerning the size, number, and order of the genes. A total of 69-70 SSR loci, 353 single nucleotide polymorphisms, and 574 indels were identified in P. phitrantha and P. caulifora. Observed evolutive features of the plastid genomes support the development of programs for the conservation and breeding of Plinia. The phylogenomic analysis based on the complete plastid genome sequence of 15 Myrteae species presented a robust phylogenetic signal and evolutive traits of the tribe. Ten hotspots of nucleotide diversity were identified, evidence of purifying selection was observed in 27 genes, and relative conservation of the plastid genomes was confirmed for Myrteae. Altogether, the outcomes of the present study provide support for planning conservation, breeding, and biotechnological programs for Plinia species.
  • Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin Genetic Of Microorganisms

    Costa, Sávio S.; Lago, Leticia, A. B.; Silva, Artur; Graças, Diego A. das; Lameira, Jerônimo; Baraúna, Rafael A.

    Abstract in English:

    Abstract Bacteriocins are antimicrobial peptides expressed by bacteria through ribosomal activity. In this study, we analyzed the diversity of bacteriocin-like genes in the Tucuruí-HPP using a whole-metagenome shotgun sequencing approach. Three layers of the water column were analyzed (photic, aphotic and sediment). Detection of bacteriocin-like genes was performed with blastx using the BAGEL4 database as subject sequences. In order to calculate the abundance of bacteriocin-like genes we also determined the number of 16S rRNA genes using blastn. Taxonomic analysis was performed using RAST server and the metagenome was assembled using IDBA-UD in order to recover the full sequence of a zoocin which had its three-dimensional structure determined. The photic zone presented the highest number of reads affiliated to bacteriocins. The most abundant bacteriocins were sonorensin, Klebicin D , pyocin and colicin. The zoocin model was composed of eight anti-parallel β-sheets and two α-helices with a Zn2+ ion in the active site. This model was considerably stable during 10 ns of molecular dynamics simulation. We observed a high diversity of bacteriocins in the Tucuruí-HPP, demonstrating that the environment is an inexhaustible source for prospecting these molecules. Finally, the zoocin model can be used for further studies of substrate binding and molecular mechanisms involving peptidoglycan degradation.
  • Genomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese Genetic Of Microorganisms

    Comerlato, Carolina Baldisserotto; Prichula, Janira; Siqueira, Franciele Maboni; Ritter, Ana Carolina; Varela, Ana Paula Muterle; Mayer, Fabiana Quoos; Brandelli, Adriano

    Abstract in English:

    Abstract Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations.
  • In the screening of alternative insecticides to control Aedes aegytpti larvae 2-methylanthraquinone showed no genotoxicity and low toxicity to zebrafish (Danio rerio) Mutagenesis

    Piau, Tathyana Benetis; Fascineli, Maria Luiza; Moura, Diego Sousa; Albernaz, Lorena Carneiro; Espindola, Laila Salmen; Grisolia, Cesar Koppe

    Abstract in English:

    Abstract The threats posed by insecticide resistance to Aedes aegypti in the context of controlling dengue have led to an urgent search for an environmentally safer alternative chemical with more effective larvicidal properties. Among many molecules tested, 2-methylanthraquinone showed the lowest LC50 for A. aegypti in a previous study and the highest LC50 for zebrafish embryos. Embryos were exposed at concentrations of 1.0, 2.19, 4.78, 10.46, 22.87, 50.0 and 100.0 mg/L, and malformations and mortality were significantly observed only at the highest exposures of 50 and 100 mg/L after 96 h. Micronucleus test and comet assay in zebrafish adults were both negative after exposures at 6.25, 12.5, 25.0, 50.0 and 100.0 mg/L for 96 h. Several biochemical biomarkers were analyzed in adults, and 2-methylanthraquinone did not interfere with acetylcholinesterase activity. The lactate dehydrogenase activity was higher at concentrations of 25 and 100 mg/L. Glutathione-S-Transferase (GST) activities were tested in the gill and body (muscle tail). The gill was more sensitive than body for GST activity after exposure to 2-methylanthraquinone, showing the highest activities, and 2-methylanthraquinone showed low toxicity to a non-target organism.
  • Perspectives in Myrtaceae evolution from plastomes and nuclear phylogenies Evolutionary Genetics

    Balbinott, Natalia; Rodrigues, Nureyev Ferreira; Guzman, Frank Lino; Turchetto-Zolet, Andreia Carina; Margis, Rogerio

    Abstract in English:

    Abstract Myrtaceae is a large and species-rich family of woody eudicots, with prevalent distribution in the Southern Hemisphere. Classification and taxonomy of species belonging to this family is quite challenging, sometimes with difficulty in species identification and producing phylogenies with low support for species relationships. Most of the current knowledge comes from few molecular markers, such as plastid genes and intergenic regions, which can be difficult to handle and produce conflicting results. Based on plastid protein-coding sequences and nuclear markers, we present a topology for the phylogenetic relationships among Myrtaceae tribes. Our phylogenetic estimate offers a contrasting topology over previous analysis with fewer markers. Plastome phylogeny groups the tribes Syzygieae and Eucalypteae and individual chloroplast genes produce divergent topologies, especially among species within Myrteae tribe, but also in regard to the grouping of Syzygieae and Eucalypteae. Results are consistent and reproducible with both nuclear and organellar datasets. It confronts previous data about the deep nodes of Myrtaceae phylogeny.
  • LINC00974 sponges miR-33a to facilitate cell proliferation, invasion, and EMT of ovarian cancer through HMGB2 upregulation Cellular, Molecular And Developmental Genetics

    Liu, Weiwei; Cheng, Jing

    Abstract in English:

    Abstract The function and mechanism of long intergenic non-protein coding RNA 974 (LINC00974) are rarely reported in ovarian cancer (OC). The study aimed to investigate how LINC00974 affects the progression of OC. The expression levels of LINC00974, microRNA-33a (miR-33a), and high mobility group box 2 (HMGB2) mRNA were detected by qRT-PCR. The LINC00974/miR-33a/HMGB2 axis was confirmed by dual-luciferase reporter, RNA-binding protein immunoprecipitation (RIP), and biotinylated RNA pull-down assays. A series of in vitro experiments were employed to assess the effects of LINC00974/miR-33a/HMGB2 axis on the proliferation, invasion and epithelial mesenchymal transition (EMT) of OC cells. Results showed that LINC00974 and HMGB2 mRNA expression were upregulated in OC cells, while miR-33a expression was downregulated. HMGB2 was a direct target gene of miR-33a. LINC00974 act as a competing endogenous RNA (ceRNA) to directly bind with miR-33a, thereby upregulated HMGB2 expression. Notably, silencing of LINC00974 suppressed cell proliferation, invasion and EMT of OC cells, whereas miR-33a knockdown partially reversed the phenotypes of LINC00974 on OC cells. Overall, our study demonstrated that LINC00974 sponges miR-33a to promote cell proliferation, invasion, and EMT of OC through HMGB2 upregulation. LINC00974/miR-33a/HMGB2 axis may be an important signaling pathway in the progression of OC.
  • MT1G inhibits the growth and epithelial-mesenchymal transition of gastric cancer cells by regulating the PI3K/AKT signaling pathway Cellular, Molecular And Developmental Genetics

    Xu, Guofeng; Fan, Linfeng; Zhao, Shufeng; OuYang, Canhui

    Abstract in English:

    Abstract Gastric carcinoma (GC) is a malignant tumor that has high mortality and morbidity worldwide. Although many efforts have been focused on the development and progression of GC, the underlying functional regulatory mechanism of GC needs more clarification. Metallothionein 1G (MT1G) is a member of the metallothionein family (MTs), and hypermethylation of MT1G occurred in a variety of cancers, including gastric cancer. However, the functional mechanism of MT1G in GC remains unclear. Here, we demonstrated that MT1G was down-regulated in GC tissues and cells. Overexpression of MT1G inhibited cell proliferation, foci formation and cell invasion, while knockdown of MT1G increased cell proliferation, foci formation and cell invasion. In addition, MT1G overexpression inhibited cell cycle progression and MT1G deficiency exerted opposite phenotype. p-AKT was negatively regulated by MT1G. In summary, our study reveals that MT1G exerts crucial role in regulating of cell proliferation and migration of gastric cancer, providing new insights for MT1G-related pathogenesis and a basis for developing new strategies for treatment of GC.
  • EPO activates PI3K-IKKα-CDK1 signaling pathway to promote the proliferation of Glial Cells under hypoxia environment Cellular, Molecular And Developmental Genetics

    Hu, Gejile; Wang, Ting; Ma, Chunjie

    Abstract in English:

    Abstract Erythropoietin (EPO), supports the function and survival of neurons through astrocytes and has a protective role in neonatal asphyxia brain injury; yet, its mechanism of action remains unclear. As a neuroprotective factor, EPO is also used in the treatment of various diseases, such as neurodegenerative diseases, Parkinson’s disease, traumatic brain injury, by decreasing inflammatory reaction, resisting apoptosis, and lowering oxidative stress. The aim of this study was to examine the effect and mechanism of EPO on promoting human brain glial cell proliferation under hypoxia in vitro. Under CoC12-induced hypoxia, after adding EPO, high-throughput sequencing was used to screen out meaningful up-regulated and significant differentially expressed genes PI3K, IKKα CDK1 related to proliferation, and make further verification by qPCR and western blotting. Under hypoxia, EPO promoted cell proliferation and the expression of PI3K while this effect was inhibited (along with a decrease of downstream genes IKKα and CDK1 decreased) after adding PI3K inhibitor to cell culture. EPO can promote cell proliferation and CDK1 expression, while after inhibiting CDK1 expression, the promotion of EPO on cell proliferation was eliminated. These data proved that EPO promotes the proliferation of U251 cells by activating the PI3K-IKKα-CDK1 signaling pathway under CoC12-induced hypoxia.
  • Comparative and phylogenetic analyses of Swertia L. (Gentianaceae) medicinal plants (from Qinghai, China) based on complete chloroplast genomes Genomics And Bioinformatics

    Xu, Xin; Li, Jinping; Chu, Ran; Luan, Mengjie; Wang, Hongyu; Song, Kexin; Wei, Shixia; Shi, Yuhua; Zhu, Shixin; Wei, Zhen

    Abstract in English:

    Abstract Swertia L. is a large genus in Swertiinae (Gentianaceae). In China, many Swertia species are used as traditional Tibetan medicines, known as “Zangyinchen” or “Dida”. However, the phylogenetic relationships among Swertia medicinal plants and their wild relatives have remained unclear. In this study, we sequenced and assembled 16 complete chloroplast (cp) genomes of 10 Swertia species, mainly distributed in Qinghai Province, China. The results showed that these species have typical structures and characteristics of plant cp genomes. The sizes of Swertia cp genomes are ranging from 149,488 bp to 154,097 bp. Most Swertia cp genomes presented 134 genes, including 85 protein coding genes, eight rRNA genes, 37 tRNA genes, and four pseudogenes. Furthermore, the GC contents and boundaries of cp genomes are similar among Swertia species. The phylogenetic analyses indicated that Swertia is a complex polyphyletic group. In addition, positive selection was found in psaI and petL genes, indicating the possible adaptation of Qinghai Swertia species to the light environment of the Qinghai-Tibet plateau. These new cp genome data could be further investigated to develop DNA barcodes for Swertia medicinal plants and for additional systematic studies of Swertia and Swertiinae species.
  • High-quality genome assembly of Pseudocercospora ulei the main threat to natural rubber trees Genomics And Bioinformatics

    González-Sayer, Sandra; Oggenfuss, Ursula; García, Ibonne; Aristizabal, Fabio; Croll, Daniel; Riaño-Pachon, Diego M.

    Abstract in English:

    Abstract Pseudocercospora ulei is the causal agent of South American Leaf Blight (SALB), the main disease affecting Hevea brasiliensis rubber tree, a native species to the Amazon. Rubber tree is a major crop in South American countries and SALB disease control strategies would benefit from the availability of genomic resources for the fungal pathogen. Here, we assembled and annotated the P. ulei genome. Shotgun sequencing was performed using second and third generation sequencing technologies. We present the first P. ulei high-quality genome assembly, the largest among Mycosphaerellaceae, with 93.8 Mbp, comprising 215 scaffolds, an N50 of 2.8 Mbp and a BUSCO gene completeness of 97.5%. We identified 12,745 protein-coding gene models in the P. ulei genome with 756 genes encoding secreted proteins and 113 genes encoding effector candidates. Most of the genome (80%) is composed of repetitive elements dominated by retrotransposons of the Gypsy superfamily. P. ulei has the largest genome size among Mycosphaerellaceae, with the highest TE content. In conclusion, we have established essential genomic resources for a wide range of studies on P. ulei and related species.
  • Mosquito long non-coding RNAs are enriched with Transposable Elements Genomics And Bioinformatics

    Melo, Elverson Soares de; Wallau, Gabriel Luz

    Abstract in English:

    Abstract Long non-coding RNAs (lncRNAs) lack coding capacity and mounting evidence suggests that they have a regulatory role in diverse organisms. Most knowledge about lncRNAs comes from studies on vertebrates, including a structural association between lncRNAs and transposable elements (TEs). TE sequences are genomic parasites found in all branches of life and are particularly active and abundant in insect genomes. Here we investigate the contribution of TEs to lncRNA biogenesis in Aedes albopictus and Culex quinquefasciatus. We found that a large fraction of lncRNA loci co-occurs with TE loci in both species. Around 40% of A. albopictus and 52% of C. quinquefasciatus lncRNAs show some association with TEs. Most of the lncRNA/TE associations are represented by TE-derived sequences that are expressed as one or all exons of lncRNAs, including five lncRNAs that seem to influence immune-related genes involved in antiviral response. The contribution of TEs to lncRNAs also varies among the different types of TEs. The Gypsi superfamily is particularly enriched in lncRNAs sequences. In sum, this study demonstrates that transposable elements substantially contribute to lncRNAs biogenesis in A. albopictus and C. quinquefasciatus and may have an impact on regulatory modulation in these species.
  • Gene Expression Analysis Platform (GEAP): A highly customizable, fast, versatile and ready-to-use microarray analysis platform Genomics And Bioinformatics

    Nunes, Itamar José Guimarães; Recamonde-Mendoza, Mariana; Feltes, Bruno César

    Abstract in English:

    Abstract There are still numerous challenges to be overcome in microarray data analysis because advanced, state-of-the-art analyses are restricted to programming users. Here we present the Gene Expression Analysis Platform, a versatile, customizable, optimized, and portable software developed for microarray analysis. GEAP was developed in C# for the graphical user interface, data querying, storage, results filtering and dynamic plotting, and R for data processing, quality analysis, and differential expression. Through a new automated system that identifies microarray file formats, retrieves contents, detects file corruption, and solves dependencies, GEAP deals with datasets independently of platform. GEAP covers 32 statistical options, supports quality assessment, differential expression from single and dual-channel experiments, and gene ontology. Users can explore results by different plots and filtering options. Finally, the entire data can be saved and organized through storage features, optimized for memory and data retrieval, with faster performance than R. These features, along with other new options, are not yet present in any microarray analysis software. GEAP accomplishes data analysis in a faster, straightforward, and friendlier way than other similar software, while keeping the flexibility for sophisticated procedures. By developing optimizations, unique customizations and new features, GEAP is destined for both advanced and non-programming users.
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