Abstract in English:Abstract Endometrial cancer (EC) harboring heterozygous POLE proofreading inactivating mutations (POLE-exo*) is associated with an increased number of somatic mutations that result in a distinctive anti-tumor immune response. However, the consequences of such POLE mutations in the context of the missing wild-type allele have not yet been described in endometrial tumors. A 72-year-old woman harboring a germline monoallelic frameshift mutation (p.Pro269fsTer26) in POLE was diagnosed with an EC having a somatic heterozygous mutation in the exonuclease domain of POLE (S459F). Targeted gene sequencing revealed an ultramutated phenotype (381 mutations/Mb) in the tumor and a 2-fold excess of mutations on the DNA leading strand. Additionally, we observed a mutational signature similar to the COSMIC signature 10, a higher mutation rate in this tumor than in endometrial tumors with heterozygous POLE-exo*, and an increased number of T lymphocytes. This is the first report of an ultramutated EC harboring a somatic POLE-exo* mutation in association with a germline loss-of-function mutation in this gene. The absence of a wild type POLE allele led to a particularly high mutational burden.
Abstract in English:Abstract Lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) are the two major subtypes of non–small-cell lung cancer (NSCLC). This study aimed to compare mRNA and circRNA expression patterns between LUSC and LUAD. Cancer tissues from 8 LUSC patients and 12 LUAD patients were collected to obtain mRNA and circRNA expression profiles. The differentially expressed mRNAs (DEmRNAs) and circRNAs (DE-circRNAs) between LUSC and LUAD were screened. Afterwards, miRNA–DEcircRNA pairs and miRNA–DEmRNA pairs were predicted to construct a competing endogenous RNAs (ceRNAs) network, followed by functional enrichment analysis and survival analysis. In total, 635 DEmRNAs and 245 DEcircRNAs were obtained. The ceRNA analysis revealed that genes, such as EPHA2, EPHA7, NTRK2, CDK6, hsa_circ_027570, hsa_circ_006089, and hsa-circ_035997, had distinct expression patterns between LUSC and LUAD. Also, functional enrichment analysis indicated that DEmRNAs were mainly enriched in ERK1 and ERK2 cascade. Survival analyses suggested that STXBP1 and PMEPA1 were associated the prognosis of with both LUAD and LUSC, whereas EPHA2 and CDK6 might serve as prognostic factors for LUSC and LUAD, respectively. In conclusion, genes such as EPHA2, EPHA7, NTRK2, and CDK6 had different patterns in the two major histological subtypes of NSCLC. Notably, EPHA2 and CDK6 might be considered as potential therapeutic targets for LUSC and LUAD, respectively.
Abstract in English:Abstract Copy number variations (CNVs) constitute an important class of variation in the human genome and the interpretation of their pathogenicity considering different frequencies across populations is still a challenge for geneticists. Since the CNV databases are predominantly composed of European and non-admixed individuals, and Brazilian genetic constitution is admixed and ethnically diverse, diagnostic screenings on Brazilian variants are greatly difficulted by the lack of populational references. We analyzed a clinical sample of 268 Brazilian individuals, including patients with neurodevelopment disorders and/or congenital malformations. The pathogenicity of CNVs was classified according to their gene content and overlap with known benign and pathogenic variants. A total of 1,504 autosomal CNVs (1,207 gains and 297 losses) were classified as benign (92.9%), likely benign (1.6%), VUS (2.6%), likely pathogenic (0.2%) and pathogenic (2.7%). Some of the CNVs were recurrent and with frequency increased in our sample, when compared to populational open resources of structural variants: 14q32.33, 22q11.22, 1q21.1, and 1p36.32 gains. Thus, these highly recurrent CNVs classified as likely benign or VUS were considered non-pathogenic in our Brazilian sample. This study shows the relevance of introducing CNV data from diverse cohorts to improve on the interpretation of clinical impact of genomic variations.
Abstract in English:Abstract TBX5 has been linked to Holt-Oram syndrome, with congenital heart defect (CHD) and atrial fibrillation (AF) being two major cardiac phenotypes. However, the prevalence of a TBX5 variation in patients with CHD and AF remains obscure. In this research, by sequencing analysis of TBX5 in 178 index patients with both CHD and AF, a novel heterozygous variation, NM_000192.3: c.577G>T; p.(Gly193*), was identified in one index patient with CHD and AF as well as bicuspid aortic valve (BAV), with an allele frequency of approximately 0.28%. Genetic analysis of the proband’s pedigree showed that the variation co-segregated with the diseases. The pathogenic variation was not detected in 292 unrelated healthy subjects. Functional analysis by using a dual-luciferase reporter assay system showed that the Gly193*-mutant TBX5 protein failed to transcriptionally activate its target genes MYH6 and NPPA. Moreover, the mutation nullified the synergistic transactivation between TBX5 and GATA4 as well as NKX2-5. Additionally, whole-exome sequencing analysis showed no other genes contributing to the diseases. This investigation firstly links a pathogenic variant in the TBX5 gene to familial CHD and AF as well as BAV, suggesting that CHD and AF as well as BAV share a common developmental basis in a subset of patients.
Abstract in English:Abstract Genome-wide association studies focused on searching genes responsible for several diseases. Admixture mapping studies proposed a more efficient alternative capable of detecting polymorphisms contributing with a small effect on the disease risk. This method focuses on the higher values of linkage disequilibrium in admixed populations. To test this, we analyzed 10 genomic regions previously defined as related with colorectal cancer among nine populations and studied the variation pattern of haplotypic structures and heterozygosity values on seven categories of SNPs. Both analyses showed differences among chromosomal regions and studied populations. Admixed Latin-American samples generally show intermediate values. Heterozygosity of the SNPs grouped in categories varies more in each gene than in each population. African related populations have more blocks per chromosomal region, coherently with their antiquity. In sum, some similarities were found among Latin American populations, but each chromosomal region showed a particular behavior, despite the fact that the study refers to genes and regions related with one particular complex disease. This study strongly suggests the necessity of developing statistical methods to deal with di- or tri-hybrid populations, as well as to carefully analyze the different historic and demographic scenarios, and the different characteristics of particular chromosomal regions and evolutionary forces.
Abstract in English:Abstract The purpose of this study was to investigate the expression and clinical value of microRNA-451a (miR-451a) in septic patients and analyze its effect on sepsis-associated cardiac dysfunction and inflammation response. A rat model of sepsis was constructed by cecal ligation and puncture. The expression of miR-451a was measured by quantitative real-time PCR. Receiver operating characteristic (ROC) analysis was used to assess the diagnostic value of serum miR-451a. The cardiac function and inflammatory responses in septic rats were measured to explore the functional role of miR-451a. Serum expression of miR-451a was increased in septic patients compared with healthy controls, and had the ability to distinguish septic patients from healthy volunteers with a sensitivity and specificity of 87.8% and 81.5%, respectively. Elevated serum miR-451a was associated with sepsis severity, as evidenced by the increased expression of miR-451a in septic shock patients and its correlation with key clinical indicators. Significantly upregulated expression of miR-451a was found in septic patients with cardiac dysfunction, and the knockdown of miR-451a in sepsis rats improved cardiac function and inhibited inflammatory responses. All the data revealed that serum miR-451a serves as a candidate diagnostic biomarker of sepsis and a potential parameter to indicate disease severity. The reduction of miR-451a may mitigate sepsis-induced cardiac dysfunction and inflammatory responses.
Abstract in English:Abstract The choline acetyltransferase (ChAT) and vesicular acetylcholine transporter (VAChT) are fundamental to neurophysiological functions of the central cholinergic system. We confirmed and quantified the presence of extracellular ChAT protein in human plasma and also characterized ChAT and VAChT polymorphisms, protein and activity levels in plasma of Alzheimer's disease patients (AD; N = 112) and in cognitively healthy controls (EC; N = 118). We found no significant differences in plasma levels of ChAT activity and protein between AD and EC groups. Although no differences were observed in plasma ChAT activity and protein concentration among ChEI-treated and untreated AD patients, ChAT activity and protein levels variance in plasma were higher among the rivastigmine-treated group (ChAT protein: p = 0.005; ChAT activity: p = 0.0002). Moreover, AD patients homozygous for SNP rs1880676 A allele exhibited higher levels of ChAT activity. Considering this is the first study to report the influence of genetic variability of CHAT locus over ChAT activity in AD patients plasma, it opens a new set of important questions on peripheral cholinergic signaling in AD.
Abstract in English:Abstract Breast cancer is the leading cause of death by cancer among women in less developed regions. In Colombia, few published studies have applied next-generation sequencing technologies to evaluate the genetic factors related to breast cancer. This study characterized the exome of three patients with breast cancer from southwestern Colombia to identify likely pathogenic or disease-related DNA sequence variants in tumor cells. For this, the exomes of three tumor tissue samples from patients with breast cancer were sequenced. The bioinformatics analysis identified two pathogenic variants in Fgfr4 and Nf1 genes, which are highly relevant for this type of cancer. Specifically, variant FGFR4-c.1162G>A predisposes individuals to a significantly accelerated progression of this pathology, while NF1-c.1915C>T negatively alters the encoded protein and should be further investigated to clarify the role of this variant in this neoplasia. Moreover, 27 novel likely pathogenic variants were found and 10 genes showed alterations of pathological interest. These results suggest that the novel variants reported here should be further studied to elucidate their role in breast cancer.
Abstract in English:Abstract Blood methylated cell-free DNA (cfDNA) as a minimally invasive cancer biomarker has great importance in cancer management. Guanylate binding protein 2 (GBP2) has been considered as a possible controlling factor in tumor development. GBP2 gene expression and its promoter methylation status in both plasma cfDNA and tumor tissues of ductal carcinoma breast cancer patients were analyzed using SYBR green comparative Real-Time RT-PCR and, Methyl-specific PCR techniques, respectively in order to find a possible cancer-related marker. The results revealed that GBP2 gene expression and promoter methylation were inversely associated. GBP2 was down-regulated in tumors with emphasis on triple negative status, nodal involvement and higher cancer stages (p<0.0001). GBP2 promoter methylation on both cfDNA and tumor tissues were positively correlated and was detected in about 88% of breast cancer patients mostly in (Lymph node positive) LN+ and higher stages. Data provided shreds of evidence that GBP2 promoter methylation in circulating DNA may be considered as a possible effective non-invasive molecular marker in poor prognostic breast cancer patients with the evidence of its relation to disease stage and lymph node metastasis. However further studies need to evaluate the involvement of GBP2 promoter methylation in progression-free survival or overall survival of the patients.
Abstract in English:Abstract Important pre-Inca civilizations, known by their great political and religious structures, inhabited the northern coast of Peru. Archeological and anthropological studies have shown that people from these villages have hierarchical strata, but the genetic structure has been poorly studied. Here, we aimed to perform a molecular characterization of the Amerindian maternal lineages and the amelogenin gene in skeletons collected from three archeological sites in Lambayeque. Ancient DNA (aDNA) samples were analyzed with conventional PCR to assess the nine-base pair (9 bp) deletion corresponding to mitochondrial haplogroup B and the identification of haplogroups A, C, and D were obtained with PCR-RFLP experiments. The sex was characterized via amplification of the AMEL(X/Y) locus. Haplogroup frequencies were compared with available data from other ancient and modern civilizations from the Peruvian coast and highlands using statistical methods. Our results showed that haplogroup C had the highest frequency, while haplogroup B showed variable diversity in the analyzed populations. The meta-analysis revealed a positive correlation among some coastal villages. We concluded that ancient populations analyzed in our study showed the presence of four Amerindian mitochondrial haplogroups, which is consistent with previous studies.
Abstract in English:Abstract Early age acute leukemia (EAL) shows a high frequency of KMT2A-rearrangements (KMT2A-r). Previous investigations highlighted double-strand breaks arising from maternal exposure to xenobiotics during pregnancy as a risk factor for EAL and KMT2A-r. In this case-control study, we investigated the relationship between EAL and genetic variants of the nonhomologous end-joining (XRCC6 rs5751129, XRCC4 rs6869366 and rs28360071), since they might affect DNA repair capacity, leading to KMT2A-r and leukemogenesis. Samples from 577 individuals (acute lymphoblastic leukemia-ALL, n=164; acute myeloid leukemia-AML, n=113; controls, n=300) were genotyped. No significant association was found for rs5751129 and rs6869366, whereas rs28360071 was associated with an increased risk for ALL with KMT2A-r (IIxID: OR - Odds ratio 2.23, CI 1.17-4.25, p=0.014). Bone marrow samples from ALL patients showed a higher expression of XRCC4 compared to AML patients (p=0.025). Human Splicing Finder 3.1 predicted that the deleted allele of rs28360071 is potentially associated with the activation of a 5’ cryptic splice site in intron 3 of XRCC4. The sequencing of cDNA did not show any differences on the splicing process for the rs28360071 genotypes. Our results suggest that the deleted allele for rs28360071 increases the risk for ALL with KMT2A-r, but not by modifying the XRCC4 expression levels or its structure.
Abstract in English:Abstract Coraciiformes contains more than 200 species with great differences on external morphology and life-style. The evolutionary relationships within Coraciiformes and the phylogenetic placement of Coraciiformes in Aves are still questioned. Mitochondrial genome (mitogenome) sequences are popular markers in molecular phylogenetic studies of birds. This study presented the genome characteristics of three new mitogenomes in Coraciiformes and explored the phylogenetic relationships among Coraciiformes and other five related orders with mitogenome data of 30 species. The sizes of three mitogenomes were 17,383 bp (Alcedo atthis), 17,892 bp (Halcyon smyrnensis) and 17,223 bp (Megaceryle lugubris). Each mitogenome contained one control region and 37 genes that were common in vertebrate mitogenomes. The organization of three mitogenomes was identical to the putative ancestral gene order in Aves. Among 13 available Coraciiform mitogenomes, 12 protein coding genes showed indications of negative selection, while the MT-ND6 presented sign of positive selection or relaxed purifying selection. The phylogenetic results supported that Upupidae and Bucerotidae should be separated from Coraciiformes, and that Coraciiformes is more closely related to Piciformes than to Strigiformes, Trogoniformes and Cuculiformes. Our study provide valuable data for further phylogenetic investigation of Coraciiformes.
Abstract in English:Abstract The freshwater family Siluridae occurs in Eurasia and is especially speciose in South and Southeast Asia, representing an important aquaculture and fishery targets. However, despite the restricted cytogenetic data, a high diploid number variation (from 2n=40 to 92) characterizes this fish group. Considering the large genomic divergence among its species, silurid genomes have experienced an enormous diversification throughout their evolutionary history. Here, we aim to investigate the chromosomal distribution of several microsatellite repeats in 12 Siluridae species and infer about their possible roles in the karyotype evolution that occurred in this group. Our results indicate divergent patterns of microsatellite distribution and accumulation among the analyzed species. Indeed, they are especially present in significant chromosome locations, such as the centromeric and telomeric regions, precisely the ones associated with several kinds of chromosomal rearrangements. Our data provide pieces of evidence that repetitive DNAs played a direct role in fostering the chromosomal differentiation and biodiversity in this fish family.
Abstract in English:Abstract In the present study, the complete characterization of cDNA and genomic sequences of IL-1β and IL-8, as well as the expression profile of these genes in the South American fish pacu (Piaractus mesopotamicus) is provided. The full-length pmIL-1β cDNA was composed of 1208 nucleotides that would produce a precursor peptide with 273 amino acid residues. A putative caspase-1 cleavage site, similar to what is found in mammalian IL-1β, was identified producing a mature peptide with a theoretical molecular weight of 17.21 kDa. The pmIL-8 cDNA sequence consisted of 1019 nucleotides which encoded a 95-amino acid protein with a theoretical molecular weight of 10.43 kDa that showed all typical CXC chemokine features, including a 20-residue signal peptide and four conserved cysteine residues. Constitutive mRNA expression was detected for both genes in the liver, head kidney, gill, intestine, skin and spleen. After a bacterial challenge, up-regulation was detected for both pmIL-1β and pmIL-8 in the spleen and head kidney at 12 h post-infection. At 24 h post-infection there was a decrease in the expression of both genes, with pmIL-8 showing a significant down-regulation in the liver and head kidney when compared to the control groups.
Abstract in English:Abstract The cytogenetic characteristics of five fish species of the Moenkhausia are described, based on the analysis of specimens collected in different headwater. All the species analyzed presented 2n=50 chromosomes. The C-banding revealed a similar distribution pattern of heterochromatic blocks in all the species, except Moenkhausia nigromarginata. The 5S rDNA sites were distributed on multiple chromosome pairs in all five species. Single and multiple histone H1 sites were observed in all the species, and histone H1 was shown to be co-located with the 18S rRNA gene in a single chromosome pair. The U2 snDNA gene was distributed at multiple sites in all the Moenkhausia species. The presence of B microchromosomes was confirmed in Moenkhausia forestii, while individuals of the three study populations of Moenkhausia oligolepis presented three morphologically distinct types of B chromosome. The chromosomal mapping of the 18S rDNA sites using the FISH technique revealed signals in the B chromosomes of M. forestii, while clusters of the H1 histone and U2 snDNA genes were found in the B chromosomes of M. forestii and M. oligolepis. The classical and molecular cytogenetic markers used in this study revealed ample variation in the Moenkhausia karyotypes, reflecting the dynamic nature of the chromosomal evolution.
Abstract in English:Abstract The Cyprinidae family is a highly diversified but demonstrably monophyletic lineage of cypriniform fishes. Among them, the genus Osteochilus contains 35 recognized valid species distributed from India, throughout Myanmar, Laos, Thailand, Malaysia, Indonesian archipelago to southern China. In this study, karyotypes and other chromosomal characteristics of five Osteochilus species occurring in Thailand, namely O. lini, O. melanopleura, O. microcephalus, O. vittatus and O. waandersii were examined using conventional and molecular cytogenetic protocols. Our results showed they possessed diploid chromosome number (2n) invariably 2n = 50, but the ratio of uni- and bi-armed chromosomes was highly variable among their karyotypes, indicating extensive chromosomal rearrangements. Only one chromosome pair bearing 5S rDNA sites occurred in most species, except O. melanopleura, where two sites were detected. In contrast, only one chromosomal pair bearing 18S rDNA sites were observed among their karyotypes, but in different positions. These cytogenetic patterns indicated that the cytogenomic divergence patterns of these Osteochilus species were largely corresponding to the inferred phylogenetic tree. Similarly, different patterns of the distributions of rDNAs and microsatellites across genomes of examined species as well as their different karyotype structures indicated significant evolutionary differentiation of Osteochilus genomes.
Abstract in English:Abstract Rodents of the genus Cerradomys belong to the tribe Oryzomyini and present high chromosome variability with diploid numbers ranging from 2n=46 to 60. Classical cytogenetics and fluorescence in situ hybridization (FISH) with telomeric and whole chromosome-specific probes of another Oryzomyini, Oligoryzomys moojeni (OMO), were used to assess the karyotype evolution of the genus. Results were integrated into a molecular phylogeny to infer the hypothetical direction of chromosome changes. The telomeric FISH showed signals in telomeres in species that diverged early in the phylogeny, plus interstitial telomeric signals (ITS) in some species from the most derived clades (C. langguthi, C. vivoi, C. goytaca, and C. subflavus). Chromosome painting revealed homology from 23 segments of C. maracajuensis and C. marinhus to 32 of C. vivoi. Extensive chromosome reorganization was responsible for karyotypic differences in closely related species. Major drivers for genomic reshuffling were in tandem and centric fusion, fission, paracentric and pericentric inversions or centromere repositioning. Chromosome evolution was associated with an increase and decrease in diploid number in different lineages and ITS indicate remnants of ancient telomeres. Cytogenetics results corroborates that C. goytaca is not a junior synonym of C. subflavus since the karyotypic differences found may lead to reproductive isolation.
Abstract in English:Abstract The expression of morphological differences between the castes of social bees is triggered by dietary regimes that differentially activate nutrient-sensing pathways and the endocrine system, resulting in differential gene expression during larval development. In the honey bee, Apis mellifera, mitochondrial activity in the larval fat body has been postulated as a link that integrates nutrient-sensing via hypoxia signaling. To understand regulatory mechanisms in this link, we measured reactive oxygen species (ROS) levels, oxidative damage to proteins, the cellular redox environment, and the expression of genes encoding antioxidant factors in the fat body of queen and worker larvae. Despite higher mean H2O2 levels in queens, there were no differences in ROS-mediated protein carboxylation levels between the two castes. This can be explained by their higher expression of antioxidant genes (MnSOD, CuZnSOD, catalase, and Gst1) and the lower ratio between reduced and oxidized glutathione (GSH/GSSG). In worker larvae, the GSG/GSSH ratio is elevated and antioxidant gene expression is delayed. Hence, the higher ROS production resulting from the higher respiratory metabolism in queen larvae is effectively counterbalanced by the up-regulation of antioxidant genes, avoiding oxidative damage. In contrast, the delay in antioxidant gene expression in worker larvae may explain their endogenous hypoxia response.
Abstract in English:Abstract Cytogenetic characterization was performed on three wandering spiders: Ctenus amphora Mello-Leitão, 1930, C. crulsi Mello-Leitão, 1930 and C. villasboasi Mello-Leitão, 1949. The three species had similar karyotypes, with 2n = 28 (26 + X1X20) in males, with sex chromosomes exhibiting positive heteropicnosis in meiotic cells. 18S rDNA mapping revealed gene sites at the terminal region of one chromosomal pair for all species, with one C. crulsi individual, showing markings in two pairs. C. villasboasi showed markers only in the pachytene phase. The distribution pattern of constitutive heterochromatin was found to be characteristic for the genus, with markings in the centromeric region of all chromosomes, suggesting an acrocentric morphology for all chromosomes of the three analysed species. The results support the fusion of sex chromosomes as an evolutionary tendency for this spider group.
Abstract in English:Abstract Hummingbirds (Trochilidae) are one of the most enigmatic avian groups, and also among the most diverse, with approximately 360 recognized species in 106 genera, of which 43 are monotypic. This fact has generated considerable interest in the evolutionary biology of the hummingbirds, which is reflected in a number of DNA-based studies. However, only a few of them explored chromosomal data. Given this, the present study provides an analysis of the karyotypes of three species of Neotropical hummingbirds, Anthracothorax nigricollis (ANI), Campylopterus largipennis (CLA), and Hylocharis chrysura (HCH), in order to analyze the chromosomal processes associated with the evolution of the Trochilidae. The diploid number of ANI is 2n=80 chromosomes, while CLA and HCH have identical karyotypes, with 2n=78. Chromosome painting with Gallus gallus probes (GGA1-12) shows that the hummingbirds have a karyotype close to the proposed ancestral bird karyotype. Despite this, an informative rearrangement was detected: an in-tandem fusion between GGA7 and GGA9 found in CLA and HCH, but absent in ANI. A comparative analysis with the tree of life of the hummingbirds indicated that this fusion must have arisen following the divergence of a number of hummingbird species.
Abstract in English:Abstract The wide variation in size and content of eukaryotic genomes is mainly attributed to the accumulation of repetitive DNA sequences, like microsatellites, which are tandemly repeated DNA sequences. Sea turtles share a diploid number (2n) of 56, however recent molecular cytogenetic data have shown that karyotype conservatism is not a rule in the group. In this study, the heterochromatin distribution and the chromosomal location of microsatellites (CA)n, (GA)n, (CAG)n, (GATA)n, (GAA)n, (CGC)n and (GACA)n in Chelonia mydas, Caretta caretta, Eretmochelys imbricata and Lepidochelys olivacea were comparatively investigated. The obtained data showed that just the (CA)n, (GA)n, (CAG)n and (GATA)n microsatellites were located on sea turtle chromosomes, preferentially in heterochromatic regions of the microchromosomes (mc). Variations in the location of heterochromatin and microsatellites sites, especially in some pericentromeric regions of macrochromosomes, corroborate to proposal of centromere repositioning occurrence in Cheloniidae species. Furthermore, the results obtained with the location of microsatellites corroborate with the temperature sex determination mechanism proposal and the absence of heteromorphic sex chromosomes in sea turtles. The findings are useful for understanding part of the karyotypic diversification observed in sea turtles, especially those that explain the diversification of Carettini from Chelonini species.
Abstract in English:Abstract Butia eriospatha is an endemic palm species from the Atlantic Rainforest in Brazil, a biodiversity hotspot. This species is currently listed in the IUCN red list as vulnerable and lacks specific plastid markers for population genetics studies. In addition, the evolutionary relationship within the genus Butia is not yet well resolved. Here, we sequenced and characterized the complete plastid genome (plastome) sequence of B. eriospatha. The complete plastome sequence is 154,048 bp in length, with the typical quadripartite structure. This plastome length and genes content is consistent with other six species from tribe Cocoseae. However, the Inverted Repeat (IR) borders show some variation among the analyzed species from this tribe. Species from the Bactridinae (Astrocaryum and Acrocomia) and Elaeidinae (Elaeis) subtribes present the rps19 gene completely duplicated in the IR region. In contrast, all plastomes sequenced from the subtribe Attaleinae (Butia, Cocos, Syagrus) present one complete CDS of rps19 and one partial copy of rps19. The difference in the IR/LSC junctions between Attaleinae and the sister clades Bactridinae + Elaeidinae might be considered an evolutionary signal and the plastome sequence of B. eriopatha may be used in future studies of population genetics and phylogeny.
Abstract in English:Abstract Terpenes produced by plants comprise a diverse range of secondary metabolites, including volatile organic compounds (VOCs). Terpene VOC production may be altered after damage or by biological stimuli such as bacterial, fungal and insects, and subsequent triggering of plant defense responses. These VOCs originate in plants from two independent pathways: the mevalonate and the methylerythritol phosphate pathways, which utilize dimethylallyl and isopentenyl diphosphates to form the terpenoidal precursors. Phakopsora pachyrhizi fungi causes Asian soybean rust, limiting soybean production and resulting in losses of up to 80% if no control strategies are applied. By using a transcriptome datasets, we investigated the regulation of genes of the mevalonate pathway under different biotic stresses. We studied the impact of P. pachyrhizi infection in vivo expression profile of genes involved in terpenoid and glyceollin biosynthesis in genotypes harboring different resistance genes (Rpp), and across the infection cycle. In addition, we used UPLC and UPGC analysis to evaluate glyceollin and VOC production, respectively, to identify metabolites associated with soybean responses to pathogen infection. The regulation of soybean genes involved in terpene production was influenced by genotypes, depending on the Rpp gene, while glyceollin was induced in all genotypes. Furthermore, a sesquiterpene was identified as a potential marker associated with rust symptoms on soybean.
Abstract in English:Abstract Peanut is a crop of the Kayabi tribe, inhabiting the Xingu Indigenous Park, Brazil. Morphological analysis of Xingu accessions showed variation exceeding that described for cultivated peanuts. This raised questions as to the origin of the Xingu accessions: are they derived from different species, or is their diversity a result of different evolutionary and selection processes? To answer these questions, cytogenetic and genotyping analyses were conducted. The karyotypes of Xingu accessions analyzed are very similar to each other, to an A. hypogaea subsp. fastigiata accession and to the wild allotetraploid A. monticola. The accessions share the number and general morphology of the chromosomes; DAPI+ bands; 5S and 45S rDNA loci distribution and a high genomic affinity with A. duranensis and A. ipaënsis genomic probes. However, the number of CMA3+ bands differs from those determined for A. hypogaea and A. monticola, which are also different from each other. SNP genotyping grouped all Arachis allotetraploids into four taxonomic groups: Xingu accessions were closer to A. monticola and A. hypogaea subsp. hypogaea. Our data suggests that the morphological diversity within these accessions is not associated with a different origin and can be attributed to morphological plasticity and different selection by the Indian tribes.
Abstract in English:Abstract Repetitive DNA is an important component of eukaryotic genomes, accounting for more than 90% of the genome size of some species, including mobile elements and satellite DNA sequences. The aim of study was to characterize the genome of Hancornia speciosa Gomes using C-value genome size estimate and repetitive DNA sequences analysis. The genome size estimate was obtained by flow cytometry and the repetitive DNA sequences were accessed using graph-based clustering. Evolutionary relationships among species of Apocynaceae was obtained using reads of Catharanthus roseus L., Rhayza stricta Decne, and Asclepias syriaca L. from the NCBI and analyzed by graph-based clustering. The genome size estimates in two botanical varieties showed 2C-values ranging from 0.88 to 1.08 pg, indicating small genome size. Clusters representing repeats making up at least 0.01% of the genome revealed the proportion of repetitive DNA ranging from 19.87% (H. speciosa) to 51.674% (A. syriaca), of which the mobile elements were more abundant. Satellite DNA sequences were not found in H. speciosa and R. stricta, while at least one satellite was detected in C. roseus and A. syriaca, suggesting that the LTR retrotransposon Ty3/Gypsy/Chromovirus may have replaced the satellite DNA in H. speciosa and R. stricta.
Abstract in English:Abstract Ralstonia solanacearum is the causal agent of Moko disease in bananas, which in the state of Sergipe in northeastern Brazil causes “Sergipe facies”. This disease induces atypical symptoms similar to those of Bugtok disease in the Philippines. This study was conducted to sequence, assemble, and annotate the genomes of the Sergipe facies-causing isolates SFC and IBSBF2570 (sequevar IIA-53) and compare their genomes with two representative isolates causing Bugtok disease. The genomes were sequenced and assembled, resulting in lengths of 5.58 Mb (SFC) and 5.46 Mb (IBSBF2570) in 185 and 174 contigs, respectively. The isolates of Sergipe facies and Bugtok disease showed similarities in their gene contents. We identified 5,668 information clusters, 3,752 of which were shared by all genomes (core genes). Moreover, 3,585 single-copy genes were identified. Isolates causing Bugtok disease exclusively shared 266 more information clusters than the isolates causing Sergipe facies. These results suggest that Sergipe facies and Bugtok disease isolates show high genomic similarity. However, the similarity is even greater between the Bugtok disease isolates. This may be because of their longer period of interaction compared to Sergipe facies isolates.
Abstract in English:Abstract Herein, we aimed to investigate the functions of ADAMTS6 in colon cancer and its potential mechanism. Based on the data acquired from TCGA database, we revealed that ADAMTS6 was highly expressed in colon cancer tissues, and high expression of ADAMTS6 predicted worse prognosis in patients with colon cancer. Moreover, qRT-PCR demonstrated that the levels of ADAMTS6 were higher in colon cancer cell lines (NCI-H508, Caco-2, CW-2 and HCT 116) than that in normal control cell line CCD-18Co. Functional experiments displayed that depletion of ADAMTS6 repressed NCI-H508 cell growth, invasion and migration whilst overexpression of ADAMTS6 facilitated Caco-2 cell growth, invasion and migration. Moreover, ADAMTS6 silencing enhanced the protein expression of E-cadherin and reduced the levels of N-cadherin, Vimentin and Snail in NCI-H508 cells, whereas ADAMTS6 overexpression showed the counter effects in Caco-2 cells. The protein levels of p-AKT and p-p65 were decreased by depletion of ADAMTS6 in NCI-H508 cells, while their levels were enhanced by overexpression of ADAMTS6 in Caco-2 cells. These consequences indicated that the accelerating effect of ADAMTS6 on colon cancer cell growth, migration and invasion might be achieved by modulating EMT and AKT/NF-κB signaling pathway, offering important foundations for colon cancer treatment.
Abstract in English:Abstract We attempted to explore the effect of Rho guanine nucleotide exchange factor 39 (ARHGEF39) on the phenotypes of clear cell renal cell carcinoma (ccRCC) cells and the underlying mechanism. Analyses of the data from The Cancer Genome Atlas (TCGA) illustrated that ARHGEF39 expression was upregulated in ccRCC and high ARHGEF39 expression was correlated with a worse prognosis. The mRNA and protein expression of ARHGEF39 in ccRCC and nontumorigenic cells was measured by qRT-PCR and western blotting, respectively. The results showed that ARHGEF39 expression was upregulated in ccRCC cells compared with nontumorigenic cells. CCK8 and clonogenic assays were used to measure the viability of ccRCC cells after knockdown or overexpression of ARHGEF39. Transwell assays were used to examine the changes in cell motility after alterations in ARHGEF39 expression and treatment with LY294002 (an AKT inhibitor) or PD98059 (an ERK inhibitor). ARHGEF39-mediated changes in the phosphorylation of AKT and ERK were measured by western blotting. The results indicated that ARHGEF39 promoted the viability, migration and invasion of ccRCC cells by regulating the activation of the AKT/ERK signaling pathway. Overall, our research suggested that ARHGEF39 was upregulated in ccRCC and possibly facilitated the malignant development of ccRCC by modulating the AKT/ERK signaling pathway.
Abstract in English:Abstract Gynostemma yixingense, an important medicinal member of the Cucurbitaceae family, is an endemic herbaceous species distributed in East China. It is morphologically similar to the plants in the same genus, which resulted in some confusion in identification and application. Meanwhile, there are still some controversies in taxonomy. Herein, the complete chloroplast genome sequence of G. yixingense was obtained by Illumina paired-end sequencing technology and compared to other chloroplast genome sequences of congeneric species. The complete chloroplast genome of G. yixingense is 157,910 bp in length with 36.94% GC content and contains a large single-copy (LSC) region of 86,791 bp, a small single-copy (SSC) region of 18,635 bp and a pair of inverted repeat (IR) regions of 26,242 bp. The whole genome contains 133 unique genes, including 87 protein-coding genes, 37 tRNA genes, eight rRNA genes and one pseudogene. In addition, 74 simple sequence repeats (SSRs) were identified, most of which were A/T rich. The phylogenetic analysis indicated that G. yixingense had the closest relationship to G. laxiflorum. The result of this study provided an important theoretical basis for chloroplast genome and phylogenetic analysis of G. yixingense.
Abstract in English:Abstract The use of post-alignment procedures has been suggested to prevent the identification of false-positives in massive DNA sequencing data. Insertions and deletions are most likely to be misinterpreted by variant calling algorithms. Using known genetic variants as references for post-processing pipelines can minimize mismatches. They allow reads to be correctly realigned and recalibrated, resulting in more parsimonious variant calling. In this work, we aim to investigate the impact of using different sets of common variants as references to facilitate variant calling from whole-exome sequencing data. We selected reference variants from common insertions and deletions available within the 1K Genomes project data and from databases from the Latin American Database of Genetic Variation (LatinGen). We used the Genome Analysis Toolkit to perform post-processing procedures like local realignment, quality recalibration procedures, and variant calling in whole exome samples. We identified an increased number of variants from the call set for all groups when no post-processing procedure was performed. We found that there was a higher concordance rate between variants called using 1K Genomes and LatinGen. Therefore, we believe that the increased number of rare variants identified in the analysis without realignment or quality recalibration indicated that they were likely false-positives.
Abstract in English:Abstract Aposematic organisms advertise their defensive toxins to predators using a variety of warning signals, including bright coloration. While most Neotropical poison frogs (Dendrobatidae) rely on crypsis to avoid predators, Oophaga poison frogs from South America advertise their chemical defenses, a complex mix of diet-derived alkaloids, by using conspicuous hues. The present study aimed to characterize the skin transcriptomic profiles of South American Oophaga poison frogs. Our analyses showed very similar transcriptomic profiles for these closely related species in terms of functional annotation and relative abundance of gene ontology terms expressed. Analyses of expression profiles of Oophaga and available skin transcriptomes of cryptic anurans allowed us to propose initial hypotheses for the active sequestration of alkaloid-based chemical defenses and to highlight some genes that may be potentially involved in resistance mechanisms to avoid self-intoxication and skin coloration. In doing so, we provide an important molecular resource for the study of warning signals that will facilitate the assembly and annotation of future poison frog genomes.