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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.