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Commercial cultivation of sugarcane is usually carried out by planting culm segments (sett) carrying buds in their internodes. However, this is an inefficient practice due to high sprouting irregularity. In this work, we inspect the first stages of the physiological preparation of the culm for sprouting, trying to identify compounds that actively participate in this process. We compared, during the first 48 h, the metabolic profile of sugarcane against energy cane, a cultivar known to have higher sprouting speed and consistency. In fact, during this short period it was possible to observe that energy cane already had a higher physiological activity than sugarcane, with significant changes in the catabolism of amino acids, increased levels of reducing sugars, lipids and metabolic activity in the phenylpropanoid pathway. On the other hand, sugarcane samples had just begun their activity during this same period, with an increase in the level of glutamate as the most significant change, which may be linked to the strategy of these cultivars to develop their roots before leaves, opposite of what is seen for energy cane. These results contribute to the development of strategies for increasing the efficiency of sprouting in sugarcane.

Agave plants are well-known for their drought resilience and commercial applications. Among them, Agave sisalana (sisal) is the species most used to produce hard fibers, and it is of great importance for semiarid regions. Agaves also show potential as bioenergy feedstocks, as they can accumulate large amounts of biomass and fermentable sugar. This study aimed to reconstruct the A. sisalana interactome, and identify key genes and modules involved in multiple plant tissues (root, stem, and leaf) through RNA-Seq analysis. We integrated A. sisalana transcriptome sequences and gene expression generated from stem, leaf, and root tissues to build global and conditional co-expression networks across the entire transcriptome. By combining the co-expression network, module classification, and function enrichment tools, we identified 20 functional modules related to at least one A. sisalana tissue, covering functions such as photosynthesis, leaf formation, auxin-activated signaling pathway, floral organ abscission, response to farnesol, brassinosteroid mediated signaling pathway, and light-harvesting. The final interactome of A. sisalana contains 2,582 nodes and 15,083 edges. In the reconstructed interactome, we identified submodules related to plant processes to validate the reconstruction. In addition, we identified 6 hub genes that were searched for in the co-expression modules. The intersection of hub genes identified by both the protein-protein interaction networks (PPI networks) and co-expression analyses using gene significance and module membership revealed six potential candidate genes for key genes. In conclusion, we identified six potential key genes for specific studies in Agave transcriptome atlas studies, biological processes related to plant survival in unfavorable environments, and provide strategies for breeding programs.

Increased demand for biofuels promotes the search for new biomass-degrading fungi. Acremonium strictum is an environmentally widespread filamentous fungi found on plant debris; that secretes lignocellulose-degrading enzymes. A recently isolated A. strictum strain, AAJ6; native to the Brazilian Cerrado biome was evaluated for its capacity to degrade lignocellulosic substrates. In this study, whole-genome sequencing of AAJ6 was performed and 775 CAZy domains were identified which correlated to those of A. strictum strain DS1bioAY4a and other lignocellulolytic fungi; suggesting AAJ6 is a high CAZyme producer. We expressed the glycoside hydrolase families GH74 and GH3 from plasmid or genome-integrated to evaluate the ethanol production from cellulosic substrates in Brazilian industrial Saccharomyces cerevisiae strains (PE-2 and SA-1) evolved for thermotolerance (AMY12 and AMY35). Those expressing the genome-integrated enzymes showed the highest β-glucosidase activity and growth in medium with cellobiose at 40°C. The strain AGY005 (integrated cassettes) showed 19, 23 and 46% higher ethanol production in SHF, pSSF (partial hydrolysis SSF) and SSF processes, respectively, using Avicel, and ∼50% more ethanol using pre-treated sugarcane bagasse, compared to the strain with a plasmid-based expression. These results indicate the improved performance of thermotolerant industrial strains with genome-integrated CAZymes in the SSF process for 2G ethanol.

Made available in DSpace on 2022-04-28T19:44:38Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-11-15 Agaves have been used for centuries as a feedstock in dryland areas for fibers, food, and beverages, and have enormous potential for biofuel production. Brazil is the world's largest producer of Agave fiber (sisal). However, since the development of synthetic fibers, the national investment in Agave research has decreased drastically, leading to the cessation of the country's breeding programs. What is left of the Brazilian elite cultivars were planted at a germplasm bank in the middle of the semiarid. Surprisingly, after 7 years of abandonment, the plants were still healthy and did not show any clear signs of stress. Here, we aimed to investigate how these plants managed to cope with this environment and the molecular basis of their biomass traits. We assembled the transcriptomic atlas of Agave sisalana, Agave fourcroydes, and Agave hybrid 11648 ((A. amaniensis x A. angustifolia) x A. amaniensis). We observed that the cultivars activated a highly overlapping set of stress-response genes, which were the most expressed transcripts. Also, raffinose was detected at high concentrations, possibly acting as an osmolyte, though differences at its biosynthesis have been found depending on cultivar. Finally, we observed differences in recalcitrance that could be attributed to lignin composition and its biosynthetic pathway. Our data contribute new insights that can help molecular breeders to correspond to emerging expectations for Agave as biorenewables feedstocks for dryland areas. Laboratório de Genômica e BioEnergia Departamento de Genética Evolução Microbiologia e Imunologia UNICAMP Departamento de Bioprocessos e Biotecnologia Faculdade de Ciências Agronômicas UNESP Departamento de Botânica Instituto de Biociências USP Laboratório de Anatomia Vegetal Departamento de Biologia Vegetal UNICAMP Empresa Brasileira de Pesquisa Agropecuária - Algodão EMBRAPA High-Throughput Sequencing Facility School of Medicine UNC Centro para Computação em Engenharia e Ciências UNICAMP Departamento de Bioprocessos e Biotecnologia Faculdade de Ciências Agronômicas UNESP

In this work, we evaluated the fermentative performance and metabolism modifications of a second generation (2G) industrial yeast by comparing an industrial condition during laboratory and industrial scale fermentations. Fermentations were done using industrial lignocellulosic hydrolysate and a synthetic medium containing inhibitors and analyses were carried out through transcriptomics and proteomics of these experimental conditions. We found that fermentation profiles were very similar, but there was an increase in xylose consumption rate during fermentations using synthetic medium when compared to lignocellulosic hydrolysate, likely due to the presence of unknown growth inhibitors contained in the hydrolysate. We also evaluated the bacterial community composition of the industrial fermentation setting and found that the presence of homofermentative and heterofermentative bacteria did not significantly change the performance of yeast fermentation. In parallel, temporal differentially expressed genes (tDEG) showed differences in gene expression profiles between compared conditions, including heat shocks and the presence of up-regulated genes from the TCA cycle during anaerobic xylose fermentation. Thus, we indicate HMF as a possible electron acceptor in this rapid respiratory process performed by yeast, in addition to demonstrating the importance of culture medium for the performance of yeast within industrial fermentation processes, highlighting the uniquenesses according to scales.

Due to the large generation of omics data on a large scale in the last few years, the extraction of information from biological data has become more complex and its integration or comparison as well. One of the ways to represent interactions of biological data is through networks, which summarize information on interactions between their nodes through edges. The comparison of two biological networks using network metrics, biological enrichment, and visualization consists of data that allows us to understand differences in the interactomes of contrasting conditions. We describe BioNetComp, a python package to compare two different interactomes through different metrics and data visualization without the need for a web platform or software, just by command-line. As a result, we present a comparison made between the interactomes generated from the differentially expressed genes at two different points during a typical bioethanol fermentation. BioNetComp is available at github.com/lmigueel/BioNetComp.

Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. Residues from the P-loop domain of the analyzed FT structures showed predominantly high destabilizing mutations which is consistent with constant selective pressure found for this region. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure experience positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

Backgroundthe scientific training to become a bioinformatician includes multidisciplinary abilities, which increase the challenges to professional development.Competition frameworkin order to improve and promote the ongoing training of the Brazilian bioinformatics community, we organize a national competition, with the main goal to develop human resources and abilities in Computational Biology at the national level. The competition framework was designed in three phases: 1) a one-day challenge composed of 60 multiple-choice questions covering Biology, Computer Science, and Bioinformatics knowledge; 2) five Computational Biology challenges to be solved in three days; and 3) development of an original project evaluated during the 15th X-meeting.Resultsthe first edition of the League of Brazilian Bioinformatics (LBB) counted 168 competitors and 59 groups, distributed into undergraduate students (14.4%), graduate students (12.6% master and 16.8%, Ph.D.), and other professional fields. The first phase selected 46 teams to proceed in the competition, while the second phase selected the three top-performing teams.Conclusionduring the competition, we were able to stimulate teamwork in the main areas of Bioinformatics, with the engagement of all research-level competitors. Furthermore, we identified opportunities to deliver and offer better training to the community and we intend to apply the acquired experience in the second edition of the LBB, which will occur in 2021.Supplementary informationSupplementary data are available at Bioinformatics

Agaves, which have been grown commercially for fiber or alcoholic beverages, are emerging as a candidate crop for biochemicals and biofuels production in semiarid regions because of their high productivity in low rainfall areas, drought tolerance, and low lignin content.In this work, we present the transcriptomic atlas of Agave sisalana, Agave fourcroydes, and agave hybrid 11648 (A. amaniensis x A. angustifolia) under prolonged drought in field conditions. Leaf, stem, and root tissues were sequenced, and gene expression profiles were correlated with biomass composition, enzymatic hydrolysis of cell wall carbohydrates, histochemical analysis, and non-structural carbohydrates content.Differences in biomass accessibility were attributed to either lignin content or lignin composition, possibly through modification of s/g ratio promoted by changes in Caffeic Acid 3-O-Methyltransferase (COMT) transcript abundance. Unlike most plants, the most highly expressed transcripts do not encode photosynthetic proteins, but rather involved in stress response. Although the three cultivars presented quantitative differences in global gene expression, they activated a highly overlapping set of genes. The main molecular strategies employed by agave to cope with high-temperature and drought seem to consist in overexpressing HSP and LEA, as well as promoting raffinose accumulation as an osmolyte.In conclusion, our data provide vital new genetic information for the study of Agave species and provide new insights into cell wall architecture, recalcitrance, and resistance to abiotic stresses for these species.

Here, we report the genome assembly of a Saccharomyces cerevisiae SA1-derived haploid (FMY097) indigenous strain isolated from a Brazilian ethanol distillery. FMY097 was recently reported to be a highly aldehyde-resistant strain capable of producing bioethanol in the presence of up to 40 mM furfural and 80 mM 5-hydroxymethylfurfural.

Sugarcane (Saccharum spp.) grows in all tropical and subtropical regions of the world, being cultivated in more than 100 countries. Modern cultivars are the results of interspecific crosses, having S. officinarum as the main genetic source, which results in high sucrose production. Energy cane is still a less rigorous definition, applied to cane cultivars that have higher biomass, although lower sucrose concentration. Despite the practical advance, little is known about the molecular and physiological basis of the energy cane productivity and robustness, a knowledge that can be very helpful for the development of cane varieties in general. In this work, we have explored the sprouting process, which is very irregular in sugarcane plantation and thereby a main cost factor. Our results could be summarized in three main contributions: first, we observed that energy cane has a physiological strategy very different from that one observed for sugarcane, starting with the shoot development and only thereafter beginning the root growth. After 10 days, the energy cane had a shoot height of 14.19 cm against of 4.24 cm of sugarcane. Nevertheless, we noticed the energy cane root presents a fast and vigorous development, overcoming the sugarcane root volume after 50 days, with 24.36 and 14.79 cm3, respectively. Second, we observed that the energy cane has homogeneity in the sprouting rate of the different internodes, regardless of their age. Finally, our data allowed us to propose that the greater growth seen in energy cane might be attributed to a vigorous rate of nocturnal growth with angulation in relation to the time of 11.89°, which is lower in sugarcane, with angulation of 5.47°.

Background The macaúba palm is a novel feedstock for oil production suitable for multiple uses, including as biodiesel and in the food and cosmetic industries. As an efficient alternative, the macaúba palm has limited genomic resources, particularly expressed sequence tag (EST) markers. We report a comprehensive set of validated EST-simple sequence repeat (SSR) markers by using transcriptome sequencing, its application in genetic diversity analysis and cross transferability in other palm trees with environmental and economic importance. Results In this study, a total of 418 EST-SSRs were identified to be unique for one transcript and region; 232 EST-SSRs were selected, with trinucleotide repeats being the most frequent motif, representing 380 (90.9%), followed by composited (4.5%), di- (3.6%), and hexanucleotides (3.6%). A total of 145 EST-SSRs (62.5%) were validated for consistent amplification in seventeen macaúba palm samples, and 100 were determined to be polymorphic with PIC values ranging from 0.25 to 0.77. Genetic diversity analysis was performed with the 20 most informative EST-SSR markers showing a distinct separation of the different groups of macaúba palm. Additionally, these 145 markers were transferred in six other palm species resulting in transferability rates of 99% (144) in Acrocomia intumescens, 98% (143) in Acrocomia totai, 80.7% (117 EST-EST) in African oil palm (Elaeis guineensis) and peach palm (Bactris gasipaes) samples, 70% (102) in the juçara palm (Euterpe edulis) and 71.7% (104) in the hat palm (Sabal causiarum). Analysis of genetic distance showed a high separation in accordance with geographic location, establishing distinct groups by genera. Conclusions The EST markers identified in our study are a valuable resource and provide a genomic tool for genetic mapping and further genetic studies, as well as evaluation of co-location between QTLs and functionally associated markers. Electronic supplementary material The online version of this article (10.1186/s12870-018-1509-9) contains supplementary material, which is available to authorized users.

We present the sequencing and annotation of the Leishmania (Leishmania) amazonensis genome, an etiological agent of human cutaneous leishmaniasis in the Amazon region of Brazil. L. (L.) amazonensis shares features with Leishmania (L.) mexicana but also exhibits unique characteristics regarding geographical distribution and clinical manifestations of cutaneous lesions (e.g. borderline disseminated cutaneous leishmaniasis). Predicted genes were scored for orthologous gene families and conserved domains in comparison with other human pathogenic Leishmania spp. Carboxypeptidase, aminotransferase, and 3′-nucleotidase genes and ATPase, thioredoxin, and chaperone-related domains were represented more abundantly in L. (L.) amazonensis and L. (L.) mexicana species. Phylogenetic analysis revealed that these two species share groups of amastin surface proteins unique to the genus that could be related to specific features of disease outcomes and host cell interactions. Additionally, we describe a hypothetical hybrid interactome of potentially secreted L. (L.) amazonensis proteins and host proteins under the assumption that parasite factors mimic their mammalian counterparts. The model predicts an interaction between an L. (L.) amazonensis heat-shock protein and mammalian Toll-like receptor 9, which is implicated in important immune responses such as cytokine and nitric oxide production. The analysis presented here represents valuable information for future studies of leishmaniasis pathogenicity and treatment.

Background High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. Results We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. Conclusions We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.