Functional Omics and Big Data Analysis in Microalgae
Gokare A. Ravishankar, Ranga Rao Ambati in Handbook of Algal Technologies and Phytochemicals, 2019
Phylogenomics is the study of the evolutionary background of biological lineages based on the comparative analysis of genome-scale data, which simultaneously allows us to refer to the various biological queries at a scale not possible earlier. Large-scale data mining and analysis of sequential data sets offer a new insight into the development of new metabolic models, providing details of the molecular evolution of metabolic pathways (Misra et al. 2012). A phylogenomic study by Misra et al. (2012) deduced that lipid biosynthetic pathway related genes among Prasinophytes, Chlorophytes, Streptophytes, and Rhodophytes clustered based on exon-intron assembly, conserved motif arrangement and functionality. Also, genomes systematically mined from species belonging to Chlorophyta, Heterokontophyta, Rhodophyta, and Haptophyta identified 289 enzymes involved in lipid metabolic pathways, consequently building the Database of Enzymes of Microalgal Biofuel Feedstock (dEMBF). dEMBF is the first database developed for the enzymes involved and is responsible for lipid synthesis from 15 algal genomes, thereby building an informative platform for enzyme queries and analysis (http://bbprof.immt.res.in/embf, Misra et al. 2016). The Algae Gene Co-expression database (ALCOdb—http://alcodb.jp) is another database providing information on various microalgal gene co-expression at the interspecies level based on comparison and network analysis, facilitating microalgal molecular understanding and evolutionary approach (Aoki et al. 2016) among two model algae, C. reinhardtii, and Cyanidioschyzon merolae, highlighti ng the major gene family belonging to higher plants. Phylogenomics study of red algae highlights the evolution of the mevalonate (MVA) pathway for isoprenoid biosynthesis in Rhodophyta and offers in-depth understanding of the origin and evolution of various genes and metabolic pathways involved in 15 red algal species of Rhodophyta (Qiu et al. 2016).
Interleukin-1β secretion induced by mucosa-associated gut commensal bacteria promotes intestinal barrier repair
Published in Gut Microbes, 2022
Wan-Jung H. Wu, Myunghoo Kim, Lin-Chun Chang, Adrien Assie, Fatima B. Saldana-Morales, Daniel F. Zegarra-Ruiz, Kendra Norwood, Buck S. Samuel, Gretchen E. Diehl
Fecal pellets from AVMN-treated mice were resuspended in PBS to 100 mg/ml and dilutions were plated on blood agar plates (Fisher) and cultured overnight at 37°C under normal or anaerobic conditions using BD GasPak (Fisher). For sequencing, genomic DNA was extracted with phenol chloroform, and DNA was sheared to 15kb using Covaris g-TUBE® devices, allowing for sizes 5 kb and larger. The library preparation was carried out using SMRTbell Template kit 1.0 Exo VII protocol and the sample was barcoded with PacBio Adaptor. Genome sequencing was performed using the Pacific Biosciences Sequel sequencing platform. Long reads were assembled de novo into two contigs (main chromosome and 1 plasmids) using Canu (v. 1.6).73 Gene prediction and annotation were carried out using the webservice PATRIC.74 Genomic visualization was performed using Circos v0.69–9.75 Genomic comparison was done using the PATRIC webservice and phylogenomic reconstructions were done using the GToTree pipeline and its associated dependencies.76–80 Sequencing reads and the genome assembly were submitted to NCBI under the bioproject PRJNA725420.
Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution
Published in Expert Review of Proteomics, 2021
Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal, Derek Caetano-Anollés
Novel phylogenomic methods are still needed to advance the science of deep history reconstruction. Phylogenetic trees lack reticulations that can account for pervasive horizontal exchange processes such as the recruitment of EFLs in domains or domains in proteins. Similarly, phylogenetic networks that could model such recruitments cannot be recovered with optimality criteria because of computational and algorithmic limitations. We therefore trust tree reconstructions can accurately extract vertical evolutionary signatures in a ‘sea’ of entanglement. Not all phylogenetic characters are suitable either. Standard alignment-dependent methods that for example focus on sequences are powerful for establishing shallow phylogenetic relationships but fail to cleanly recover deep evolution [106]. Alignment-free methodologies overcome some of the challenges but depend on the accuracy of machine-learning methodologies or the levels of evolutionary conservation embedded for example in the hierarchy of loops or domain taxonomies. Finally, networks that exploit sequence or structure similarity lack an homology-based phylogenetic rationale and must be carefully validated with other phylogenetic approaches. Learning how to interface levels of protein structural complexity and tree and network reconstruction will remain an important task for the future.
Atypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis
Published in Gut Microbes, 2022
Maximilian Baumgartner, Rebecca Zirnbauer, Sabine Schlager, Daniel Mertens, Nikolaus Gasche, Barbara Sladek, Craig Herbold, Olga Bochkareva, Vera Emelianenko, Harald Vogelsang, Michaela Lang, Anton Klotz, Birgit Moik, Athanasios Makristathis, David Berry, Stefanie Dabsch, Vineeta Khare, Christoph Gasche
Bacterial DNA was extracted using a phenol chloroform-based method. Whole-genome sequencing was performed using HiSeqV4 PE125 methodology. For genome assembly, the spades pipeline was used. Assemblies were submitted to NCBI for annotation. The CFSAN SNP pipeline was used with the E. coli reference genome O103:H2 12009 to construct an SNP matrix with the 57 strains from this study and 348 publicly available AEEC genomes of diverse pathotypes and one E. albertii genome. For phylogenomic maximum likelihood inference, IQ-TREE was applied with the best-fit model automatically selected by ModelFinder.41 For pangenome analysis, the Roary pipeline was used with standard parameters, followed by Scoary for the identification of associations between all genes in the accessory genome and EspG2 and EspV positivity.42 Pangenome composition was visualized with Phandango. To investigate the presence of known virulence factors, the VFDB database was used. For the detection of novel hypothetical secreted proteins and additional secretion systems, the EffectiveDB was applied. Pairwise comparison between EspG2-pos and EspV-pos genomes was performed with the Mann–Whitney U test, prevalences were compared using Fisher’s exact test, with Bonferroni correction for multiple comparisons. Sequencing data and assemblies are publicly accessible at NCBI under the project number PRJNA528578. Additional information on bioinformatic analysis can be found in the supplementary method section.