A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of themoeBGene

Abstract

We report the database of plastid protein families from red algae, secondary and tertiary rhodophyte-derived plastids, and Apicomplexa constructed with the novel method to infer orthology. The families contain proteins with maximal sequence similarity and minimal paralogous content. The database contains 6509 protein entries, 513 families and 278 nonsingletons (from which 230 are paralog-free, and among the remaining 48, 46 contain at maximum two proteins per species, and 2 contain at maximum three proteins per species). The method is compared with other approaches. Expression regulation of the moeB gene is studied using this database and the model of RNA polymerase competition. An analogous database obtained for green algae and their symbiotic descendants, and applications based on it are published earlier.

Highly Conserved Elements and Chromosome Structure Evolution in Mitochondrial Genomes in Ciliates

“…Proteins were clustered using the method described and tested in [23,31,32,33,34]. BLAST hit threshold E = 0.001 and the most relaxed values for additional parameters: L = 0, H = 1, and very high p were used for clustering.…”

“…This method was used previously to identify binding sites of transcription factors in algal plastids [23,33,34]. …”

Bioinformatic screening of genes present only in well regenerating vertebrates reveals novel FGF and purinergic signaling modulator - c-Answer

“…We developed an approach aimed at identifying genes present in cold-blooded animals that have no orthologs, i.e. direct homologs, in warm-blooded species (Lyubetsky et al, 2017;Zverkov et al, 2015). For the purposes of our study, we regarded orthologs as a pair of homologs in distinct species which keep local genomic synteny, i.e.…”

“…The genome of Xenopus tropicalis, which presumably contains a full collection of genes present in cold-blooded animals and is well-sequenced, was used as a reference, or basic species. At the first step, by using previously developed algorithm (called ClusterZSL) (Lyubetsky et al, 2013;Rubanov et al, 2016;Zverkov et al, 2012Zverkov et al, , 2015 for each gene of X. tropicalis we formed a cluster of the most homologous genes from the selected representatives of cold-and warm-blooded species with well sequenced and annotated genomes. Several orthology inference methods including the local synteny consideration were compared previously using five mammalian genomes (Jun et al, 2009a).…”

Molecular Phylogenetics 2016

“…Even simple computation of distances between genes, leader genes, or hairpins in RNA can be nontrivial [5]. An alternative approach is to extract phylogenetic signal from syntenic patterns of regulatory elements [6], but this comes with its own computational challenges.…”