Biology subjects

Beilstein, M. A.

Publications and source records attributed to Beilstein, M. A..

3 recordsLinked to original sources

bioRxiv2018

Evidence for a unique DNA-dependent RNA polymerase in cereal crops

Gene duplication is an important driver for the evolution of new genes and protein functions. Duplication of DNA-dependent RNA polymerase (Pol) II subunits within plants led to the emergence of RNA Pol IV and V complexes, each of which possess unique functions necessary for RNA-directed DNA Methylation. Comprehensive identification of Pol V subunit orthologs across the monocot radiation revealed a duplication of the largest two subunits within the grasses (Poaceae), including critical cereal crops. These paralogous Pol subunits display sequence conservation within catalytic domains, but their carboxy terminal domains differ in length and character of the Ago-binding platform, suggesting unique functional interactions. Phylogenetic analysis of the catalytic region indicates positive selection on one paralog following duplication, consistent with retention via neofunctionalization. Positive selection on residue pairs that are predicted to interact between subunits suggests that paralogous subunits have evolved specific assembly partners. Additional Pol subunits as well as Pol-interacting proteins also possess grass-specific paralogs, supporting the hypothesis that a novel Pol complex with distinct function has evolved in the grass family, Poaceae.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC=\"FIGDIR/small/272708_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@13d3515org.highwire.dtl.DTLVardef@16831d5org.highwire.dtl.DTLVardef@19f99b8org.highwire.dtl.DTLVardef@1253e70_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG Significance statementThe grass family is critically important for humans, as this group contains cereal grains such as rice, wheat, and corn that form the bulk of the human diet. Here we provide evidence that grasses have evolved a unique polymerase complex of unknown function, suggesting a novel mechanism of gene regulation in the grass lineage. In addition to implications for the biology of grasses, this system offers an opportunity to understand how evolution shapes multi-subunit complexes through duplication of individual components.

plant biology↗

bioRxiv2017

Epistatic interactions drive biased gene retention in the face of massive nuclear introgression

Phylogenomic analyses are recovering previously hidden histories of hybridization, revealing the genomic consequences of these events on the architecture of extant genomes. We exploit a suite of genomic resources to show that introgressive hybridization occurred between close relatives of Arabidopsis, impacting our understanding of species relationships in the group. The composition of introgressed and retained genes indicates that selection against incompatible cytonuclear and nuclear-nuclear interactions likely acted during introgression, while neutral processes also contributed to genome composition through the retention of ancient haplotype blocks. We also developed a divergence-based test to distinguish donor from recipient lineages without the requirement of additional taxon-sampling. Finally, to our great surprise, we find that cytonuclear discordance appears to have arisen via extensive nuclear, rather than cytoplasmic, introgression, meaning that most of the genome was displaced during introgression, while only a small proportion of native alleles were retained.

evolutionary biology↗

bioRxiv2017

Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifyingsequence conserved lincRNAs for functional analysis.

Long intergenic non-coding RNAs (lincRNAs) are an abundant and functionally diverse class of eukaryotic transcripts. Reported lincRNA repertoires in mammals vary, but are commonly in the thousands to tens of thousands of transcripts, covering ~90% of the genome. In addition to elucidating function, there is particular interest in understanding the origin and evolution of lincRNAs. Aside from mammals, lincRNA populations have been sparsely sampled, precluding evolutionary analyses focused on lincRNA emergence and persistence. Here we present Evolinc, a two-module pipeline designed to facilitate lincRNA discovery and characterize aspects of lincRNA evolution. The first module (Evolinc-I) is a lincRNA identification workflow that also facilitates downstream differential expression analysis and genome browser visualization of identified lincRNAs. The second module (Evolinc-II) is a genomic and transcriptomic comparative analyses workflow that determines the phylogenetic depth to which a lincRNA locus is conserved within a user-defined group of related species. Evolinc-II builds families of homologous lincRNA loci, aligns constituent sequences, infers gene trees, and then uses gene tree / species tree reconciliation to reconstruct evolutionary processes such as gain, loss, or duplication of the locus. Here we demonstrate that Evolinc-I is agnostic to target organism by validating against previously annotated Arabidopsis and human lincRNA data. Using Evolinc-II, we examine ways in which conservation can rapidly be used to winnow down large lincRNA datasets to a small set of candidates for functional analysis. Finally, we show how Evolinc-II can be used to recover the evolutionary history of a known lincRNA, the human telomerase RNA (TERC). The analyses revealed unexpected duplication events as well as the loss and subsequent acquisition of a novel TERC locus in the lineage leading to mice and rats. The Evolinc pipeline is currently integrated in CyVerses Discovery Environment and is free to use by researchers.

bioinformatics↗