All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3ʹ-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.KEYWORDS RNA polymerase IV; transcription; gene regulation; transposons; paramutation E UKARYOTES use at least three DNA-dependent RNA polymerases (RNAPs) to transcribe their genomes into functional RNAs. RNAP Pol II generates messenger RNAs (mRNAs) and noncoding RNAs involved in various RNA-mediated regulatory pathways (reviewed by Sabin et al. 2013). Flowering plant genomes encode additional RNAP subunits comprising Pol IV and Pol V, which are central to a small interfering RNA (siRNA)-based silencing pathway primarily targeting repetitive sequences such as transposable elements (TEs) (Matzke and Mosher 2014;Matzke et al. 2015). These additional RNAPs derive from duplications of specific Pol II subunits followed by subfunctionalization during plant evolution (Tucker et al. 2011), yet the holoenzyme complexes still share some Pol II subunits (Ream et al. 2009;Haag et al. 2014).Zea mays (maize) has distinct largest subunits for Pol IV and V and, unlike Arabidopsis thaliana, three second-largest subunits Sidorenko et al. 2009;Stonaker et al. 2009) that in distinct combinations form two Pol IV and three Pol V isoforms (Haag et al. 2014). Genetic analyses of rna polymerase d/e 2a (rpd/e2a) encoding one of the secondlargest subunits (Sidorenko et al. 2009;Stonaker et al. 2009) together with recent proteomic data showing association of a putative RNA-dependent RNA polymerase (RDR2) with only RPD/E2a-containing isoforms (Haag et al. 2014) indicate that maize Pol IV isoforms have diverse functional roles in managing genome homeostasis.Loss of Pol IV function has different consequences in Arabidopsis, Brassica rapa (a close relative of Arabidops...

Zoonomia is the largest comparative genomics resource for mammals produced to date. By aligning genomes for 240 species, we identify bases that, when mutated, are likely to affect fitness and alter disease risk. At least 332 million bases (~10.7%) in the human genome are unusually conserved across species (evolutionarily constrained) relative to neutrally evolving repeats, and 4552 ultraconserved elements are nearly perfectly conserved. Of 101 million significantly constrained single bases, 80% are outside protein-coding exons and half have no functional annotations in the Encyclopedia of DNA Elements (ENCODE) resource. Changes in genes and regulatory elements are associated with exceptional mammalian traits, such as hibernation, that could inform therapeutic development. Earth’s vast and imperiled biodiversity offers distinctive power for identifying genetic variants that affect genome function and organismal phenotypes.

Annotating coding genes and inferring orthologs are two classical challenges in genomics and evolutionary biology that have traditionally been approached separately, limiting scalability. We present TOGA (Tool to infer Orthologs from Genome Alignments), a method that integrates structural gene annotation and orthology inference. TOGA implements a different paradigm to infer orthologous loci, improves ortholog detection and annotation of conserved genes compared with state-of-the-art methods, and handles even highly fragmented assemblies. TOGA scales to hundreds of genomes, which we demonstrate by applying it to 488 placental mammal and 501 bird assemblies, creating the largest comparative gene resources so far. Additionally, TOGA detects gene losses, enables selection screens, and automatically provides a superior measure of mammalian genome quality. TOGA is a powerful and scalable method to annotate and compare genes in the genomic era.

We examined transposable element (TE) content of 248 placental mammal genome assemblies, the largest de novo TE curation effort in eukaryotes to date. We found that although mammals resemble one another in total TE content and diversity, they show substantial differences with regard to recent TE accumulation. This includes multiple recent expansion and quiescence events across the mammalian tree. Young TEs, particularly long interspersed elements, drive increases in genome size, whereas DNA transposons are associated with smaller genomes. Mammals tend to accumulate only a few types of TEs at any given time, with one TE type dominating. We also found association between dietary habit and the presence of DNA transposon invasions. These detailed annotations will serve as a benchmark for future comparative TE analyses among placental mammals.