THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree and $\sigma$ an assignment of leaves to species. The best graph $(G,\sigma)$ is digraph that contains arc from $x$ $y$ if genes reside different species one possibly many (evolutionary) closest relatives compared all other contained $\sigma(y)$. Here, we characterize show it can...

A wide variety of problems in computational biology, most notably the assessment orthology, are solved with help reciprocal best matches. Using an evolutionary definition matches that captures intuition behind concept we clarify rigorously relationships between matches, and events under assumption duplication/loss scenarios. We show orthology graph is a subgraph match (RBMG). furthermore give conditions which RBMG cograph identifies correct orthlogy relation. computer simulations find false...

The structure of eukaryotic genes is generally a combination exons interrupted by intragenic non-coding DNA regions (introns) removed RNA splicing to generate the mature mRNA. A fraction genes, however, comprise single coding exon with introns in their untranslated or are intronless (IGs), lacking entirely. latter code for essential proteins involved development, growth, and cell proliferation expression has been proposed be highly specialized neuro-specific functions linked cancer,...

Many of the commonly used methods for orthology detection start from mutually most similar pairs genes (reciprocal best hits) as an approximation evolutionary closely related matches). This matches by hits becomes exact ultrametric dissimilarities, i.e., under Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level noise into input data best-hit-based methods.

Abstract A detailed knowledge of gene function in the monarch butterfly is still lacking. Here we generate a genome assembly from Mexican nonmigratory population and used RNA-seq data 14 biological samples for annotation to construct an atlas portraying breadth expression during most life cycle. Two thirds genes show changes, with long noncoding RNAs being particularly finely regulated adulthood, male-biased four times more common than female-biased. The two portions heterochromosome Z , one...

Gene regulatory factors (GRFs), such as transcription factors, co-factors and histone-modifying enzymes, play many important roles in modifying gene expression biological processes. They have also been proposed to underlie speciation adaptation. To investigate potential contributions of GRFs primate evolution, we analyzed GRF genes 27 publicly available genomes. Genes coding for zinc finger (ZNF) proteins, especially ZNFs with a Krüppel-associated box (KRAB) domain were the most abundant TFs...

Cographs are exactly the hereditarily well-colored graphs, i.e., graphs for which a greedy vertex coloring of every induced subgraph uses only minimally necessary number colors χ(G). Greedy colorings shown to be subclass hierarchical that naturally appear in phylogenetic combinatorics. The cographs form special class minimal colorings. fact cotrees modular decomposition trees suggests natural generalization: A σ is modularly-minimal if |σ(M)| = χ(M) strong module M G. We show graph admits...

Cographs are exactly hereditarily well-colored graphs, i.e., the graphs for which a greedy coloring of every induced subgraph uses only minimally necessary number colors $\chi(G)$. In recent work on reciprocal best match so-called hierarchically play an important role. Here we show that colorings special case hierarchical coloring, also require no more than $\chi(G)$ colors.

ABSTRACT The monarch butterfly epitomizes insect biodiversity decline. Understanding the genetic basis of adaptation to a changing environment requires genomic and transcriptomic resources that better reflect its diversity while being informative about gene functionality during life cycle. We report reference-quality genome assembly from an individual resident at nonmigratory colony in Mexico, new annotation expression atlas for 14,865 genes, including 492 unreported long noncoding RNA...

A wide variety of problems in computational biology, most notably the assessment orthology, are solved with help reciprocal best matches. Using an evolutionary definition matches that captures intuition behind concept we clarify rigorously relationships between matches, and events under assumption duplication/loss scenarios. We show orthology graph is a subgraph match (RBMG). furthermore give conditions which RBMG cograph identifies correct orthlogy relation. computer simulations find false...

Cographs are exactly the hereditarily well-colored graphs, i.e., graphs for which a greedy vertex coloring of every induced subgraph uses only minimally necessary number colors $\chi(G)$. We show that colorings special case more general hierarchical colorings, recently were introduced in phylogenetic combinatorics. Replacing cotrees by modular decomposition trees generalizes concept to arbitrary graphs. graph has modularly-minimal $\sigma$ satisfying $|\sigma(M)|=\chi(M)$ strong module $M$...

Many of the commonly used methods for orthology detection start from mutually most similar pairs genes (reciprocal best hits) as an approximation evolutionary closely related matches). This matches by hits becomes exact ultrametric dissimilarities, i.e., under Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level noise into input data best-hit-based methods. If additive...

The availability of cellphone geolocation data provides a remarkable opportunity to study human mobility patterns and how these are affected by the recent pandemic. Two simple centrality metrics allow us measure two different aspects in origin-destination networks constructed with this type data: variety places connected certain node (degree) number people that travel or from given (strength). In contribution, we present an analysis degree strength daily for Greater Mexico City during 2020....

Abstract Eukaryotic gene structure is a combination of exons generally interrupted by intragenic non-coding DNA regions termed introns removed RNA splicing to generate the mature mRNA. Thus, eukaryotic genes can be either single exon (SEGs) or multiple (MEGs). Among SEGs, intronless (IGs) are subgroup that additionally lacks at their UTRs, and code for proteins essentially involved in development, growth, cell proliferation. Gene expression IGs has been proposed highly specialized...