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Species-aware DNA language models capture regulatory elements and their evolution
BackgroundThe rise of large-scale multi-species genome sequencing projects promises to shed new light on how genomes encode gene regulatory...
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A chromosome-scale genome sequence of sudangrass (Sorghum sudanense) highlights the genome evolution and regulation of dhurrin biosynthesis
Key messageSudangrass is more similar to US commercial sorghums than to cultivated sorghums from Africa sequence-wise and contain significantly lower...
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Bioinformatics tools for the sequence complexity estimates
We review current methods and bioinformatics tools for the text complexity estimates (information and entropy measures). The search DNA regions with...
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Protein folding rate evolution upon mutations
Despite the spectacular success of cutting-edge protein fold prediction methods, many critical questions remain unanswered, including why proteins...
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Molecular Evolution of Rhodopsin Protein
AbstractRhodopsins are light-sensitive proteins which universally exist in prokaryotes and eukaryotes. Type I rhodopsins exist in microbes and are...
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Promoter evolution of mammalian gene duplicates
BackgroundGene duplication is thought to be a central process in evolution to gain new functions. The factors that dictate gene retention following...
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Adaptive evolution and co-evolution of chloroplast genomes in Pteridaceae species occupying different habitats: overlap** residues are always highly mutated
BackgroundThe evolution of protein residues depends on the mutation rates of their encoding nucleotides, but it may also be affected by co-evolution...
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The evolution and mutational robustness of chromatin accessibility in Drosophila
BackgroundThe evolution of genomic regulatory regions plays a critical role in sha** the diversity of life. While this process is primarily...
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Evolution of rhizobial symbiosis islands through insertion sequence-mediated deletion and duplication
Symbiosis between organisms influences their evolution via adaptive changes in genome architectures. Immunity of soybean carrying the Rj2 allele is...
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Molecular Evolution in Australasian Marsupials
This chapter outlines the history of molecular evolutionary research in australidelphian marsupials, along with the genetic and genomic advances that...
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Molecular Evolution in Australasian Marsupials
This chapter outlines the history of molecular evolutionary research in australidelphian marsupials, along with the genetic and genomic advances that...
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Eighty million years of rapid evolution of the primate Y chromosome
The Y chromosome usually plays a critical role in determining male sex and comprises sequence classes that have experienced unique evolutionary...
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Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids
BackgroundThe Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution,...
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dgfr: an R package to assess sequence diversity of gene families
BackgroundGene families are groups of homologous genes that often have similar biological functions. These families are formed by gene duplication...
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Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution
BackgroundInsect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the...
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Actomyosin organelle functions of SPIRE actin nucleators precede animal evolution
An important question in cell biology is how cytoskeletal proteins evolved and drove the development of novel structures and functions. Here we...
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Evolution Between Species: Phylogeny
In 1834 Charles Darwin (1809–1882) wrote in his notebook “I think”—but instead of writing down what he was thinking, he drew a phylogeny. When he...
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Understand Evolution Better Applying the Computer
The evolution of populations creates new species; the individual living being or protein is, after all, determined within narrow limits by the...
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Whole genome sequence analysis of shallot virus X from India reveals it to be a natural recombinant with positive selection pressure
BackgroundShallots are infected by various viruses like Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV)...
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Definition of Species and Mysteries of Evolution
We have already discussed that the nucleotide composition at each letter position of the codon is highly skewed from a completely random composition,...