19 papers · ranked by Valyu relevance
Samuel H Church, Cassandra G Extavour, Michael Rosenberg
Island radiations present natural laboratories for studying the evolutionary process. The Hawaiian Drosophilidae are one such radiation, with nearly 600 described species and substantial morphological and ecological diversification. These species are largely divided into a few major clades, but the relationship between…
Wend Yam D D Ouedraogo, Aida Ouangraoua
Eukaryotic genes can encode multiple distinct transcripts through the alternative splicing (AS) of genes. Interest in the AS mechanism and its evolution across different species has stimulated numerous studies, leading to several databases that provide information on AS and transcriptome data across multiple eukaryotic…
Wend Yam D. D. Ouedraogo, Aida Ouangraoua
Background SimSpliceEvol is a tool for simulating the evolution of eukaryotic gene sequences that integrates exon-intron structure evolution as well as the evolution of the sets of transcripts produced from genes. It takes a guide gene tree as input and generates a gene sequence with its transcripts for each node of…
Zhan Liu, Shanjun Deng, Hui Zeng, Mendong Zhang + 6 more
Combining cell lineage tracing with single-cell RNA sequencing can reconstruct a phylogenetic tree to integrate single-cell transcriptomic atlas. However, the internal nodes of this tree - representing ancestral cells - remain transcriptionally silent, preventing along-lineage longitudinal tracing of cell state…
James Titus‐McQuillan, Adalena V. Nanni, Lauren M. McIntyre, Rebekah L. Rogers
'Rebekah L. Rogers'] Genomic complexity is a growing field of evolution, with case studies for comparative evolutionary analyses in model and emerging non-model systems. Understanding complexity and the functional components of the genome is an untapped wealth of knowledge ripe for exploration. With the "remarkable…
Yu-Hao Huang, Yi-Fei Sun, Hao Li, Hao-Sen Li + 1 more
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, traditional methods typically involve intricate and time-consuming procedures prior to core analyses. These procedures encompass assembly from high-throughput reads, decontamination, gene prediction, homology search…
Lucas Vandenabeele, Anaïs Gibert, Pascaline Salvado, Roselyne Buscail + 4 more
Ophrys orchids (or bee orchids) provide an outstanding example of a plant adaptive radiation. Over the last five million years, this genus has diversified into hundreds of taxa as a result of its unconventional pollination strategy, known as ‘sexual swindling’. However, the rapid and substantial diversification of this…
David Mark Emms, Steven Kelly
Determining the evolutionary relationships between genes is fundamental to comparative biological research. Here, we present SHOOT. SHOOT searches a user query sequence against a database of phylogenetic trees and returns a tree with the query sequence correctly placed within it. We show that SHOOT performs this…
Anna Grandchamp, Peter Czuppon, Erich Bornberg-Bauer
Most of the transcribed eukaryotic genomes are composed of non-coding transcripts. Among these transcripts, some are newly transcribed when compared to outgroups and are referred to as de novo transcripts. De novo transcripts have been shown to play a major role in genomic innovations. However, little is known about…
Rafiuddin, S M
Phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To estimate a phylogenetic tree there are certain necessary steps have to be…
Gaurav D. Diwan, Paschalis Natsidis, Mu-en Chung, Juan-Carlos Gonzalez Sanchez + 4 more
In the biodiversity genomics era, vast gene catalogs have rapidly accumulated, but how gene functions map onto major evolutionary transitions remains vague. We integrated phylogenomics with functional annotations to trace the emergence of ∼4.5 million genes and their associated functions in 508 representative species…
Laura E. Tibbs-Cortes, Oliva C. Haley, John Portwood, Ethalinda Cannon + 2 more
Phylostratigraphic analysis identifies the evolutionary origins and level of conservation of proteins, facilitating research in evolutionary biology and comparative genomics. We developed the MaizeGDB Phylostrata Tool, a custom web application that enables users to explore the evolutionary origins of maize proteins.…
Logan Blair, Julie Cridland, Yige Luo, David Begun + 1 more
The evolution of genes de novo from ancestrally nongenic sequences is a significant mechanism of gene origin. Many studies have focused on distant evolutionary comparisons, which bias the sample of de novo genes towards older genes that have acquired important functions and have been refined by selection. In this…
Julia A. Palacios, Anand Bhaskar, Filippo Disanto, Noah A. Rosenberg
Evolutionary models used for describing molecular sequence variation suppose that at a non-recombining genomic segment, sequences share ancestry that can be represented as a genealogy—a rooted, binary, timed tree, with tips corresponding to individual sequences. Under the infinitely-many-sites mutation model, mutations…
Ray Han
Phylogeny can be inferred using two sources of data from an organism: morphological data and molecular data. Historically, phylogenies were usually inferred using morphological characters (Lee and Palci, 2015), but some morphological features may not necessarily indicate shared heritage (Zou and Zhang, 2016). With the…
Marc Hellmuth, Peter F. Stadler
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to…
Guillaume Hummel, David Pflieger, Alexandre Berr, Laurence Drouard
Transfer RNAs (tRNAs) are universal adaptors of the genetic code, yet their evolutionary dynamics across photosynthetic eukaryotes remain underexplored. Here, we present the largest comparative re-analysis integrating the PlantRNA database with published data to explore tRNA gene evolution. We find that tRNA gene…
Bethan S. Jones, Connie M. Ross, Gabriel Foley, Nico Kress + 5 more
Selective, one-step C-H activation of fatty acids from biomass is an attractive concept in sustainable chemistry. Biocatalysis has shown promise for generating high-value hydroxy acids but to date enzyme discovery has relied on laborious screening and produced limited hits, which predominantly oxidise the sub-terminal…
Pavel Kohout, Michal Vasina, Marika Majerova, Veronika Novakova + 5 more
Enzymes play a crucial role in sustainable industrial applications, with their optimization posing a formidable challenge due to the intricate interplay among residues. Computational methodologies predominantly rely on evolutionary insights, leveraging homologous sequences to pinpoint conserved and functionally…