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1. Developing Asparagaceae1726: An Asparagaceae‐specific probe set targeting 1726 loci for Hyb‐Seq and phylogenomics in the family

   https://doi.org/10.1002/aps3.11597  

   Bentz, Philip C; Leebens‐Mack, Jim (September 2024, Applications in Plant Sciences)

   Abstract PremiseTarget sequence capture (Hyb‐Seq) is a cost‐effective sequencing strategy that employs RNA probes to enrich for specific genomic sequences. By targeting conserved low‐copy orthologs, Hyb‐Seq enables efficient phylogenomic investigations. Here, we present Asparagaceae1726—a Hyb‐Seq probe set targeting 1726 low‐copy nuclear genes for phylogenomics in the angiosperm family Asparagaceae—which will aid the often‐challenging delineation and resolution of evolutionary relationships within Asparagaceae. MethodsHere we describe and validate the Asparagaceae1726 probe set (https://github.com/bentzpc/Asparagaceae1726) in six of the seven subfamilies of Asparagaceae. We perform phylogenomic analyses with these 1726 loci and evaluate how inclusion of paralogs and bycatch plastome sequences can enhance phylogenomic inference with target‐enriched data sets. ResultsWe recovered at least 82% of target orthologs from all sampled taxa, and phylogenomic analyses resulted in strong support for all subfamilial relationships. Additionally, topology and branch support were congruent between analyses with and without inclusion of target paralogs, suggesting that paralogs had limited effect on phylogenomic inference. DiscussionAsparagaceae1726 is effective across the family and enables the generation of robust data sets for phylogenomics of any Asparagaceae taxon. Asparagaceae1726 establishes a standardized set of loci for phylogenomic analysis in Asparagaceae, which we hope will be widely used for extensible and reproducible investigations of diversification in the family. 

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2. Extensive paraphyly in the typical owl family (Strigidae)

   https://doi.org/10.1093/auk/ukz070  

   Salter, Jessie F.; Oliveros, Carl H.; Hosner, Peter A.; Manthey, Joseph D.; Robbins, Mark B.; Moyle, Robert G.; Brumfield, Robb T.; Faircloth, Brant C. (December 2019, The Auk)

   Abstract The typical owl family (Strigidae) comprises 194 species in 28 genera, 14 of which are monotypic. Relationships within and among genera in the typical owls have been challenging to discern because mitochondrial data have produced equivocal results and because many monotypic genera have been omitted from previous molecular analyses. Here, we collected and analyzed DNA sequences of ultraconserved elements (UCEs) from 43 species of typical owls to produce concatenated and multispecies coalescent-based phylogenetic hypotheses for all but one genus in the typical owl family. Our results reveal extensive paraphyly of taxonomic groups across phylogenies inferred using different analytical approaches and suggest the genera Athene, Otus, Asio, Megascops, Bubo, and Strix are paraphyletic, whereas Ninox and Glaucidium are polyphyletic. Secondary analyses of protein-coding mitochondrial genes harvested from off-target sequencing reads and mitochondrial genomes downloaded from GenBank generally support the extent of paraphyly we observe, although some disagreements exist at higher taxonomic levels between our nuclear and mitochondrial phylogenetic hypotheses. Overall, our results demonstrate the importance of taxon sampling for understanding and describing evolutionary relationships in this group, as well as the need for additional sampling, study, and taxonomic revision of typical owl species. Additionally, our findings highlight how both divergence and convergence in morphological characters have obscured our understanding of the evolutionary history of typical owls, particularly those with insular distributions. 

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3. Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function

   https://doi.org/10.1186/s12864-024-10630-6  

   Vo, Nguyen_N T; Yang, Ally; Leesutthiphonchai, Wiphawee; Liu, Yulong; Hughes, Timothy R; Judelson, Howard S (December 2024, BMC Genomics)

   Abstract BackgroundIdentifying the DNA-binding specificities of transcription factors (TF) is central to understanding gene networks that regulate growth and development. Such knowledge is lacking in oomycetes, a microbial eukaryotic lineage within the stramenopile group. Oomycetes include many important plant and animal pathogens such as the potato and tomato blight agentPhytophthora infestans, which is a tractable model for studying life-stage differentiation within the group. ResultsMining of the P. infestans genome identified 197 genes encoding proteins belonging to 22 TF families. Their chromosomal distribution was consistent with family expansions through unequal crossing-over, which were likely ancient since each family had similar sizes in most oomycetes. Most TFs exhibited dynamic changes in RNA levels through the P. infestanslife cycle. The DNA-binding preferences of 123 proteins were assayed using protein-binding oligonucleotide microarrays, which succeeded with 73 proteins from 14 families. Binding sites predicted for representatives of the families were validated by electrophoretic mobility shift or chromatin immunoprecipitation assays. Consistent with the substantial evolutionary distance of oomycetes from traditional model organisms, only a subset of the DNA-binding preferences resembled those of human or plant orthologs. Phylogenetic analyses of the TF families withinP. infestansoften discriminated clades with canonical and novel DNA targets. Paralogs with similar binding preferences frequently had distinct patterns of expression suggestive of functional divergence. TFs were predicted to either drive life stage-specific expression or serve as general activators based on the representation of their binding sites within total or developmentally-regulated promoters. This projection was confirmed for one TF using synthetic and mutated promoters fused to reporter genesin vivo. ConclusionsWe established a large dataset of binding specificities forP. infestansTFs, representing the first in the stramenopile group. This resource provides a basis for understanding transcriptional regulation by linking TFs with their targets, which should help delineate the molecular components of processes such as sporulation and host infection. Our work also yielded insight into TF evolution during the eukaryotic radiation, revealing both functional conservation as well as diversification across kingdoms. 

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4. Data Associated with PhyloFisher

   https://doi.org/10.6084/m9.figshare.15141900.v1  

   Brown, Matthew (January 2021, figshare)

   PhyloFisher is a software package, written in Python3, that contains a protocol designed for phylogenomic dataset assembly and data exploration. This software package aids in the construction and curation of protein sequence-based phylogenomic datasets, conducts post-assembly analyses, and allows visualization of the results. In addition, PhyloFisher currently includes a manually curated starting dataset of 240 proteins from 304 eukaryotic taxa representing the full breadth of known diversity in the eukaryotic tree of life. Importantly, this dataset also includes identified paralogs of each of the 240 proteins from all investigated taxa which is crucial for the identification of probable orthologs. Although PhyloFisher includes this pan-eukaryotic dataset, the tool is flexible and can work with any dataset consisting of protein sequences derived from eukaryotes. The combination of all of the foregoing features makes PhyloFisher a broadly-useful, user-friendly software tool for sophisticated phylogenomic analyses of eukaryotes.</div></div>PROJECT WEBSITE: http://amoeba.msstate.edu/phylofisher/ </div>PROJECT GITHUB: http://github.com/TheBrownLab/PhyloFisher</div></div>This dataset contains files for endusers to retrieve for installation of PhyloFisher as well as accompanying data from the PhyloFisher manuscript.</div></div>Tice_etal.PhyloFisher.archives.tar.gz | Installation requirements for PIP installation</div>Tice_etal.PhyloFisher1.FINAL_DATASET_RENAMED.tar.gz | File dataset associated with the manuscript including matrices and phylogenetic analyses</div>Tice_etal.PhyloFisher_v1.0_input_proteomes_LongNames.tar.gz | Input proteome data from taxa that was used to construct PhyloFisher v1.0</div>Tice_etal.PhyloFisherDatabase_v1.0_Jan.28.2021.tar.gz | PhyloFisher v1.0 starting database</div>Tice_etal.PhyloFisher_FOR_CUSTOM_DATASET_Jan.28.2021.tar.gz | Necessary files and directory structure to be used in custom database construction.</div>Tice_etal.PhyloFisher.DATA.tgz | All data associated with the figures (Fig 3, 4, A-Y) along with all phylogenomic trees and analyses. </div></div></div> 

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5. Specialization Restricts the Evolutionary Paths Available to Yeast Sugar Transporters

   https://doi.org/10.1093/molbev/msae228  

   Crandall, Johnathan_G; Zhou, Xiaofan; Rokas, Antonis; Hittinger, Chris_Todd; Townsend, ed., Jeffrey (November 2024, Molecular Biology and Evolution)

   Abstract Functional innovation at the protein level is a key source of evolutionary novelties. The constraints on functional innovations are likely to be highly specific in different proteins, which are shaped by their unique histories and the extent of global epistasis that arises from their structures and biochemistries. These contextual nuances in the sequence–function relationship have implications both for a basic understanding of the evolutionary process and for engineering proteins with desirable properties. Here, we have investigated the molecular basis of novel function in a model member of an ancient, conserved, and biotechnologically relevant protein family. These Major Facilitator Superfamily sugar porters are a functionally diverse group of proteins that are thought to be highly plastic and evolvable. By dissecting a recent evolutionary innovation in an α-glucoside transporter from the yeast Saccharomyces eubayanus, we show that the ability to transport a novel substrate requires high-order interactions between many protein regions and numerous specific residues proximal to the transport channel. To reconcile the functional diversity of this family with the constrained evolution of this model protein, we generated new, state-of-the-art genome annotations for 332 Saccharomycotina yeast species spanning ∼400 My of evolution. By integrating phylogenetic and phenotypic analyses across these species, we show that the model yeast α-glucoside transporters likely evolved from a multifunctional ancestor and became subfunctionalized. The accumulation of additive and epistatic substitutions likely entrenched this subfunction, which made the simultaneous acquisition of multiple interacting substitutions the only reasonably accessible path to novelty. 

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