BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

Bond, Stephen R.; Keat, Karl; Baxevanis, Andreas D.

doi:10.1101/040675

Cited by 2 publications

(2 citation statements)

References 13 publications

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“…Multiple sequence alignments were predicted with Clustal Omega (56) and maximum likelihood phylogenies were inferred against the LG-gamma model using PhyML (57). Alignments and phylogenies were performed using Align-Buddy and PhyloBuddy, respectively (55). Time course RNA-Seq data published in Ref.…”

Section: Bioinformatics In Silico Sequence Analysesmentioning

confidence: 99%

Functional and phylogenetic characterization of noncanonical vitamin B12–binding proteins in zebrafish suggests involvement in cobalamin transport

Benoit

Stanton

Tartanian

et al. 2018

Journal of Biological Chemistry

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Edited by Ruma Banerjee In humans, transport of food-derived cobalamin (vitamin B 12) from the digestive system into the bloodstream involves three paralogous proteins: transcobalamin (TC), haptocorrin (HC), and intrinsic factor (IF). Each of these proteins contains two domains, an ␣-domain and a ␤-domain, which together form a cleft in which cobalamin binds. Zebrafish (Danio rerio) are thought to possess only a single cobalamin transport protein, referred to as Tcn2, which is a transcobalamin homolog. Here, we used CRISPR/Cas9 mutagenesis to create null alleles of tcn2 in zebrafish. Fish homozygous for tcn2-null alleles were viable and exhibited no obvious developmentally or behaviorally abnormal phenotypes. For this reason, we hypothesized that previously unidentified cobalamin-carrier proteins encoded in the zebrafish genome may provide an additional pathway for cobalamin transport. We identified genes predicted to code for two such proteins, Tcn-beta-a (Tcnba) and Tcn-beta-b (Tcnbb), which differ from all previously characterized cobalamin transport proteins as they lack the ␣-domain. These ␤-domainonly proteins are representative of an undescribed class of cobalamin-carrier proteins that are highly conserved throughout the ray-finned fishes. We observed that the genes encoding the three cobalamin transport homologs, tcn2, tcnba, and tcnbb, are expressed in unique spatial and temporal patterns in the developing zebrafish. Moreover, exogenously expressed recombinant Tcnba and Tcnbb bound cobalamin with high affinity, comparable with binding by full-length Tcn2. Taken together, our results suggest that this noncanonical protein structure has evolved to fully function as a cobalamin-carrier protein, thereby allowing for a compensatory cobalamin transport mechanism in the tcn2 ؊/؊ zebrafish. Vitamin B 12 , also referred to as cobalamin, is a micronutrient that acts as a cofactor for two enzymes: methionine synthase, This article contains Figs. S1-S4 and Table S1.

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Section: Bioinformatics In Silico Sequence Analysesmentioning

confidence: 99%

Functional and phylogenetic characterization of noncanonical vitamin B12–binding proteins in zebrafish suggests involvement in cobalamin transport

Benoit

Stanton

Tartanian

et al. 2018

Journal of Biological Chemistry

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“…The resulting alignments frequently contained indel‐rich stretches of poorly aligned non‐exonic sequences which were several thousand base pairs long. We used BuddySuite v1.3.0 (Bond et al, 2017) to reduce the number of these regions by trimming alignment positions that consisted of more than 50% gaps. Any alignments that were missing more than 20% of the samples or the S. hirsuta sample were also excluded from further analysis.…”

Section: Methodsmentioning

confidence: 99%

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

Gerschwitz-Eidt

Dillenberger

Kadereit

2023

Ecology and Evolution

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Saxifraga section Saxifraga subsection Arachnoideae is a lineage of 12 species distributed mainly in the European Alps. It is unusual in terms of ecological diversification by containing both high elevation species from exposed alpine habitats and low elevation species from shady habitats such as overhanging rocks and cave entrances. Our aims are to explore which of these habitat types is ancestral, and to identify the possible drivers of this remarkable ecological diversification. Using a Hybseq DNA‐sequencing approach and a complete species sample we reconstructed and dated the phylogeny of subsection Arachnoideae . Using Landolt indicator values, this phylogenetic tree was used for the reconstruction of the evolution of temperature, light and soil pH requirements in this lineage. Diversification of subsection Arachnoideae started in the late Pliocene and continued through the Pleistocene. Both diversification among and within clades was largely allopatric, and species from shady habitats with low light requirements are distributed in well‐known refugia. We hypothesize that low light requirements evolved when species persisting in cold‐stage refugia were forced into marginal habitats by more competitive warm‐stage vegetation. While we do not claim that such competition resulted in speciation, it very likely resulted in adaptive evolution.

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BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

Cited by 2 publications

References 13 publications

Functional and phylogenetic characterization of noncanonical vitamin B12–binding proteins in zebrafish suggests involvement in cobalamin transport

Functional and phylogenetic characterization of noncanonical vitamin B12–binding proteins in zebrafish suggests involvement in cobalamin transport

Phylogeny of Saxifraga section Saxifraga subsection Arachnoideae (Saxifragaceae) and the origin of low elevation shade‐dwelling species

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