Bacterial contribution to genesis of the novel germ line determinant oskar
- Department of Molecular and Cellular Biology, Harvard University, United States
- Department of Organismic and Evolutionary Biology, Harvard University, United States
Figures
Figure 1
Sequence analysis of the Oskar gene.
(a) Schematic representation of the Oskar gene. The LOTUS and OSK hydrolase-like domains are separated by a poorly conserved region of predicted high disorder and variable length between species. In …
Figure 2 with 13 supplements
Phylogenetic analysis of the LOTUS and OSK domains.
(a) Bayesian consensus tree for the LOTUS domain. Three major LOTUS-containing protein families are represented within the tree: Tudor 5, Tudor 7, and Oskar. Oskar LOTUS domains form two clades, one …
Figure 2—figure supplement 1
LOTUS Domain RaxML MUSCLE Tree.
Phylogenetic tree of the HMMER sequences retrieved from the UniProt database using the LOTUS alignment HMM model. The top 97 hits were selected for phylogenetic analysis, and the only three …
Figure 2—figure supplement 2
LOTUS Domain Bayesian MUSCLE Tree.
Phylogenetic tree of the HMMER sequences retrieved from the UniProt database using the LOTUS alignment HMM model. 100 sequences were chosen for analysis as described for Figure 2—figure supplement 1.…
Figure 2—figure supplement 3
OSK Domain RaxML MUSCLE Tree.
Phylogenetic tree of the HMMER sequences retrieved from the UniProt database using the OSK alignment HMM model. The top 95 hits were selected for phylogenetic analysis, and the only five non-Oskar …
Figure 2—figure supplement 4
OSK Domain Bayesian MUSCLE Tree.
Phylogenetic tree of the HMMER sequences hit on the UniProt database using the OSK alignment HMM model. 87 sequences were chosen for analysis as described for Figure 2—figure supplement 3.The tree …
Figure 2—figure supplement 5
SOWHAT constrained trees and results.
Two trees constrained by alternative relationships that would be expected under vertical transmission of sequences were designed and tested against our result supporting a putative HGT event of the …
Figure 2—figure supplement 6
LOTUS Domain RaxML PRANK Tree.
Phylogenetic tree of the same sequences used for the previous LOTUS trees. The sequences were aligned using PRANK and the tree generated with RaxML as described in Phylogenetic Analysis Based on …
Figure 2—figure supplement 7
OSK Domain RaxML PRANK Tree.
Phylogenetic tree of the same sequences used for the previous OSK trees. The sequences were aligned using PRANK and the tree generated with RaxML as described in Phylogenetic Analysis Based on PRANK …
Figure 2—figure supplement 8
OSK Tree PRANK Comparison.
Comparison of the tree obtained with RaxML starting from the MUSCLE alignment (left) versus the PRANK alignment (right) for the OSK domain. Similarity scores for the branching events are color coded …
Figure 2—figure supplement 9
LOTUS Tree PRANK Comparison.
Comparison of the tree obtained with RaxML starting from the MUSCLE alignment (left) versus the PRANK alignment (right) for the LOTUS domain. Similarity scores for the branching events are color …
Figure 2—figure supplement 10
LOTUS Domain RaxML T-Coffee Tree.
Phylogenetic tree of the same sequences used for the previous LOTUS trees. The sequences were aligned using T-Coffee and the tree generated with RaxML as described in Phylogenetic Analysis Based on …
Figure 2—figure supplement 11
OSK Domain RaxML T-Coffee Tree.
Phylogenetic tree of the same sequences used for the previous OSK trees. The sequences were aligned using T-Coffee and the tree generated with RaxML as described in Phylogenetic Analysis Based on …
Figure 2—figure supplement 12
OSK Tree T-Coffee Comparison.
Comparison of the tree obtained with RaxML starting from the MUSCLE alignment (left) versus the T-Coffee alignment (right) for the OSK domain. Similarity scores for the branching events are color …
Figure 2—figure supplement 13
LOTUS Tree T-Coffee Comparison.
Comparison of the tree obtained with RaxML starting from the MUSCLE alignment (left) versus the T-Coffee alignment (right) for the LOTUS domain. Similarity scores for the branching events are color …
Figure 3
Hypothesis for the origin of oskar.
Integration of the OSK domain close to a LOTUS domain in an ancestral insect genome. (a) DNA containing a GDSL-like domain from an endosymbiotic germ line bacterium is transferred to the nucleus of …
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Additional files
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Source data 1
Alignment and Sequence Classification Tools & Data.
Subfolder "Alignments": All sequences identified and analyzed in this study, in FASTA format and with corresponding Alignments. Subfolder BLAST search results: Results of BLASTP searches with full length Oskar, OSK or LOTUS domains as queries. Subfolder "Data": Necessary files for running the different IPython notebooks: a. Subfolder "HMM": HMM models used for iterative searching for sequences similar to full-length Oskar, LOTUS and OSK domains; b. Subfolder "Taxonomy": Conversion table for UniProt ID to taxon information (uniprot_ID_taxa.tsv); c. Subfolder "Trees": Contains the tree files obtained from i. RaxML phylogenetic analyses of the OSK and LOTUS domains aligned with MUSCLE, T-Coffee or PRANK; ii. MrBayes phylogenetic analyses of the OSK and LOTUS domains aligned with MUSCLE; iii. SOWHAT analyses.
- https://cdn.elifesciences.org/articles/45539/elife-45539-data1-v2.zip
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Supplementary file 1
Supplementary tables.
(A) List of genomes and transcriptomes used for automated oskar search. (B) List of Oskar sequences used in the final alignment. (C) List of sequences used for phylogenetic analysis of the LOTUS domain. (D) List of sequences used for phylogenetic analysis of the OSK domain.
- https://cdn.elifesciences.org/articles/45539/elife-45539-supp1-v2.pdf
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Transparent reporting form
- https://cdn.elifesciences.org/articles/45539/elife-45539-transrepform-v2.docx
