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Nucleotide substitution rates of diatom plastid encoded protein genes are correlated with genome architecture

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Nucleotide substitution rates of diatom plastid encoded protein genes are correlated with genome architecture https://t.co/oG27cT8hkU https://t.co/BYKfldSKQR
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Supplemental Information

Fig. S1. Maximum likelihood phylogeny of 40 diatom species and outgroup Triparma laevis

Maximum likelihood phylogeny of 40 diatom species and outgroup Triparma laevis. Phylogeny was used as constraint tree in substitution rate analyses. Bootstrap values less than 100% are indicated at the nodes. * indicates bootstrap of 100%. Scale is substitutions per codon.

DOI: 10.7287/peerj.preprints.27636v1/supp-1

Fig. S2. Distribution of nonsynonymous (dN) substitution rates for groups of genes and individual genes

Distribution of nonsynonymous (dN) substitution rates for groups of genes and individual genes. The top and bottom lines of each box represent the 75th and 25th percentiles, respectively and the middle line in each box represents the 50th percentile. The whisker lines represent the minimum to the maximum points and the points outside of the whisker lines are outliers.

DOI: 10.7287/peerj.preprints.27636v1/supp-2

Fig. S3. Distribution of synonymous (dS) substitution rates for groups of genes and individual genes

Distribution of synonymous (dS) substitution rates for groups of genes and individual genes. The top and bottom lines of each box represent the 75th and 25th percentiles, respectively and the middle line in each box represents the 50th percentile. The whisker lines represent the minimum to the maximum points and the points outside of the whisker lines are outliers.

DOI: 10.7287/peerj.preprints.27636v1/supp-3

Fig S4. Relationship between the plastome size (one IR copy was excluded) and substitution rate

DOI: 10.7287/peerj.preprints.27636v1/supp-4

Table S1. Taxa included in diatom plastome analyses and NCBI accession numbers

DOI: 10.7287/peerj.preprints.27636v1/supp-5

Table S2. Plastid genes and functional groups included in rates analyses

DOI: 10.7287/peerj.preprints.27636v1/supp-6

Table S3. Local collinear blocks (LCBs) for each of the 40 diatom plastomes identified by Mauve

DOI: 10.7287/peerj.preprints.27636v1/supp-7

Table S4. Pairwise inversion distance inferred by GRIMM of 40 diatom plastomes

DOI: 10.7287/peerj.preprints.27636v1/supp-8

Table S5. Nucleotide substitution rates and plastome features included in correlation analyses

DOI: 10.7287/peerj.preprints.27636v1/supp-9

Table S6. Correlation coefficient and adjusted P-values for correlation between substitution rates and plastome rearrangement measured by inversion distance

DOI: 10.7287/peerj.preprints.27636v1/supp-10

Additional Information

Competing Interests

There are no competing interests

Author Contributions

Mengjie Yu conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, approved the final draft.

Tracey A Ruhlman analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Nahid H Hajrah authored or reviewed drafts of the paper, approved the final draft.

Mohammad A Khiyami authored or reviewed drafts of the paper, approved the final draft, secured funding.

Mumdooh J Sabir analyzed the data, approved the final draft.

Mohammed H. Alblowi authored or reviewed drafts of the paper, approved the final draft.

Alawiah M. Alhebshi authored or reviewed drafts of the paper, approved the final draft.

Abdulrahman Al-Malki L. Al-Malki authored or reviewed drafts of the paper, approved the final draft.

Jamal S.M. Sabir conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft, secured funding.

Edward C. Theriot conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Robert K Jansen conceived and designed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

NCBI Genbank and accession numbers are listed in Supplemental table S1

Funding

The President of King Abdulaziz University, Prof. Abdulrahman O. Alyoubi, provided funding support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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