Data supporting the thesis "The Evolutionary Genomics of Chlamydomonas"

  • Rory Craig (Depositor)

Dataset

Abstract

Files from the PhD thesis "The Evolutionary Genomics of Chlamydomonas" by Rory Craig.

Appendix C:
Supplementary Material for Chapter 3:
Note S1. High molecular weight DNA extraction protocol for Chlamydomonas.
Dataset S1: Annotation notes for curated transposable elements from Chlamydomonas incerta, Chlamydomonas schloesseri, Edaphochlamys debaryana, Eudorina sp. and Volvox carteri. See Appendix E, Dataset S1 for Chlamydomonas reinhardtii transposable element annotation notes.

Dataset S2: Assembly metrics for genome assemblies of all available Reinhardtinia species and selected outgroups.

Dataset S3: Gene model annotation metrics for all available Reinhardtinia species and selected outgroups.

Dataset S4. List of contigs terminating in telomeric repeats.

Dataset S5. Orthogroup and InterPro domain annotation for Chlamydomonas-specific orthogroups with annotated domains.

Dataset S6: Orthogroup and InterPro domain annotation for E. debaryana gene family expansions (log2-transformed ratios >1) and contractions (ratios <-1) .

Dataset S7: Presence-absence of C. reinhardtii MT– genes in C. incerta, C. schloesseri and E. debaryana.

Dataset S8: New genes identified with significant blastp homology to proteins from the C. reinhardtii v4.3 annotation.

Dataset S9: Core-Reinhardtinia ultraconserved elements (elements >=50 bp, 100% conservation within Chlamydomonas and >=95% conservation across eight core-Reinhardtinia species).


Appendix D: Supplementary Material for Chapter 4:

Dataset S1: Metrics and sequence context of all CC-503 v6 assembly gaps.

Dataset S2: Curated structural mutations unique to the CC-503 v6 assembly.

Dataset S3: Curated structural mutations unique to the CC-4532 v6 assembly.

Dataset S4. Metrics and sequence context of all CC-4532 v6 assembly gaps.

Dataset S5. Curated TE transposition events unique to the CC-503 v6 assembly.

Dataset S6: Curated TE transposition events unique to the CC-4452 v6 assembly.


Appendix E: Supplementary Material for Chapter 5:
Dataset S1: Annotation notes for the updated transposable element library for Chlamydomonas reinhardtii.

Dataset S2: Chlamys annotation notes.

Dataset S3: Naiad annotation notes.

Dataset S4. Chlamys-like annotation notes.

Dataset S5. Hydra annotation notes.

Data Citation

University of Edinburgh. School of Biological Sciences. Institute of Evolutionary Biology. (2021). Data supporting the thesis "The Evolutionary Genomics of Chlamydomonas", [dataset]. https://doi.org/10.7488/ds/3103.
Date made available2 Aug 2021
PublisherEdinburgh DataShare

Cite this