Comparative genomics reveals insight into the evolutionary origin of massively scrambled genomes

Abstract
Data availability
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Abstract

Ciliates are microbial eukaryotes that undergo extensive programmed genome rearrangement, a natural genome editing process that converts long germline chromosomes into smaller gene-rich somatic chromosomes. Three well-studied ciliates include Oxytricha trifallax, Tetrahymena thermophila and Paramecium tetraurelia, but only the Oxytricha lineage has a massively scrambled genome, whose assembly during development requires hundreds of thousands of precise programmed DNA joining events, representing the most complex genome dynamics of any known organism. Here we study the emergence of such complex genomes by examining the origin and evolution of discontinuous and scrambled genes in the Oxytricha lineage. This study compares six genomes from three species, the germline and somatic genomes for Euplotes woodruffi, Tetmemena sp., and the model ciliate Oxytricha trifallax. To complement existing data, we sequenced, assembled and annotated the germline and somatic genomes of Euplotes woodruffi, which provides an outgroup, and the germline genome of Tetmemena sp.. We find that the germline genome of Tetmemena is as massively scrambled and interrupted as Oxytricha's : 13.6% of its gene loci require programmed translocations and/or inversions, with some genes requiring hundreds of precise gene editing events during development. This study revealed that the earlier-diverged spirotrich, E. woodruffi, also has a scrambled genome, but only roughly half as many loci (7.3%) are scrambled. Furthermore, its scrambled genes are less complex, together supporting the position of Euplotes as a possible evolutionary intermediate in this lineage, in the process of accumulating complex evolutionary genome rearrangements, all of which require extensive repair to assemble functional coding regions. Comparative analysis also reveals that scrambled loci are often associated with local duplications, supporting a gradual model for the origin of complex, scrambled genomes via many small events of DNA duplication and decay.

Data availability

Custom scripts are public on https://github.com/yifeng-evo/Oxytricha_Tetmemena_Euplotes. DNA-seq reads and genome assemblies are available at GenBank under Bioprojects PRJNA694964 (Tetmemena sp.) and PRJNA781979 (Euplotes woodruffi). Genbank accession numbers for genomes are JAJKFJ000000000 (Tetmemena sp. Micronucleus genome), JAJLLS000000000 (Euplotes woodruffi Micronucleus genome), and JAJLLT000000000 (Euplotes woodruffi Macronucleus genome).Three replicates of RNA-seq reads for vegetative cells are available at GenBank under accession numbers of SRR21815378, SRR21815379, SRR21815380 for E. woodruffi and SRR21817702, SRR21817703 and SRR21817704 for Tetmemena sp..MDSs annotations for three species are available at https://doi.org/10.5061/dryad.5dv41ns96 and https://knot.math.usf.edu/mds_ies_db/2022/downloads.html (please select species from the drop-down menu).

The following data sets were generated

(2022) Euplotes woodruffi genome sequencing and assembly
NCBI Bioproject, PRJNA781979.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA781979
(2022) etmemena sp. micronucleus genome sequencing and assembly
NCBI Bioproject, PRJNA694964.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA694964
(2022) Euplotes woodruffi RNA-seq for vegetative cells
NCBI Bioproject, PRJNA781602.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA781602
(2022) Tetmemena sp. RNA-seq for vegetative cells
NCBI Bioproject, PRJNA887426.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887426
(2022) MDS-IES database
https://knot.math.usf.edu/mds_ies_db/2022/downloads.html.

https://knot.math.usf.edu/mds_ies_db/2022/downloads.html
1. Feng Y
2. Neme R
3. Beh L
4. Chen X
5. Braun J
6. Lu M
7. Landweber L
(2022) MDS and IES annotations for Euplotes woodruff, Tetmemena sp. and Oxytricha trifallax
Dryad Digital Repository, doi:10.5061/dryad.5dv41ns96.

https://doi.org/10.5061/dryad.5dv41ns96

The following previously published data sets were used

1. Chen X
2. Bracht JR
3. Goldman AD
4. Dolzhenko E
5. Clay DM
6. Swart EC
7. Perlman DH
8. Doak TG
9. Stuart A
10. Amemiya CT
11. Sebra RP
12. Landweber LF
(2014) Oxytricha trifallax micronucleus genome
Genbank GCA_000711775.1.

https://www.ncbi.nlm.nih.gov/assembly/GCA_000711775.1
1. Swart EC
2. Bracht JR
3. Magrini V
4. Minx P
5. Chen X
6. Zhou Y
7. Khurana JS
8. Goldman AD
9. Nowacki M
10. Schotanus K
11. Jung S
12. Ly A
13. McGrath S
14. Haub K
15. Wiggins JL
16. Storton D
17. Matese JC
18. Parsons L
19. Chang WJ
20. Bowen MS
21. Stover NA
22. Jones TA
23. Eddy SR
24. Herrick GA
25. Doak TG
26. Wilson RK
27. Mardis ER
28. Landweber LF
(2013) Oxytricha trifallax macronucleus genome
Genbank GCA_000295675.1.

https://www.ncbi.nlm.nih.gov/assembly/GCA_000295675.1/
1. Chen X
2. Jung S
3. Beh LY
4. Eddy SR
5. Landweber LF.
(2015) Tetmemena sp. macronucleus genome
Genbank GCA_001273295.2.

https://www.ncbi.nlm.nih.gov/assembly/GCA_001273295.2
(2019) Oxytricha trifallax RNA-seq for vegetative cells
NCBI SRA SRX5944382, SRX5944383 and SRX5944384.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE94421

Article and author information

Author details

Yi Feng

Department of Biological Sciences, Columbia University, New York, United States

Competing interests
No competing interests declared.
Rafik Neme

Department of Chemistry and Biology, Universidad del Norte, Barranquilla, Colombia

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0001-8462-5291
Leslie Y Beh

Department of Biochemistry, Columbia University, New York, United States

Competing interests
Leslie Y Beh, The author is currently employed by Illumina.
Xiao Chen

Pacific Biosciences, Menlo Park, United States

Competing interests
Xiao Chen, employed by Pacific Biosciences.

"This ORCID iD identifies the author of this article:" 0000-0002-1432-268X
Jasper Braun

Department of Mathematics and Statistics, University of South Florida, Tampa, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-1250-4399
Michael W Lu

Department of Biochemistry, Columbia University, New York, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-4926-8839
Laura F Landweber

Department of Biochemistry, Columbia University, New York, United States

For correspondence
Laura.Landweber@columbia.edu

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-7030-8540

Funding

National Institutes of Health (R35GM122555)

Yi Feng

National Science Foundation (DMS1764366)

Yi Feng

Pew Latin American Fellows Program (no)

Rafik Neme

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.