dc.contributor.author |
Sharma, Diksha |
|
dc.contributor.author |
Denmat, Sylvie Hermann-Le |
|
dc.contributor.author |
Matzke, Nicholas J |
|
dc.contributor.author |
Hannan, Katherine |
|
dc.contributor.author |
Hannan, Ross D |
|
dc.contributor.author |
O'Sullivan, Justin M |
|
dc.contributor.author |
Ganley, Austen RD |
|
dc.coverage.spatial |
United States |
|
dc.date.accessioned |
2022-08-15T00:20:29Z |
|
dc.date.available |
2022-08-15T00:20:29Z |
|
dc.date.issued |
2022-07-10 |
|
dc.identifier.citation |
(2022). Genomics, 114(4), 110430-. |
|
dc.identifier.issn |
0888-7543 |
|
dc.identifier.uri |
https://hdl.handle.net/2292/60786 |
|
dc.description.abstract |
Ribosomal DNA genes (rDNA) encode the major ribosomal RNAs and in eukaryotes typically form tandem repeat arrays. Species have characteristic rDNA copy numbers, but there is substantial intra-species variation in copy number that results from frequent rDNA recombination. Copy number differences can have phenotypic consequences, however difficulties in quantifying copy number mean we lack a comprehensive understanding of how copy number evolves and the consequences. Here we present a genomic sequence read approach to estimate rDNA copy number based on modal coverage to help overcome limitations with existing mean coverage-based approaches. We validated our method using Saccharomyces cerevisiae strains with known rDNA copy numbers. Application of our pipeline to a global sample of S. cerevisiae isolates showed that different populations have different rDNA copy numbers. Our results demonstrate the utility of the modal coverage method, and highlight the high level of rDNA copy number variation within and between populations. |
|
dc.format.medium |
Print-Electronic |
|
dc.language |
eng |
|
dc.publisher |
Elsevier |
|
dc.relation.ispartofseries |
Genomics |
|
dc.rights |
Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher. |
|
dc.rights.uri |
https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm |
|
dc.rights.uri |
https://creativecommons.org/licenses/by/4.0/ |
|
dc.subject |
Bioinformatics method |
|
dc.subject |
Copy number |
|
dc.subject |
Ribosomal DNA |
|
dc.subject |
Saccharomyces cerevisiae |
|
dc.subject |
Sequence read coverage |
|
dc.subject |
Tandem repeats |
|
dc.subject |
Genetics |
|
dc.subject |
Human Genome |
|
dc.subject |
0604 Genetics |
|
dc.subject |
0806 Information Systems |
|
dc.title |
A new method for determining ribosomal DNA copy number shows differences between Saccharomyces cerevisiae populations. |
|
dc.type |
Journal Article |
|
dc.identifier.doi |
10.1016/j.ygeno.2022.110430 |
|
pubs.issue |
4 |
|
pubs.begin-page |
110430 |
|
pubs.volume |
114 |
|
dc.date.updated |
2022-07-23T00:11:10Z |
|
dc.rights.holder |
Copyright: The authors |
en |
dc.identifier.pmid |
35830947 (pubmed) |
|
pubs.author-url |
https://www.ncbi.nlm.nih.gov/pubmed/35830947 |
|
pubs.publication-status |
Published |
|
dc.rights.accessrights |
http://purl.org/eprint/accessRights/OpenAccess |
en |
pubs.subtype |
Journal Article |
|
pubs.elements-id |
912242 |
|
pubs.org-id |
Liggins Institute |
|
pubs.org-id |
Science |
|
pubs.org-id |
Biological Sciences |
|
dc.identifier.eissn |
1089-8646 |
|
dc.identifier.pii |
S0888-7543(22)00175-6 |
|
pubs.number |
110430 |
|
pubs.record-created-at-source-date |
2022-07-23 |
|
pubs.online-publication-date |
2022-07 |
|