Using sequencing coverage statistics to identify sex chromosomes in minke whales
The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems and identifying genes on sex chromosomes. This not only hel...
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ftdatacite:10.48550/arxiv.1902.06654 2023-05-15T14:06:26+02:00 Using sequencing coverage statistics to identify sex chromosomes in minke whales Malde, Ketil Skern, Rasmus Glover, Kevin A. 2019 https://dx.doi.org/10.48550/arxiv.1902.06654 https://arxiv.org/abs/1902.06654 unknown arXiv Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 CC-BY Genomics q-bio.GN FOS Biological sciences Preprint Article article CreativeWork 2019 ftdatacite https://doi.org/10.48550/arxiv.1902.06654 2022-04-01T08:46:59Z The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems and identifying genes on sex chromosomes. This not only helps reveal mechanisms behind sex determination in the species under study, but their characteristics make sex chromosomes a unique tool for studying the mechanisms and effects of recombination and genomic rearrangements and how they affect adaption and selection. Despite this, many sequencing projects omit such investigations. Here, we apply a simple method using sequencing coverage statistics to identify scaffolds belonging to the sex chromosomes of minke whale, and show how the sex chromosome system can be determined using coverage statistics alone. Using publicly available data, we identify the previously unknown sex of an Antarctic minke whale as female. We further investigate public sequence data from the different species and sub-species of minke whale, and classify genomic scaffolds from a published minke whale assembly as X or Y chromosomal sequences. Our findings are consistent with previous results that identified a handful of scaffolds as sex chromosomal, but we are able to identify a much larger set of scaffolds, likely to represent close to the complete sex chromosomal sequences for the minke whale. Sequence coverage statistics provides a readily available tool for investigating the sex determination system and locate genes on sex chromosomes. This analysis is straightforward and can often be performed with existing resources. Report Antarc* Antarctic Antarctic Minke whale minke whale DataCite Metadata Store (German National Library of Science and Technology) Antarctic |
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DataCite Metadata Store (German National Library of Science and Technology) |
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Genomics q-bio.GN FOS Biological sciences |
spellingShingle |
Genomics q-bio.GN FOS Biological sciences Malde, Ketil Skern, Rasmus Glover, Kevin A. Using sequencing coverage statistics to identify sex chromosomes in minke whales |
topic_facet |
Genomics q-bio.GN FOS Biological sciences |
description |
The ever-increasing number of genome sequencing and resequencing projects is a central source of insights into the ecology and evolution of non-model organisms. An important aspect of genomics is the elucidation of sex determination systems and identifying genes on sex chromosomes. This not only helps reveal mechanisms behind sex determination in the species under study, but their characteristics make sex chromosomes a unique tool for studying the mechanisms and effects of recombination and genomic rearrangements and how they affect adaption and selection. Despite this, many sequencing projects omit such investigations. Here, we apply a simple method using sequencing coverage statistics to identify scaffolds belonging to the sex chromosomes of minke whale, and show how the sex chromosome system can be determined using coverage statistics alone. Using publicly available data, we identify the previously unknown sex of an Antarctic minke whale as female. We further investigate public sequence data from the different species and sub-species of minke whale, and classify genomic scaffolds from a published minke whale assembly as X or Y chromosomal sequences. Our findings are consistent with previous results that identified a handful of scaffolds as sex chromosomal, but we are able to identify a much larger set of scaffolds, likely to represent close to the complete sex chromosomal sequences for the minke whale. Sequence coverage statistics provides a readily available tool for investigating the sex determination system and locate genes on sex chromosomes. This analysis is straightforward and can often be performed with existing resources. |
format |
Report |
author |
Malde, Ketil Skern, Rasmus Glover, Kevin A. |
author_facet |
Malde, Ketil Skern, Rasmus Glover, Kevin A. |
author_sort |
Malde, Ketil |
title |
Using sequencing coverage statistics to identify sex chromosomes in minke whales |
title_short |
Using sequencing coverage statistics to identify sex chromosomes in minke whales |
title_full |
Using sequencing coverage statistics to identify sex chromosomes in minke whales |
title_fullStr |
Using sequencing coverage statistics to identify sex chromosomes in minke whales |
title_full_unstemmed |
Using sequencing coverage statistics to identify sex chromosomes in minke whales |
title_sort |
using sequencing coverage statistics to identify sex chromosomes in minke whales |
publisher |
arXiv |
publishDate |
2019 |
url |
https://dx.doi.org/10.48550/arxiv.1902.06654 https://arxiv.org/abs/1902.06654 |
geographic |
Antarctic |
geographic_facet |
Antarctic |
genre |
Antarc* Antarctic Antarctic Minke whale minke whale |
genre_facet |
Antarc* Antarctic Antarctic Minke whale minke whale |
op_rights |
Creative Commons Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/legalcode cc-by-4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.48550/arxiv.1902.06654 |
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1766278137450070016 |