Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa
Abstract The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome‐level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antar...
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crwiley:10.1002/jez.b.21341 2024-06-02T07:58:16+00:00 Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa Detrich, H. William Stuart, Andrew Schoenborn, Michael Parker, Sandra K. Methé, Barbara A. Amemiya, Chris T. 2010 http://dx.doi.org/10.1002/jez.b.21341 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjez.b.21341 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.21341 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Journal of Experimental Zoology Part B: Molecular and Developmental Evolution volume 314B, issue 5, page 369-381 ISSN 1552-5007 1552-5015 journal-article 2010 crwiley https://doi.org/10.1002/jez.b.21341 2024-05-03T11:24:36Z Abstract The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome‐level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high‐quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus . Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species ( n =6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66–1.83 pg ( n =4 species). The BAC libraries VMRC‐19 ( N. coriiceps ) and VMRC‐21 ( C. aceratus ) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library (∼0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus ) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus . Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life. J. Exp. Zool. (Mol. Dev. Evol.) 314B:369–381, 2010 . © 2010 Wiley‐Liss, Inc. Article in Journal/Newspaper Antarc* Antarctic Antarctica Icefish Southern Ocean Wiley Online Library Antarctic Southern Ocean Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 314B 5 369 381 |
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Open Polar |
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Wiley Online Library |
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English |
description |
Abstract The perciform suborder Notothenoidei provides a compelling opportunity to study the adaptive radiation of a marine species flock in the cold Southern Ocean surrounding Antarctica. To enable genome‐level studies of these psychrophilic fishes, we estimated the sizes of the genomes of 11 Antarctic species and generated high‐quality BAC libraries for 2, the notothen Notothenia coriiceps and the icefish Chaenocephalus aceratus . Our results indicate that evolution of phylogenetically derived notothenioid families, [e.g., the icefishes (Channichthyidae)], was accompanied by genome expansion. Species ( n =6) of the basal family Nototheniidae had C values that ranged between 0.98 and 1.20 pg, whereas those of the icefishes, the notothenioid crown group, were 1.66–1.83 pg ( n =4 species). The BAC libraries VMRC‐19 ( N. coriiceps ) and VMRC‐21 ( C. aceratus ) comprised 12X and 10X coverage of the respective genomes and had average insert sizes of 138 and 168 kb. Greater than 60% of paired BAC ends sampled from each library (∼0.1% of each genome) contained repetitive sequences, and the repetitive element landscapes of the 2 genomes (13.4% of the N. coriiceps genome and 14.5% for C. aceratus ) were similar. The representation and depth of coverage of the libraries were verified by identification of multiple Hox gene contigs: six discrete Hox clusters were found in N. coriiceps and at least five Hox clusters were found in C. aceratus . Given the unusual anatomical and physiological adaptations of the notothenioids, the availability of these BAC libraries sets the stage for expanded analysis of the psychrophilic mode of life. J. Exp. Zool. (Mol. Dev. Evol.) 314B:369–381, 2010 . © 2010 Wiley‐Liss, Inc. |
format |
Article in Journal/Newspaper |
author |
Detrich, H. William Stuart, Andrew Schoenborn, Michael Parker, Sandra K. Methé, Barbara A. Amemiya, Chris T. |
spellingShingle |
Detrich, H. William Stuart, Andrew Schoenborn, Michael Parker, Sandra K. Methé, Barbara A. Amemiya, Chris T. Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
author_facet |
Detrich, H. William Stuart, Andrew Schoenborn, Michael Parker, Sandra K. Methé, Barbara A. Amemiya, Chris T. |
author_sort |
Detrich, H. William |
title |
Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
title_short |
Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
title_full |
Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
title_fullStr |
Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
title_full_unstemmed |
Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 Representative Taxa |
title_sort |
genome enablement of the notothenioidei: genome size estimates from 11 species and bac libraries from 2 representative taxa |
publisher |
Wiley |
publishDate |
2010 |
url |
http://dx.doi.org/10.1002/jez.b.21341 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fjez.b.21341 https://onlinelibrary.wiley.com/doi/pdf/10.1002/jez.b.21341 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Antarctica Icefish Southern Ocean |
genre_facet |
Antarc* Antarctic Antarctica Icefish Southern Ocean |
op_source |
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution volume 314B, issue 5, page 369-381 ISSN 1552-5007 1552-5015 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1002/jez.b.21341 |
container_title |
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution |
container_volume |
314B |
container_issue |
5 |
container_start_page |
369 |
op_container_end_page |
381 |
_version_ |
1800741561936379904 |