Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome
Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats l...
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ftunivtroemsoe:oai:munin.uit.no:10037/4993 2023-05-15T14:30:32+02:00 Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome Zhuang, Xuan Yang, Chun Fevolden, Svein-Erik Cheng, Chi-Hing Christina 2012 https://hdl.handle.net/10037/4993 https://doi.org/10.1186/1471-2164-13-293 eng eng BMC Genomics (2012), vol. 13 (293) FRIDAID 933303 http://dx.doi.org/10.1186/1471-2164-13-293 1471-2164 https://hdl.handle.net/10037/4993 URN:NBN:no-uit_munin_4688 openAccess VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 Journal article Tidsskriftartikkel Peer reviewed 2012 ftunivtroemsoe https://doi.org/10.1186/1471-2164-13-293 2021-06-25T17:53:30Z Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits. Article in Journal/Newspaper Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua polar cod University of Tromsø: Munin Open Research Archive Arctic BMC Genomics 13 1 293 |
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Open Polar |
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University of Tromsø: Munin Open Research Archive |
op_collection_id |
ftunivtroemsoe |
language |
English |
topic |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 |
spellingShingle |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 Zhuang, Xuan Yang, Chun Fevolden, Svein-Erik Cheng, Chi-Hing Christina Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
topic_facet |
VDP::Mathematics and natural science: 400::Basic biosciences: 470::Genetics and genomics: 474 VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Genetikk og genomikk: 474 |
description |
Highly repetitive sequences are the bane of genome sequence assembly, and the short read lengths produced by current next generation sequencing technologies further exacerbates this obstacle. An adopted practice is to exclude repetitive sequences in genome data assembly, as the majority of repeats lack protein-coding genes. However, this could result in the exclusion of important genotypes in newly sequenced non-model species. The absence of the antifreeze glycoproteins (AFGP) gene family in the recently sequenced Atlantic cod genome serves as an example. The Atlantic cod (Gadus morhua) genome was assembled entirely from Roche 454 short reads, demonstrating the feasibility of this approach. However, a well-known major adaptive trait, the AFGP, essential for survival in frigid Arctic marine habitats was absent in the annotated genome. To assess whether this resulted from population difference, we performed Southern blot analysis of genomic DNA from multiple individuals from the North East Arctic cod population that the sequenced cod belonged, and verified that the AFGP genotype is indeed present. We searched the raw assemblies of the Atlantic cod using our G. morhua AFGP gene, and located partial AFGP coding sequences in two sequence scaffolds. We found these two scaffolds constitute a partial genomic AFGP locus through comparative sequence analyses with our newly assembled genomic AFGP locus of the related polar cod, Boreogadus saida. By examining the sequence assembly and annotation methodologies used for the Atlantic cod genome, we deduced the primary cause of the absence of the AFGP gene family from the annotated genome was the removal of all repetitive Roche 454 short reads before sequence assembly, which would exclude most of the highly repetitive AFGP coding sequences. Secondarily, the model teleost genomes used in projection annotation of the Atlantic cod genome have no antifreeze trait, perpetuating the unawareness that the AFGP gene family is missing. We recovered some of the missing AFGP coding sequences and reconstructed a partial AFGP locus in the Atlantic cod genome, bringing to light that not all repetitive sequences lack protein coding information. Also, reliance on genomes of model organisms as reference for annotating protein-coding gene content of a newly sequenced non-model species could lead to omission of novel genetic traits. |
format |
Article in Journal/Newspaper |
author |
Zhuang, Xuan Yang, Chun Fevolden, Svein-Erik Cheng, Chi-Hing Christina |
author_facet |
Zhuang, Xuan Yang, Chun Fevolden, Svein-Erik Cheng, Chi-Hing Christina |
author_sort |
Zhuang, Xuan |
title |
Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
title_short |
Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
title_full |
Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
title_fullStr |
Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
title_full_unstemmed |
Protein genes in repetitive sequence—antifreeze glycoproteins in Atlantic cod genome |
title_sort |
protein genes in repetitive sequence—antifreeze glycoproteins in atlantic cod genome |
publishDate |
2012 |
url |
https://hdl.handle.net/10037/4993 https://doi.org/10.1186/1471-2164-13-293 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua polar cod |
genre_facet |
Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua polar cod |
op_relation |
BMC Genomics (2012), vol. 13 (293) FRIDAID 933303 http://dx.doi.org/10.1186/1471-2164-13-293 1471-2164 https://hdl.handle.net/10037/4993 URN:NBN:no-uit_munin_4688 |
op_rights |
openAccess |
op_doi |
https://doi.org/10.1186/1471-2164-13-293 |
container_title |
BMC Genomics |
container_volume |
13 |
container_issue |
1 |
container_start_page |
293 |
_version_ |
1766304371093536768 |