Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)
Striped catfish ( Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong...
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ftunivqespace:oai:espace.library.uq.edu.au:UQ:360885 2023-05-15T15:27:45+02:00 Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) Thanh, Nguyen Minh Jung, Hyungtaek Lyons, Russell E. Njaci, Isaac Yoon, Byoung-Ha Chand, Vincent Tuan, Nguyen Viet Thu, Vo Thi Minh Mather, Peter 2015-05-12 https://espace.library.uq.edu.au/view/UQ:360885 eng eng Elsevier doi:10.1016/j.margen.2015.05.001 issn:1874-7787 issn:1876-7478 orcid:0000-0002-0795-7994 106.99-2011.63 Ion Torrent Pangasianodon hypophthalmus Salinity tolerance Simple sequence repeat 1104 Aquatic Science 1311 Genetics Journal Article 2015 ftunivqespace https://doi.org/10.1016/j.margen.2015.05.001 2020-11-30T23:48:20Z Striped catfish ( Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97. bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478. bp and N50 length of 506. bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species. Article in Journal/Newspaper atlantic cod The University of Queensland: UQ eSpace Marine Genomics 23 87 97 |
institution |
Open Polar |
collection |
The University of Queensland: UQ eSpace |
op_collection_id |
ftunivqespace |
language |
English |
topic |
Ion Torrent Pangasianodon hypophthalmus Salinity tolerance Simple sequence repeat 1104 Aquatic Science 1311 Genetics |
spellingShingle |
Ion Torrent Pangasianodon hypophthalmus Salinity tolerance Simple sequence repeat 1104 Aquatic Science 1311 Genetics Thanh, Nguyen Minh Jung, Hyungtaek Lyons, Russell E. Njaci, Isaac Yoon, Byoung-Ha Chand, Vincent Tuan, Nguyen Viet Thu, Vo Thi Minh Mather, Peter Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
topic_facet |
Ion Torrent Pangasianodon hypophthalmus Salinity tolerance Simple sequence repeat 1104 Aquatic Science 1311 Genetics |
description |
Striped catfish ( Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97. bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478. bp and N50 length of 506. bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species. |
format |
Article in Journal/Newspaper |
author |
Thanh, Nguyen Minh Jung, Hyungtaek Lyons, Russell E. Njaci, Isaac Yoon, Byoung-Ha Chand, Vincent Tuan, Nguyen Viet Thu, Vo Thi Minh Mather, Peter |
author_facet |
Thanh, Nguyen Minh Jung, Hyungtaek Lyons, Russell E. Njaci, Isaac Yoon, Byoung-Ha Chand, Vincent Tuan, Nguyen Viet Thu, Vo Thi Minh Mather, Peter |
author_sort |
Thanh, Nguyen Minh |
title |
Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
title_short |
Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
title_full |
Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
title_fullStr |
Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
title_full_unstemmed |
Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus) |
title_sort |
optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (pangasianodon hypophthalmus) |
publisher |
Elsevier |
publishDate |
2015 |
url |
https://espace.library.uq.edu.au/view/UQ:360885 |
genre |
atlantic cod |
genre_facet |
atlantic cod |
op_relation |
doi:10.1016/j.margen.2015.05.001 issn:1874-7787 issn:1876-7478 orcid:0000-0002-0795-7994 106.99-2011.63 |
op_doi |
https://doi.org/10.1016/j.margen.2015.05.001 |
container_title |
Marine Genomics |
container_volume |
23 |
container_start_page |
87 |
op_container_end_page |
97 |
_version_ |
1766358163043385344 |