Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles
Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-...
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ftmdpi:oai:mdpi.com:/2076-2615/10/7/1130/ 2023-08-20T04:07:18+02:00 Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles Rui-Yi Chen Bui Thi Ngoc Hieu Gilbert Audira Bao Lou Ming-Der Lin Chung-Der Hsiao agris 2020-07-03 application/pdf https://doi.org/10.3390/ani10071130 EN eng Multidisciplinary Digital Publishing Institute Animal Genetics and Genomics https://dx.doi.org/10.3390/ani10071130 https://creativecommons.org/licenses/by/4.0/ Animals; Volume 10; Issue 7; Pages: 1130 myoglobin hemoglobin fish meta-transcriptomic Text 2020 ftmdpi https://doi.org/10.3390/ani10071130 2023-07-31T23:43:30Z Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish. Text Icefish MDPI Open Access Publishing Animals 10 7 1130 |
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myoglobin hemoglobin fish meta-transcriptomic |
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myoglobin hemoglobin fish meta-transcriptomic Rui-Yi Chen Bui Thi Ngoc Hieu Gilbert Audira Bao Lou Ming-Der Lin Chung-Der Hsiao Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
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myoglobin hemoglobin fish meta-transcriptomic |
description |
Oxygen-binding proteins, such as myoglobin, hemoglobin, neuroglobin, and cytoglobin, play a role in oxygen binding and delivery to tissues. In icefish, the loss of myoglobin and hemoglobin genes has been reported to be an adaptive evolution event. This interesting finding prompted us to exam oxygen-binding protein expression in diverse fish species. Taking advantage of substantial RNAseq data deposited in the NCBI (National Center for Biotechnology Information) database, we adopted a meta-transcriptomic approach to explore and compare four oxygen-binding protein gene expression levels in the skeletal muscle of 25 diverse fish species for the first time. RNAseq data were downloaded from the NCBI Sequence Read Archive (SRA) database, and de novo assembly was performed to generate transcript contigs. The genes encoding oxygen-binding proteins were then identified by the BLAST search, and the relative expression level of oxygen-binding protein genes was normalized by the RPKM (Reads per Kilobase Million) method. By performing expression profiling, hierarchy clustering, and principal component analysis, pacu and loach fish were noticed by their high myoglobin expression levels in skeletal muscle tissues among 25 diverse fish species. In conclusion, we demonstrated that meta-transcriptomic analysis of RNAseq data is an informative approach to compare the oxygen-binding protein expression and putative gene expansion event in fish. |
format |
Text |
author |
Rui-Yi Chen Bui Thi Ngoc Hieu Gilbert Audira Bao Lou Ming-Der Lin Chung-Der Hsiao |
author_facet |
Rui-Yi Chen Bui Thi Ngoc Hieu Gilbert Audira Bao Lou Ming-Der Lin Chung-Der Hsiao |
author_sort |
Rui-Yi Chen |
title |
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
title_short |
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
title_full |
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
title_fullStr |
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
title_full_unstemmed |
Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
title_sort |
meta-transcriptomic analysis of rnaseq data reveals pacu and loach fish with unusually high levels of myoglobin expression in skeletal muscles |
publisher |
Multidisciplinary Digital Publishing Institute |
publishDate |
2020 |
url |
https://doi.org/10.3390/ani10071130 |
op_coverage |
agris |
genre |
Icefish |
genre_facet |
Icefish |
op_source |
Animals; Volume 10; Issue 7; Pages: 1130 |
op_relation |
Animal Genetics and Genomics https://dx.doi.org/10.3390/ani10071130 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.3390/ani10071130 |
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Animals |
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7 |
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1130 |
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1774718814477352960 |