Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles
Simple Summary Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a me...
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ftchinacadsciihb:oai:ir.ihb.ac.cn:342005/38567 2023-05-15T16:42:08+02:00 Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles Chen, Rui-Yi Hieu, Bui Thi Ngoc Audira, Gilbert Lou, Bao Lin, Ming-Der Hsiao, Chung-Der 2020-07-01 http://ir.ihb.ac.cn/handle/342005/38567 https://doi.org/10.3390/ani10071130 英语 eng MDPI ANIMALS http://ir.ihb.ac.cn/handle/342005/38567 doi:10.3390/ani10071130 myoglobin hemoglobin fish meta-transcriptomic Agriculture Veterinary Sciences Dairy & Animal Science PIARACTUS-MESOPOTAMICUS HOLMBERG BELTFISH TRICHIURUS-LEPTURUS GENE-EXPRESSION CYTOGLOBIN CARP 期刊论文 2020 ftchinacadsciihb https://doi.org/10.3390/ani10071130 2020-12-04T01:07:25Z Simple Summary Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a meta-transcriptomic approach. By using RNAseq data, this is the first study to examine the high level of myoglobin, one of the oxygen-binding proteins, transcripts in pacu and loach fish that might be related to their high tolerance for the oxygen-deficient environment. In addition, this study presents the power of the current method to compare the fish oxygen-binding protein expression and its putative gene expansion event. 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. Report Icefish Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR Animals 10 7 1130 |
institution |
Open Polar |
collection |
Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR |
op_collection_id |
ftchinacadsciihb |
language |
English |
topic |
myoglobin hemoglobin fish meta-transcriptomic Agriculture Veterinary Sciences Dairy & Animal Science PIARACTUS-MESOPOTAMICUS HOLMBERG BELTFISH TRICHIURUS-LEPTURUS GENE-EXPRESSION CYTOGLOBIN CARP |
spellingShingle |
myoglobin hemoglobin fish meta-transcriptomic Agriculture Veterinary Sciences Dairy & Animal Science PIARACTUS-MESOPOTAMICUS HOLMBERG BELTFISH TRICHIURUS-LEPTURUS GENE-EXPRESSION CYTOGLOBIN CARP Chen, Rui-Yi Hieu, Bui Thi Ngoc Audira, Gilbert Lou, Bao Lin, Ming-Der Hsiao, Chung-Der Meta-Transcriptomic Analysis of RNAseq Data Reveals Pacu and Loach Fish with Unusually High Levels of Myoglobin Expression in Skeletal Muscles |
topic_facet |
myoglobin hemoglobin fish meta-transcriptomic Agriculture Veterinary Sciences Dairy & Animal Science PIARACTUS-MESOPOTAMICUS HOLMBERG BELTFISH TRICHIURUS-LEPTURUS GENE-EXPRESSION CYTOGLOBIN CARP |
description |
Simple Summary Oxygen-binding proteins that mediate oxygen-binding for storage and consumption, to reduce energy, are very diverse in fish, depending on their habitats. In the present study, oxygen-binding protein gene expression in the skeletal muscle of 25 diverse fish species was examined by a meta-transcriptomic approach. By using RNAseq data, this is the first study to examine the high level of myoglobin, one of the oxygen-binding proteins, transcripts in pacu and loach fish that might be related to their high tolerance for the oxygen-deficient environment. In addition, this study presents the power of the current method to compare the fish oxygen-binding protein expression and its putative gene expansion event. 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 |
Report |
author |
Chen, Rui-Yi Hieu, Bui Thi Ngoc Audira, Gilbert Lou, Bao Lin, Ming-Der Hsiao, Chung-Der |
author_facet |
Chen, Rui-Yi Hieu, Bui Thi Ngoc Audira, Gilbert Lou, Bao Lin, Ming-Der Hsiao, Chung-Der |
author_sort |
Chen, Rui-Yi |
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 |
MDPI |
publishDate |
2020 |
url |
http://ir.ihb.ac.cn/handle/342005/38567 https://doi.org/10.3390/ani10071130 |
genre |
Icefish |
genre_facet |
Icefish |
op_relation |
ANIMALS http://ir.ihb.ac.cn/handle/342005/38567 doi:10.3390/ani10071130 |
op_doi |
https://doi.org/10.3390/ani10071130 |
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Animals |
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10 |
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1130 |
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1766032571816214528 |