Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis
Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which...
Published in: | Comparative Biochemistry and Physiology Part D: Genomics and Proteomics |
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ftchinacadsciihb:oai:ir.ihb.ac.cn:342005/42874 2023-05-15T15:32:42+02:00 Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis Luo, Weiwei Wang, Junru Yu, Xiaomu Zhou, Ying Tong, Jingou 2020-12-01 http://ir.ihb.ac.cn/handle/342005/42874 https://doi.org/10.1016/j.cbd.2020.100752 英语 eng ELSEVIER SCIENCE INC COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS http://ir.ihb.ac.cn/handle/342005/42874 doi:10.1016/j.cbd.2020.100752 Bighead carp Body deformity Transcriptome Muscles Vertebrae Differentially expressed genes (DEGs) Biochemistry & Molecular Biology Genetics & Heredity SALMO-SALAR L ATLANTIC SALMON SEA BREAM MORPHOLOGICAL DEFORMITIES SKELETAL DEVELOPMENT JAPANESE FLOUNDER ANGUILLA-JAPONICA CULTURED LARVAE BONE EXPRESSION 期刊论文 2020 ftchinacadsciihb https://doi.org/10.1016/j.cbd.2020.100752 2021-03-12T01:07:47Z Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differen-tially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis. Report Atlantic salmon Salmo salar Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 36 100752 |
institution |
Open Polar |
collection |
Institute of Hydrobiology, Chinese Academy of Sciences: IHB OpenIR |
op_collection_id |
ftchinacadsciihb |
language |
English |
topic |
Bighead carp Body deformity Transcriptome Muscles Vertebrae Differentially expressed genes (DEGs) Biochemistry & Molecular Biology Genetics & Heredity SALMO-SALAR L ATLANTIC SALMON SEA BREAM MORPHOLOGICAL DEFORMITIES SKELETAL DEVELOPMENT JAPANESE FLOUNDER ANGUILLA-JAPONICA CULTURED LARVAE BONE EXPRESSION |
spellingShingle |
Bighead carp Body deformity Transcriptome Muscles Vertebrae Differentially expressed genes (DEGs) Biochemistry & Molecular Biology Genetics & Heredity SALMO-SALAR L ATLANTIC SALMON SEA BREAM MORPHOLOGICAL DEFORMITIES SKELETAL DEVELOPMENT JAPANESE FLOUNDER ANGUILLA-JAPONICA CULTURED LARVAE BONE EXPRESSION Luo, Weiwei Wang, Junru Yu, Xiaomu Zhou, Ying Tong, Jingou Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
topic_facet |
Bighead carp Body deformity Transcriptome Muscles Vertebrae Differentially expressed genes (DEGs) Biochemistry & Molecular Biology Genetics & Heredity SALMO-SALAR L ATLANTIC SALMON SEA BREAM MORPHOLOGICAL DEFORMITIES SKELETAL DEVELOPMENT JAPANESE FLOUNDER ANGUILLA-JAPONICA CULTURED LARVAE BONE EXPRESSION |
description |
Body deformity occurs both in wild and farmed fishes, which is one of the most challenging problems for aquaculture industry. In most cases, such body deformities are linked to skeletal deformities. Currently, very limited information is available on skeletal deformities of farmed fish species which may be caused by genetic factor. In this study, we performed muscle and vertebra transcriptome analyses in body deformity and normality of bighead carp Hypophthalmichthys nobilis (from one meiotic gynogenesis family) using RNA-Seq. A total of 43,923 and 44,416 unigenes were predicted in muscles and vertebrae, respectively. Based on these data, we further explored the gene expression profiles in gynogenetic normal and abnormal bighead carp. No differen-tially expressed gene (DEG) was found in transcriptome data of muscles. Totally, 20 key DEGs were identified in transcriptome data of vertebrae, such as low density lipoprotein-related protein 2 (lrp2), bone morphogenetic protein 2B (bmp2b) and collagen alpha-1(IV) (col4a1). 12 potential pathways were also identified in vertebra transcriptome data, which were mainly involved in development, growth, cytoskeleton and energy metabolism, such as MAPK signaling pathway, regulation of actin cytoskeleton and TGF-beta signaling pathway. Results of this study will be informative for the understanding of genetic mechanisms for body shape formation and also provide potential candidate genes for selection program involved in body shape and skeletal development in H. nobilis. |
format |
Report |
author |
Luo, Weiwei Wang, Junru Yu, Xiaomu Zhou, Ying Tong, Jingou |
author_facet |
Luo, Weiwei Wang, Junru Yu, Xiaomu Zhou, Ying Tong, Jingou |
author_sort |
Luo, Weiwei |
title |
Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
title_short |
Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
title_full |
Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
title_fullStr |
Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
title_full_unstemmed |
Comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp Hypophthalmichthys nobilis |
title_sort |
comparative transcriptome analyses and identification of candidate genes involved in vertebral abnormality of bighead carp hypophthalmichthys nobilis |
publisher |
ELSEVIER SCIENCE INC |
publishDate |
2020 |
url |
http://ir.ihb.ac.cn/handle/342005/42874 https://doi.org/10.1016/j.cbd.2020.100752 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS http://ir.ihb.ac.cn/handle/342005/42874 doi:10.1016/j.cbd.2020.100752 |
op_doi |
https://doi.org/10.1016/j.cbd.2020.100752 |
container_title |
Comparative Biochemistry and Physiology Part D: Genomics and Proteomics |
container_volume |
36 |
container_start_page |
100752 |
_version_ |
1766363199310921728 |