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Wang H, Wan HT, Wu B, Jian J, Ng AHM, Chung CYL, Chow EYC, Zhang J, Wong AOL, Lai KP, Chan TF, Zhang EL, Wong CKC. A Chromosome-level assembly of the Japanese eel genome, insights into gene duplication and chromosomal reorganization. Gigascience 2022; 11:6883318. [PMID: 36480030 PMCID: PMC9730501 DOI: 10.1093/gigascience/giac120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Japanese eels (Anguilla japonica) are commercially important species, harvested extensively for food. Currently, this and related species (American and European eels) are challenging to breed on a commercial basis. As a result, the wild stock is used for aquaculture. Moreover, climate change, habitat loss, water pollution, and altered ocean currents affect eel populations negatively. Accordingly, the International Union for Conservation of Nature lists Japanese eels as endangered and on its red list. Here we presented a high-quality genome assembly for Japanese eels and demonstrated that large chromosome reorganizations occurred in the events of third-round whole-genome duplications (3R-WRDs). Several chromosomal fusions and fissions have reduced the ancestral protochromosomal number of 25 to 19 in the Anguilla lineage. A phylogenetic analysis of the expanded gene families showed that the olfactory receptors (group δ and ζ genes) and voltage-gated Ca2+ channels expanded significantly. Both gene families are crucial for olfaction and neurophysiology. Additional tandem and proximal duplications occurred following 3R-WGD to acquire immune-related genes for an adaptive advantage against various pathogens. The Japanese eel assembly presented here can be used to study other Anguilla species relating to evolution and conservation.
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Affiliation(s)
- Hongbo Wang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR
| | - Hin Ting Wan
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR
| | - Bin Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Alice H M Ng
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Baptist University, Hong Kong SAR
| | - Claire Yik-Lok Chung
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Eugene Yui-Ching Chow
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Jizhou Zhang
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Anderson O L Wong
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,School of Biological Sciences, the University of Hong Kong, Hong Kong SAR
| | - Keng Po Lai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,Key Laboratory of Environmental Pollution and Integrative Omics, Guilin Medical University, Guilin, China
| | - Ting Fung Chan
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), China,School of Life Sciences, State Key Laboratory of Agrobiotechnology, Hong Kong Bioinformatics Centre, the Chinese University of Hong Kong, Hong Kong SAR
| | - Eric Lu Zhang
- Correspondence address. Eric Lu Zhang, Department of Computer Science, Hong Kong Baptist University, Hong Kong SAR. E-mail:
| | - Chris Kong-Chu Wong
- Correspondence address. Chris K.C. Wong, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Croucher Institute for Environmental Sciences, Department of Biology, Hong Kong Baptist University, Hong Kong SAR. E-mail:
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Cao Q, Wang H, Fan C, Sun Y, Li J, Cheng J, Chu P, Yin S. Environmental salinity influences the branchial expression of TCR pathway related genes based on transcriptome of a catadromous fish. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100815. [PMID: 33610026 DOI: 10.1016/j.cbd.2021.100815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 11/17/2022]
Abstract
Environmental salinity not only affects the physiological processes such as osmoregulation and hormonal control, but also changes the immune system in fishes. Studies are limited in fish on the roles of the T cell receptor (TCR)-related genes in relation to changes in environmental salinity. A large group of salinity-challenged transcripts was obtained in gills of marbled eel (Anguilla marmorata). Moreover, bioinformatic ways were used to identify the enriched TCR pathway related genes which were significantly different expressed in fresh water (FW), brackish water (BW) and seawater (SW). Meanwhile, the RT-qPCR results were validated and consistent with the RNA-seq results. TCR a, TCR b, CD45, CD28, PI3K, LCK and LAT were up-regulated when the salinity increases in BW and SW, which connected with the related signaling pathways (Ras-MAPK and PKC pathway). CD4 and Zap70 were down-regulated when the salinity increases in BW and SW, which connected with the PLC pathway. The research offers a novel viewpoint to explore the immune pathways including the TCR pathway in fish based on transcriptome.
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Affiliation(s)
- Quanquan Cao
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Hongyu Wang
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Chengxu Fan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475000, China
| | - Yiru Sun
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Jie Li
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Jinghao Cheng
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Peng Chu
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China
| | - Shaowu Yin
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang 222005, China.
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Cao Q, Yin S. The influence of environmental calcium on the branchial morphology in a catadromous fish. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:8945-8952. [PMID: 33405148 DOI: 10.1007/s11356-020-11922-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Eels are exposed to Ca2+ changes during migration between seawater and freshwater. The gill is the main organ of active calcium transport and has a large surface area to be particularly sensitive to environmental changes in the aquatic environment. In this research, we focused on the morphological changes of gill tissues when eels are faced with the environmental calcium challenges. Based on the results of hematoxylin and eosin (HE) staining and immunohistochemistry, compared with the control group (normal Ca2+ environment), the filament and lamella lengths and lamellar frequency (LF) appeared higher in high calcium environment and lower in deficient calcium environment, while the lamella width and filamental lamellar surface area (SAFL) decreased in high calcium environment and increased in deficient calcium environment. And there was no difference in the number filaments in first right gill arch in the three Ca2+ water environment. Transmission electron microscopy was employed to examine the ultrastructural changes in gills in different Ca2+ water environment. The nucleus and endoplasmic reticulum had a tendency to expand in calcium-deficient water, but had a tendency to shrink in high-calcium water comparing with the control group. This study provides the support that branchial surface areas are regulated in different Ca2+ waters through a list of calcium transporters including CACNB2.
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Affiliation(s)
- Quanquan Cao
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, Jiangsu, China
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China
| | - Shaowu Yin
- College of Marine Science and Engineering, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing, 210023, Jiangsu, China.
- Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, 222005, China.
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Krzywoszyńska K, Witkowska D, Świątek-Kozłowska J, Szebesczyk A, Kozłowski H. General Aspects of Metal Ions as Signaling Agents in Health and Disease. Biomolecules 2020; 10:biom10101417. [PMID: 33036384 PMCID: PMC7600656 DOI: 10.3390/biom10101417] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 02/07/2023] Open
Abstract
This review focuses on the current knowledge on the involvement of metal ions in signaling processes within the cell, in both physiological and pathological conditions. The first section is devoted to the recent discoveries on magnesium and calcium-dependent signal transduction-the most recognized signaling agents among metals. The following sections then describe signaling pathways where zinc, copper, and iron play a key role. There are many systems in which changes in intra- and extra-cellular zinc and copper concentrations have been linked to important downstream events, especially in nervous signal transduction. Iron signaling is mostly related with its homeostasis. However, it is also involved in a recently discovered type of programmed cell death, ferroptosis. The important differences in metal ion signaling, and its disease-leading alterations, are also discussed.
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Affiliation(s)
- Karolina Krzywoszyńska
- Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; (J.Ś.-K.); (A.S.); (H.K.)
- Correspondence: (K.K.); (D.W.); Tel.: +48-77-44-23-549 (K.K); +48-77-44-23-548 (D.W.)
| | - Danuta Witkowska
- Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; (J.Ś.-K.); (A.S.); (H.K.)
- Correspondence: (K.K.); (D.W.); Tel.: +48-77-44-23-549 (K.K); +48-77-44-23-548 (D.W.)
| | - Jolanta Świątek-Kozłowska
- Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; (J.Ś.-K.); (A.S.); (H.K.)
| | - Agnieszka Szebesczyk
- Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; (J.Ś.-K.); (A.S.); (H.K.)
| | - Henryk Kozłowski
- Institute of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland; (J.Ś.-K.); (A.S.); (H.K.)
- Faculty of Chemistry, University of Wrocław, 14 F. Joliot-Curie St., 50-383 Wrocław, Poland
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