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Koyama H, Yamashita K, Narita H, Hiraoka H, Sasaki Y, Kamiya K, Yamakawa R, Kuniyoshi H, Piyapattanakorn S, Watabe S. Cloning and expression profile of the alanine aminotransferase gene from kuruma shrimp Penaeus japonicus exposed to different salinities. J Exp Zool A Ecol Integr Physiol 2024; 341:615-626. [PMID: 38529846 DOI: 10.1002/jez.2811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
Several crustaceans including shrimps change the amount of specific free amino acids to regulate the osmotic pressure in their bodies. Kuruma shrimp Penaeus japonicus also increases the concentration of alanine (Ala) in the abdominal muscle following the increase of environmental salinity. In the present study, to elucidate the mechanisms of changes in Ala accumulation of kuruma shrimp depending on salinity, we cloned the gene encoding alanine aminotransferase (ALT), an enzyme involved in Ala biosynthesis, and examined its expression profile. It was found that the full-length kuruma shrimp ALT1 cDNA consisted of 3,301 bp, encoding 514 amino acids, and that all amino acid residues important for ALT activity were conserved. Phylogenetic analysis also indicated that the ALT gene cloned in this study was classified as ALT1. Moreover, we examined the expression levels of the ALT1 gene in the abdominal muscle and the hepatopancreas of kuruma shrimp acclimated at 17‰, 34‰, and 40‰ salinities, resulting that the mRNA levels of the ALT1 genes in both tissues of the shrimp acclimated at 40‰ were significantly higher than those at 17‰ for 12 h (p < 0.05). The mRNA levels of the ALT1 gene in the abdominal muscle of the shrimp acclimated for more than 24 h tended to increase following the increase of environmental salinity. These results indicate that ALT1 is responsible for the increase of free Ala concentration in the abdominal muscle of kuruma shrimp to regulate osmotic pressure at high salinity.
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Affiliation(s)
- Hiroki Koyama
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Kyoko Yamashita
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hinano Narita
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Haruki Hiraoka
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yuka Sasaki
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Kanna Kamiya
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Rin Yamakawa
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Hisato Kuniyoshi
- Program of Food and AgriLife Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Seto Inland Sea Carbon-neutral Research Center, Hiroshima University, Hiroshima, Japan
| | - Sanit Piyapattanakorn
- Department of Marine Science, Center of Excellence for Marine Biotechnology, Chulalongkorn University, Bangkok, Thailand
| | - Shugo Watabe
- Department of Marine Biochemistry, School of Marine Biosciences, Kitasato University, Kanagawa, Japan
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Chen S, Du T, Huang Z, He K, Yang M, Gao S, Yu T, Zhang H, Li X, Chen S, Liu CM, Li H. The Spartina alterniflora genome sequence provides insights into the salt-tolerance mechanisms of exo-recretohalophytes. Plant Biotechnol J 2024. [PMID: 38685729 DOI: 10.1111/pbi.14368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 03/24/2024] [Accepted: 04/11/2024] [Indexed: 05/02/2024]
Abstract
Spartina alterniflora is an exo-recretohalophyte Poaceae species that is able to grow well in seashore, but the genomic basis underlying its adaptation to salt tolerance remains unknown. Here, we report a high-quality, chromosome-level genome assembly of S. alterniflora constructed through PacBio HiFi sequencing, combined with high-throughput chromosome conformation capture (Hi-C) technology and Illumina-based transcriptomic analyses. The final 1.58 Gb genome assembly has a contig N50 size of 46.74 Mb. Phylogenetic analysis suggests that S. alterniflora diverged from Zoysia japonica approximately 21.72 million years ago (MYA). Moreover, whole-genome duplication (WGD) events in S. alterniflora appear to have expanded gene families and transcription factors relevant to salt tolerance and adaptation to saline environments. Comparative genomics analyses identified numerous species-specific genes, significantly expanded genes and positively selected genes that are enriched for 'ion transport' and 'response to salt stress'. RNA-seq analysis identified several ion transporter genes including the high-affinity K+ transporters (HKTs), SaHKT1;2, SaHKT1;3 and SaHKT1;8, and high copy number of Salt Overly Sensitive (SOS) up-regulated under high salt conditions, and the overexpression of SaHKT2;4 in Arabidopsis thaliana conferred salt tolerance to the plant, suggesting specialized roles for S. alterniflora to adapt to saline environments. Integrated metabolomics and transcriptomics analyses revealed that salt stress activate glutathione metabolism, with differential expressions of several genes such as γ-ECS, GSH-S, GPX, GST and PCS in the glutathione metabolism. This study suggests several adaptive mechanisms that could contribute our understanding of evolutional basis of the halophyte.
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Affiliation(s)
- Shoukun Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
- Hainan Seed Industry Laboratory, Sanya, Hainan, China
| | - Tingting Du
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Zhangping Huang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Kunhui He
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Maogeng Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Shang Gao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Tingxi Yu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Hao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
| | - Xiang Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Shihua Chen
- Key Laboratory of Plant Molecular & Developmental Biology, College of Life Sciences, Yantai University, Yantai, Shandong, China
| | - Chun-Ming Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Huihui Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Nanfan Research Institute, CAAS, Sanya, Hainan, China
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Shukla N, Vemula H, Raval I, Kumar S, Shrivastava V, Chaudhari A, Patel AK, Joshi CG. Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita. Front Genet 2023; 14:1209843. [PMID: 37719712 PMCID: PMC10500595 DOI: 10.3389/fgene.2023.1209843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/17/2023] [Indexed: 09/19/2023] Open
Abstract
Introduction: Brain being the master regulator of the physiology of animal, the current study focuses on the gene expression pattern of the brain tissue with special emphasis on regulation of growth, developmental process of an organism and cellular adaptation of Labeo rohita against unfavourable environmental conditions. Methods: RNA-seq study was performed on collected brain samples at 8ppt salt concentration and analyzed for differential gene expression, functional annotation and miRNA-mRNA regulatory network. Results: We found that 2450 genes were having significant differential up and down regulation. The study identified 20 hub genes based on maximal clique centrality algorithm. These hub genes were mainly involved in various signaling pathways, energy metabolism and ion transportation. Further, 326 up and 1214 down regulated genes were found to be targeted by 7 differentially expressed miRNAs i.e., oni-miR-10712, oni-miR-10736, ssa-miR-221-3p, ssa-miR-130d-1-5p, ssa-miR-144-5p and oni-miR-10628. Gene ontology analysis of these differentially expressed genes led to the finding that these genes were involved in signal transduction i.e., calcium, FOXO, PI3K-AKT, TGF-β, Wnt and p53 signalling pathways. Differentially expressed genes were also involved in regulation of immune response, environmental adaptation i.e., neuroactive ligand-receptor interaction, ECM-receptor interaction, cell adhesion molecules and circadian entrainment, osmoregulation and energy metabolism, which are critical for salinity adaptation. Discussion: The findings of whole transcriptomic study on brain deciphered the miRNA-mRNA interaction patterns and pathways associated with salinity adaptation of L. rohita.
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Affiliation(s)
- Nitin Shukla
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Harshini Vemula
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Ishan Raval
- Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India
| | - Sujit Kumar
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Vivek Shrivastava
- Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India
| | - Aparna Chaudhari
- Central Institute of Fisheries Education, Mumbai, Maharashtra, India
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Zafirah Ghazali S, Lavoué S, Sukmono T, Habib A, Min Pau T, Azizah Mohd Nor S. Cenozoic colonisation of the Indian Ocean region by the Australian freshwater originating glassperch family Ambassidae (Teleostei). Mol Phylogenet Evol 2023:107832. [PMID: 37263456 DOI: 10.1016/j.ympev.2023.107832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/29/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023]
Abstract
We examined the phylogeny and biogeography of the glassperch family Ambassidae (Teleostei), which is widely distributed in the freshwater, brackish and marine coastal habitats across the Indo-West Pacific region. We first built a comprehensive time-calibrated phylogeny of Ambassidae using five genes. We then used this tree to reconstruct the evolution of the salinity preference and ancestral areas. Our results indicate that the two largest genera of Ambassidae, Ambassis and Parambassis, are each not monophyletic. The most recent common ancestor of Ambassidae was freshwater adapted and lived in Australia about 56 million years ago. Three independent freshwater-to-marine transitions are inferred, but no marine-to-freshwater ones. To explain the distribution of ambassids, we hypothesise two long-distance marine dispersal events from Australia. A first event was towards Southeast Asia during the early Cenozoic, followed by a second one towards Africa during mid-Cenozoic. The phylogenetic signal associated with the salinity adaptation of these events was not detected, possibly because of the selective extinction of intermediate marine lineages. The Ambassidae shares two characteristics with other freshwater fish groups distributed in continental regions surrounding the Indian Ocean: They are too young to support the hypothesis that their distribution is the result of the fragmentation of Gondwana, but they did not retain the phylogenetic signal of their marine dispersal.
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Affiliation(s)
- Siti Zafirah Ghazali
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Sébastien Lavoué
- School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia.
| | - Tedjo Sukmono
- Department of Biology, Universitas Jambi, Jalan Lintas Jambi - Muara Bulian Km15, 36122 Jambi, Sumatra, Indonesia
| | - Ahasan Habib
- Faculty of Fisheries and Food Science, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh
| | - Tan Min Pau
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia
| | - Siti Azizah Mohd Nor
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, 21030 Kuala Terengganu, Terengganu, Malaysia; School of Biological Sciences, Universiti Sains Malaysia, 11800 Pulau Pinang, Malaysia
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Ma X, Ru D, Morales-Briones DF, Mei F, Wu J, Liu J, Wu S. Genome sequence and salinity adaptation of the desert shrub Nitraria sibirica (Nitrariaceae, Sapindales). DNA Res 2023:7160319. [PMID: 37167434 DOI: 10.1093/dnares/dsad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 05/13/2023] Open
Abstract
The genetic bases of halophytes for salinity tolerance are crucial for genetically breeding salt-tolerant crops. All natural Nitrariaceae species that exclusively occur in arid environments are highly tolerant to salt stress, but the underlying genomic bases to this adaptation remain unknown. Here we present a high-quality, chromosome-level genome sequence of Nitraria sibirica, with an assembled size of 456.66 Mb and 23,365 annotated genes. Phylogenomic analyses confirmed N. sibirica as the sister to all other sampled representatives from other families in Sapindales, and no lineage-specific whole-genome duplication was found except the gamma triplication event. Still, we found that the genes involved in K + retention, energy supply, and Fe absorption expanded greatly in N. sibirica. Deep transcriptome analyses showed that leaf photosynthesis and cuticular wax formation in roots were enhanced under salt treatments. Furthermore, many transcription factors involved in salt tolerance changed their expressions significantly and displayed tissue- and concentration-dependent signaling in response to salt stress. Additionally, we found vacuolar Na + compartmentalization is an ongoing process under salt treatment, while Na + exclusion tends to function at high salt concentrations. These genomic and transcriptomic changes conferred salt tolerance in N. sibirica and pave the way for future breeding of salt-tolerant crops.
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Affiliation(s)
- Xiaohui Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Dafu Ru
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Diego F Morales-Briones
- Princess Therese von Bayern chair of Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 Munich, Germany
| | - Fengyuan Mei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jingjing Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
| | - Shengdan Wu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China
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Liu JN, Fang H, Liang Q, Dong Y, Wang C, Yan L, Ma X, Zhou R, Lang X, Gai S, Wang L, Xu S, Yang KQ, Wu D. Genomic analyses provide insights into the evolution and salinity adaptation of halophyte Tamarix chinensis. Gigascience 2022; 12:giad053. [PMID: 37494283 PMCID: PMC10370455 DOI: 10.1093/gigascience/giad053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/09/2023] [Accepted: 06/29/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND The woody halophyte Tamarix chinensis is a pioneer tree species in the coastal wetland ecosystem of northern China, exhibiting high resistance to salt stress. However, the genetic information underlying salt tolerance in T. chinensis remains to be seen. Here we present a genomic investigation of T. chinensis to elucidate the underlying mechanism of its high resistance to salinity. RESULTS Using a combination of PacBio and high-throughput chromosome conformation capture data, a chromosome-level T. chinensis genome was assembled with a size of 1.32 Gb and scaffold N50 of 110.03 Mb. Genome evolution analyses revealed that T. chinensis significantly expanded families of HAT and LIMYB genes. Whole-genome and tandem duplications contributed to the expansion of genes associated with the salinity adaptation of T. chinensis. Transcriptome analyses were performed on root and shoot tissues during salt stress and recovery, and several hub genes responding to salt stress were identified. WRKY33/40, MPK3/4, and XBAT31 were critical in responding to salt stress during early exposure, while WRKY40, ZAT10, AHK4, IRX9, and CESA4/8 were involved in responding to salt stress during late stress and recovery. In addition, PER7/27/57/73 encoding class III peroxidase and MCM3/4/5/7 encoding DNA replication licensing factor maintained up/downregulation during salt stress and recovery stages. CONCLUSIONS The results presented here reveal the genetic mechanisms underlying salt adaptation in T. chinensis, thus providing important genomic resources for evolutionary studies on tamarisk and plant salt tolerance genetic improvement.
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Affiliation(s)
- Jian Ning Liu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Hongcheng Fang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Qiang Liang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Yuhui Dong
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Changxi Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Liping Yan
- Shandong Provincial Academy of Forestry, Jinan 250014, China
| | - Xinmei Ma
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Rui Zhou
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Xinya Lang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shasha Gai
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Lichang Wang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Shengyi Xu
- College of Forestry, Shandong Agricultural University, Taian 271018, China
| | - Ke Qiang Yang
- College of Forestry, Shandong Agricultural University, Taian 271018, China
- State Forestry and Grassland Administration Key Laboratory of Silviculture in the Downstream Areas of the Yellow River, Shandong Agricultural University, Taian 271018, China
- Shandong Taishan Forest Ecosystem Research Station, Shandong Agricultural University, Taian 271018, China
| | - Dejun Wu
- Shandong Provincial Academy of Forestry, Jinan 250014, China
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Yuan F, Wang X, Zhao B, Xu X, Shi M, Leng B, Dong X, Lu C, Feng Z, Guo J, Han G, Zhang H, Huang J, Chen M, Wang BS. The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution. Mol Plant 2022; 15:1024-1044. [PMID: 35514085 DOI: 10.1016/j.molp.2022.04.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 06/14/2023]
Abstract
Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.
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Affiliation(s)
- Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xi Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Boqing Zhao
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xiaojing Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Miao Shi
- Berry Genomics Corporation, Beijing, China
| | - Bingying Leng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Xinxiu Dong
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Chaoxia Lu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Zhongtao Feng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Jianrong Guo
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | - Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China
| | | | | | - Min Chen
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.
| | - Bao-Shan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji'nan, Shandong, China.
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Tian Y, Gao Q, Dong S, Zhou Y, Yu H, Liu D, Yang W. Genome-Wide Analysis of Alternative Splicing (AS) Mechanism Provides Insights into Salinity Adaptation in the Livers of Three Euryhaline Teleosts, including Scophthalmus maximus, Cynoglossus semilaevis and Oncorhynchus mykiss. Biology (Basel) 2022; 11:222. [PMID: 35205090 DOI: 10.3390/biology11020222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/21/2022] [Accepted: 01/27/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Alternative splicing (AS) is a key post-transcriptional regulatory mechanism that acts an important regulator in response to environmental stimuli in organisms. In the present study, 18 RNA-Seq datasets were utilized to investigate the potential roles of AS in response to different salinity environments in the livers of three euryhaline teleosts, including turbot (Scophthalmus maximus), tongue sole (Cynoglossus semilaevis) and steelhead trout (Oncorhynchus mykiss). The results indicated that different salinity environments changed the splicing patterns of numerous RNA splicing regulators, which might affect the splicing decisions of many downstream target genes in response to salinity changes. This study provides preliminary evidence for the important roles of AS events in salinity adaptation in teleosts. Abstract Salinity is an important environmental factor that directly affects the survival of aquatic organisms, including fish. However, the underlying molecular mechanism of salinity adaptation at post-transcriptional regulation levels is still poorly understood in fish. In the present study, 18 RNA-Seq datasets were utilized to investigate the potential roles of alternative splicing (AS) in response to different salinity environments in the livers of three euryhaline teleosts, including turbot (Scophthalmus maximus), tongue sole (Cynoglossus semilaevis) and steelhead trout (Oncorhynchus mykiss). A total of 10,826, 10,741 and 10,112 AS events were identified in the livers of the three species. The characteristics of these AS events were systematically investigated. Furthermore, a total of 940, 590 and 553 differentially alternative splicing (DAS) events were determined and characterized in the livers of turbot, tongue sole and steelhead trout, respectively, between low- and high-salinity environments. Functional enrichment analysis indicated that these DAS genes in the livers of three species were commonly enriched in some GO terms and KEGG pathways associated with RNA processing. The most common DAS genes work as RNA-binding proteins and play crucial roles in the regulation of RNA splicing. The study provides new insights into uncovering the molecular mechanisms of salinity adaptation in teleosts.
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Lv J, Li R, Su Z, Gao B, Ti X, Yan D, Liu G, Liu P, Wang C, Li J. A chromosome-level genome of Portunus trituberculatus provides insights into its evolution, salinity adaptation and sex determination. Mol Ecol Resour 2021; 22:1606-1625. [PMID: 34854556 DOI: 10.1111/1755-0998.13564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 01/14/2023]
Abstract
Portunus trituberculatus (Crustacea: Decapoda: Brachyura), commonly known as the swimming crab, is of major ecological importance, as well as being important to the fisheries industry. P. trituberculatus is also an important farmed species in China due to its rapid growth rate and high economic value. Here, we report the genome sequence of the swimming crab, which was assembled at the chromosome scale, covering ~1.2 Gb, with 79.99% of the scaffold sequences assembled into 53 chromosomes. The contig and scaffold N50 values were 108.7 kb and 15.6 Mb, respectively, with 19,981 protein-coding genes. Based on comparative genomic analyses of crabs and shrimps, the C2H2 zinc finger protein family was found to be the only gene family expanded in crab genomes, suggesting it was closely related to the evolution of crabs. The combination of transcriptome and bulked segregant analysis provided insights into the genetic basis of salinity adaptation and rapid growth in P. trituberculatus. In addition, the specific region of the Y chromosome was located for the first time in the genome of P. trituberculatus, and three genes were preliminarily identified as candidate genes for sex determination in this region. Decoding the swimming crab genome not only provides a valuable genomic resource for further biological and evolutionary studies, but is also useful for molecular breeding of swimming crabs.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Aoshanwei Town, Jimo, Qingdao, China
| | - Ronghua Li
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Zhencheng Su
- Novogene Bioinformatics Institute, Beijing, China
| | - Baoquan Gao
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Aoshanwei Town, Jimo, Qingdao, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Deping Yan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | | | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Aoshanwei Town, Jimo, Qingdao, China
| | - Chunlin Wang
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education, Ningbo University, Ningbo, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, China, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Aoshanwei Town, Jimo, Qingdao, China
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10
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Ordóñez-Grande B, Guerreiro PM, Sanahuja I, Fernández-Alacid L, Ibarz A. Environmental Salinity Modifies Mucus Exudation and Energy Use in European Sea Bass Juveniles. Animals (Basel) 2021; 11:ani11061580. [PMID: 34071210 PMCID: PMC8230262 DOI: 10.3390/ani11061580] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 12/24/2022] Open
Abstract
The European sea bass (Dicentrarchus labrax) is a euryhaline marine teleost that can often be found in brackish and freshwater or even in hypersaline environments. Here, we exposed sea bass juveniles to sustained salinity challenges for 15 days, simulating one hypoosmotic (3‰), one isosmotic (12‰) and one hyperosmotic (50‰) environment, in addition to control (35‰). We analyzed parameters of skin mucus exudation and mucus biomarkers, as a minimally invasive tool, and plasma biomarkers. Additionally, Na+/K+-ATPase activity was measured, as well as the gill mucous cell distribution, type and shape. The volume of exuded mucus increased significantly under all the salinity challenges, increasing by 130% at 50‰ condition. Significantly greater amounts of soluble protein (3.9 ± 0.6 mg at 50‰ vs. 1.1 ± 0.2 mg at 35‰, p < 0.05) and lactate (4.0 ± 1.0 µg at 50‰ vs. 1.2 ± 0.3 µg at 35‰, p < 0.05) were released, with clear energy expenditure. Gill ATPase activity was significantly higher at the extreme salinities, and the gill mucous cell distribution was rearranged, with more acid and neutral mucin mucous cells at 50‰. Skin mucus osmolality suggested an osmoregulatory function as an ion-trap layer in hypoosmotic conditions, retaining osmosis-related ions. Overall, when sea bass cope with different salinities, the hyperosmotic condition (50‰) demanded more energy than the extreme hypoosmotic condition.
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Affiliation(s)
- Borja Ordóñez-Grande
- Department of Cell Biology, Physiology and Immunology, University of Barcelona (UB), 08028 Barcelona, Spain; (B.O.-G.); (I.S.); (A.I.)
| | - Pedro M. Guerreiro
- CCMAR—Centre for Marine Sciences, University of Algarve, 8005-139 Faro, Portugal;
| | - Ignasi Sanahuja
- Department of Cell Biology, Physiology and Immunology, University of Barcelona (UB), 08028 Barcelona, Spain; (B.O.-G.); (I.S.); (A.I.)
| | - Laura Fernández-Alacid
- Department of Cell Biology, Physiology and Immunology, University of Barcelona (UB), 08028 Barcelona, Spain; (B.O.-G.); (I.S.); (A.I.)
- Correspondence:
| | - Antoni Ibarz
- Department of Cell Biology, Physiology and Immunology, University of Barcelona (UB), 08028 Barcelona, Spain; (B.O.-G.); (I.S.); (A.I.)
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11
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Chen Y, Gao Y, Huang X, Li S, Zhan A. Local environment-driven adaptive evolution in a marine invasive ascidian ( Molgula manhattensis). Ecol Evol 2021; 11:4252-4266. [PMID: 33976808 PMCID: PMC8093682 DOI: 10.1002/ece3.7322] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/04/2022] Open
Abstract
Elucidating molecular mechanisms of environment-driven adaptive evolution in marine invaders is crucial for understanding invasion success and further predicting their future invasions. Although increasing evidence suggests that adaptive evolution could contribute to organisms' adaptation to varied environments, there remain knowledge gaps regarding how environments influence genomic variation in invaded habitats and genetic bases underlying local adaptation for most marine invaders. Here, we performed restriction-site-associated DNA sequencing (RADseq) to assess population genetic diversity and further investigate genomic signatures of local adaptation in the marine invasive ascidian, Molgula manhattensis. We revealed that most invasive populations exhibited significant genetic differentiation, low recent gene flow, and no signal of significant population bottleneck. Based on three genome scan approaches, we identified 109 candidate loci potentially under environmental selection. Redundancy analysis and variance partitioning analysis suggest that local environmental factors, particularly the salinity-related variables, represent crucial evolutionary forces in driving adaptive divergence. Using the newly developed transcriptome as a reference, 14 functional genes were finally obtained with potential roles in salinity adaptation, including SLC5A1 and SLC9C1 genes from the solute carrier gene (SLC) superfamily. Our findings confirm that differed local environments could rapidly drive adaptive divergence among invasive populations and leave detectable genomic signatures in marine invaders.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Yangchun Gao
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
- Guangdong Key Laboratory of Animal Conservation and Resource UtilizationInstitute of ZoologyGuangdong Academy of SciencesHaizhu DistrictGuangzhouChina
| | - Xuena Huang
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
| | - Shiguo Li
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
| | - Aibin Zhan
- Research Center for Eco‐Environmental SciencesChinese Academy of SciencesHaidian DistrictBeijingChina
- University of Chinese Academy of SciencesChinese Academy of SciencesShijingshan DistrictBeijingChina
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12
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Sun C, Li J, Dong J, Niu Y, Hu J, Lian J, Li W, Li J, Tian Y, Shi Q, Ye X. Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water. Mol Ecol Resour 2020; 21:301-315. [PMID: 32985096 DOI: 10.1111/1755-0998.13256] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/19/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022]
Abstract
Largemouth bass (LMB; Micropterus salmoides) has been an economically important fish in North America, Europe, and China. This study obtained a chromosome-level genome assembly of LMB using PacBio and Hi-C sequencing. The final assembled genome is 964 Mb, with contig N50 and scaffold N50 values of 1.23 Mb and 36.48 Mb, respectively. Combining with RNA sequencing data, we annotated a total of 23,701 genes. Chromosomal assembly and syntenic analysis proved that, unlike most Perciformes with the popular haploid chromosome number of 24, LMB has only 23 chromosomes (Chr), among which the Chr1 seems to be resulted from a chromosomal fusion event. LMB is phylogenetically closely related to European seabass and spotted seabass, diverging 64.1 million years ago (mya) from the two seabass species. Eight gene families comprising 294 genes associated with ionic regulation were identified through positive selection, transcriptome and genome comparisons. These genes involved in iron facilitated diffusion (such as claudin, aquaporins, sodium channel protein and so on) and others related to ion active transport (such as sodium/potassium-transporting ATPase and sodium/calcium exchanger). The claudin gene family, which is critical for regulating cell tight junctions and osmotic homeostasis, showed a significant expansion in LMB with 27 family members and 68 copies for salinity adaptation. In summary, we reported the first high-quality LMB genome, and provided insights into the molecular mechanisms of LMB adaptation to fresh and brackish water. The chromosome-level LMB genome will also be a valuable genomic resource for in-depth biological and evolutionary studies, germplasm conservation and genetic breeding of LMB.
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Affiliation(s)
- Chengfei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jia Li
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Junjian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Jie Hu
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | | | - Wuhui Li
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Jiang Li
- Biozeron Shenzhen Inc., Shenzhen, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Qiong Shi
- Shenzhen Key Laboratory of Marine Genomics, Guangdong Provincial Key Laboratory of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
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13
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Hong M, Li N, Li J, Li W, Liang L, Li Q, Wang R, Shi H, Storey KB, Ding L. Adenosine Monophosphate-Activated Protein Kinase Signaling Regulates Lipid Metabolism in Response to Salinity Stress in the Red-Eared Slider Turtle Trachemys scripta elegans. Front Physiol 2019; 10:962. [PMID: 31417422 PMCID: PMC6684833 DOI: 10.3389/fphys.2019.00962] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/11/2019] [Indexed: 12/25/2022] Open
Abstract
Aquatic animals have developed various mechanisms to live in either hyperionic or hypoionic environments, and, as such, not many species are capable of surviving in both. The red-eared slider turtle, Trachemys scripta elegans, a well-known freshwater species, has recently been found to invade and inhabit brackish water. Herein, we focus on some of the metabolic adaptations that are required to survive and cope with salinity stress. The regulation of the adenosine monophosphate (AMP)-activated protein kinase (AMPK), a main cellular “energy sensor,” and its influence on lipid metabolism were evaluated with a comparison of three groups of turtles: controls in freshwater, and turtles held in water of either 5‰ salinity (S5) or 15‰ salinity (S15) with sampling at 6, 24, and 48 h and 30 days of exposure. When subjected to elevated salinities of 5 or 15‰, AMPK mRNA levels and AMPK enzyme activity increased strongly. In addition, the high expression of the peroxisome proliferator activated receptor-α (PPARα) transcription factor that, in turn, facilitated upregulation of target genes including carnitine palmitoyltransferase (CPT) and acyl-CoA oxidase (ACO). Furthermore, the expression of transcription factors involved in lipid synthesis such as the carbohydrate-responsive element-binding protein (ChREBP) and sterol regulatory element-binding protein 1c (SREBP-1c) was inhibited, and two of their target genes, acetyl-CoA carboxylase (ACC) and fatty acid synthase (FAS), were significantly decreased. Moreover, exposure to saline environments also increased plasma triglyceride (TG) content. Interestingly, the content of low-density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) in plasma was markedly higher than the control in the S15 group after 30 days, which indicated that lipid metabolism was disrupted by chronic exposure to high salinity. These findings demonstrate that activation of AMPK might regulate lipid metabolism in response to salinity stress through the inhibition of lipid synthesis and promotion of lipid oxidation in the liver of T. s. elegans. This may be an important component of the observed salinity tolerance of these turtles that allow for invasion of brackish waters.
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Affiliation(s)
- Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Na Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Jiangyue Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Weihao Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Lingyue Liang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Qian Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Runqi Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, China
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14
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Tang J, Du LM, Liang YM, Daroch M. Complete Genome Sequence and Comparative Analysis of Synechococcus sp. CS-601 (SynAce01), a Cold-Adapted Cyanobacterium from an Oligotrophic Antarctic Habitat. Int J Mol Sci 2019; 20:E152. [PMID: 30609821 DOI: 10.3390/ijms20010152] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 12/24/2022] Open
Abstract
Marine picocyanobacteria belonging to Synechococcus are major contributors to the global carbon cycle, however the genomic information of its cold-adapted members has been lacking to date. To fill this void the genome of a cold-adapted planktonic cyanobacterium Synechococcus sp. CS-601 (SynAce01) has been sequenced. The genome of the strain contains a single chromosome of approximately 2.75 MBp and GC content of 63.92%. Gene prediction yielded 2984 protein coding sequences and 44 tRNA genes. The genome contained evidence of horizontal gene transfer events during its evolution. CS-601 appears as a transport generalist with some specific adaptation to an oligotrophic marine environment. It has a broad repertoire of transporters of both inorganic and organic nutrients to survive in inhospitable environments. The cold adaptation of the strain exhibited characteristics of a psychrotroph rather than psychrophile. Its salt adaptation strategy is likely to rely on the uptake and synthesis of osmolytes, like glycerol or glycine betaine. Overall, the genome reveals two distinct patterns of adaptation to the inhospitable environment of Antarctica. Adaptation to an oligotrophic marine environment is likely due to an abundance of genes, probably acquired horizontally, that are associated with increased transport of nutrients, osmolytes, and light harvesting. On the other hand, adaptations to low temperatures are likely due to prolonged evolutionary changes.
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Olmos E, García De La Garma J, Gomez-Jimenez MC, Fernandez-Garcia N. Arabinogalactan Proteins Are Involved in Salt-Adaptation and Vesicle Trafficking in Tobacco by-2 Cell Cultures. Front Plant Sci 2017; 8:1092. [PMID: 28676820 PMCID: PMC5476920 DOI: 10.3389/fpls.2017.01092] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/06/2017] [Indexed: 05/21/2023]
Abstract
Arabinogalactan proteins (AGPs) are a highly diverse family of glycoproteins that are commonly found in most plant species. However, little is known about the physiological and molecular mechanisms of their function. AGPs are involved in different biological processes such as cell differentiation, cell expansion, tissue development and somatic embryogenesis. AGPs are also involved in abiotic stress response such as salinity modulating cell wall expansion. In this study, we describe how salt-adaptation in tobacco BY-2 cell cultures induces important changes in arabinogalactan proteins distribution and contents. Using the immuno-dot blot technique with different anti-AGP antibodies (JIM13, JIM15, and others), we observed that AGPs were highly accumulated in the culture medium of salt-adapted tobacco cells, probably due to the action of phospholipases. We located these AGP epitopes using immunogold labeling in the cytoplasm associated to the endoplasmic reticulum, the golgi apparatus, and vesicles, plasma membrane and tonoplast. Our results show that salt-adaptation induced a significant reduction of the cytoplasm, plasma membrane and tonoplast content of these epitopes. Yariv reagent was added to the control and salt-adapted tobacco cell cultures, leading to cell death induction in control cells but not in salt-adapted cells. Ultrastructural and immunogold labeling revealed that cell death induced by Yariv reagent in control cells was due to the interaction of Yariv reagent with the AGPs linked to the plasma membranes. Finally, we propose a new function of AGPs as a possible sodium carrier through the mechanism of vesicle trafficking from the apoplast to the vacuoles in salt-adapted tobacco BY-2 cells. This mechanism may contribute to sodium homeostasis during salt-adaptation to high saline concentrations.
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Affiliation(s)
- Enrique Olmos
- Department of Abiotic Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC)Murcia, Spain
| | - Jesús García De La Garma
- Department of Abiotic Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC)Murcia, Spain
| | - Maria C. Gomez-Jimenez
- Department of Plant Physiology, Faculty of Science, University of ExtremaduraBadajoz, Spain
| | - Nieves Fernandez-Garcia
- Department of Abiotic Stress and Plant Pathology, Centro de Edafología y Biología Aplicada del Segura (CSIC)Murcia, Spain
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16
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Ip YK, Hiong KC, Wong SZH, Ching B, Chen XL, Soh MML, Chng YR, Ong JLY, Wilson JM, Chew SF. Branchial Na(+):K(+):2Cl(-) cotransporter 1 and Na(+)/K(+)-ATPase α-subunit in a brackish water-type ionocyte of the euryhaline freshwater white-rimmed stingray, Himantura signifer. Front Physiol 2013; 4:362. [PMID: 24339817 PMCID: PMC3857534 DOI: 10.3389/fphys.2013.00362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 11/23/2013] [Indexed: 11/13/2022] Open
Abstract
Himantura signifer is a freshwater stingray which inhabits rivers in Southeast Asia. It can survive in brackish water but not seawater. In brackish water, it becomes partially ureosmotic, but how it maintains its plasma hypoionic to the external medium is enigmatic because of the lack of a rectal gland. Here, we report for the first time the expression of Na(+):K(+):2Cl(-) cotransporter 1 (nkcc1) in the gills of freshwaterH. signifer, and its moderate up-regulation (~2-fold) in response to brackish water (salinity 20) acclimation. The absence of the Ste20-related proline-alanine-rich kinase and oxidation stress response kinase 1 interaction site from the N-terminus of H. signifer Nkcc1 suggested that it might not be effectively activated by stress kinases in response to salinity changes as in more euryhaline teleosts. The increased activity of Nkcc1 during salt excretion in brackish water would lead to an influx of Na(+) into ionocytes, and the maintenance of intracellular Na(+) homeostasis would need the cooperation of Na(+)/K(+)-ATPase (Nka). We demonstrated for the first time the expression of nkaα1, nkaα2 and nkaα3 in the gills of H. signifer, and the up-regulation of the mRNA expression of nkaα3 and the overall protein abundance of Nkaα in response to acclimation to brackish water. Immunofluorescence microscopy revealed the presence of a sub-type of ionocyte, co-expressing Nkcc1 and Nkaα, near the base of the secondary lamellae in the gills of H. signifer acclimated to brackish water, but this type of ionocyte was absent from the gills of fish kept in fresh water. Hence, there could be a change in the function of the gills of H. signifer from salt absorption to salt excretion during brackish water acclimation in the absence of a functioning rectal gland.
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Affiliation(s)
- Yuen K Ip
- Department of Biological Sciences, National University of Singapore Singapore, Singapore
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