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Wi J, Park EJ, Hwang MS, Choi DW. A subfamily of the small heat shock proteins of the marine red alga Neopyropia yezoensis localizes in the chloroplast. Cell Stress Chaperones 2023; 28:835-846. [PMID: 37632625 PMCID: PMC10746837 DOI: 10.1007/s12192-023-01375-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 12/21/2022] [Accepted: 08/21/2023] [Indexed: 08/28/2023] Open
Abstract
Small heat shock proteins (sHSPs) play a crucial role under abiotic stress and are present in all organisms, from eukaryotes to prokaryotes. However, studies on the sHSP gene family in red alga are limited. In this study, we aimed to identify and characterize NysHSP genes from the genome of N. yezoensis, a marine red alga adapted to the stressful intertidal zone. We identified seven NysHSP genes distributed on all three chromosomes. Expression analysis revealed that all NysHSP genes responded to H2O2 and heat stress in the gametophytic thalli, but these genes responded only to heat stress in the sporophytic conchocelis. NysHSP20.3, which has an acidic isoelectric point (pI) and short N-terminal region, was localized as granules in the cytosol. Fluorescence imaging of the NysHSP25.8-GFP and NysHSP28.4-GFP fusion proteins revealed that these proteins were located in the chloroplast. Based on their characteristics and cellular localization, the NysHSPs are divided into two subfamilies. Subfamily I includes four sHSP genes that strongly respond to heat stress and encode a protein localized in the cytosol. The NysHSP gene of subfamily II encodes a polypeptide with a long N-terminal region located in the chloroplast. This study provides insights into the evolution and function of the sHSP gene family of the marine red alga N. yezoensis and how it adapts to the stressful intertidal zone.
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Affiliation(s)
- Jiwoong Wi
- Department of Biology Education and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Eun-Jeong Park
- Aquatic Plant Variety Center, National Institute of Fisheries Science, Mokpo, 59002, Republic of Korea
| | - Mi-Sook Hwang
- Fisheries Seed and Breeding Research Institute, National Institute of Fisheries Science, Haenam, 58746, Republic of Korea
| | - Dong-Woog Choi
- Department of Biology Education and Kumho Life Science Laboratory, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Acquisition of desiccation tolerance in Haematococcus pluvialis requires photosynthesis and coincides with lipid and astaxanthin accumulation. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Schomaker RA, Dudycha JL. De novo transcriptome assembly of the green alga Ankistrodesmus falcatus. PLoS One 2021; 16:e0251668. [PMID: 33989339 PMCID: PMC8121315 DOI: 10.1371/journal.pone.0251668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/30/2021] [Indexed: 01/11/2023] Open
Abstract
Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.
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Affiliation(s)
- Rachel A Schomaker
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
| | - Jeffry L Dudycha
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States of America
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Wi J, Na Y, Yang E, Lee JH, Jeong WJ, Choi DW. Arabidopsis AtMPV17, a homolog of mice MPV17, enhances osmotic stress tolerance. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:1341-1348. [PMID: 32647452 PMCID: PMC7326884 DOI: 10.1007/s12298-020-00834-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/28/2020] [Accepted: 06/07/2020] [Indexed: 06/11/2023]
Abstract
Mutation in the human MPV17 gene or the functional yeast orthologue SYM1 result in mitochondrial DNA depletion. MPV17 homologs are also found in plants including Arabidopsis, but the function of these genes remain unclear. Arabidopsis genome contains 10 MPV17 homologs. Among these, the AtMPV17 protein was localized in mitochondria as MPV17 and SYM1. The yeast sym1 knock out mutant cannot grow on ethanol-containing medium at 37 °C. AtMPV17 complements the ethanol growth defection of sym1 yeast MPV17 ortholog cells at 37 °C, suggesting that AtMPV17 is a functional ortholog of SYM1. AtMPV17 knock out mutant, atmpv17 show similar growth and seed development to those of the wild-type plant on normal growth condition. However, atmpv17 mutant is more sensitive to ABA and mannitol during germination and seedling growth than wild type plants. Growth retardation of the atmpv17 knock out mutant on medium containing ABA and mannitol is complemented by AtMPV17 overexpression. These results suggest that the AtMPV17 contributes to osmotic stress tolerance in plants.
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Affiliation(s)
- Jiwoong Wi
- Department of Biology Education, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Yeonju Na
- Department of Biology Education, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Eunju Yang
- Department of Biology Education, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141 Republic of Korea
| | - Dong-Woog Choi
- Department of Biology Education, Chonnam National University, Gwangju, 61186 Republic of Korea
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Li BJ, Zhu ZX, Qin H, Meng ZN, Lin HR, Xia JH. Genome-Wide Characterization of Alternative Splicing Events and Their Responses to Cold Stress in Tilapia. Front Genet 2020; 11:244. [PMID: 32256528 PMCID: PMC7093569 DOI: 10.3389/fgene.2020.00244] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) is an important post-transcriptional regulatory mechanism for cells to generate transcript variability and proteome diversity. No systematic investigation of AS events among different tissues in response to stressors is available for tilapia currently. In this study, AS among different tissues was identified and the cold stress-related AS events were explored in a Nile tilapia (Oreochromis niloticus) line based on 42 RNA-seq datasets using a bioinformatics pipeline. 14,796 (82.76%; SD = 2,840) of the expression genes showed AS events. The two most abundant AS types were alternative transcription start site (TSS) and terminal site (TTS) in tilapia. Testis, brain and kidney possess the most abundant AS gene number, while the blood, muscle and liver possess the least number in each tissue. Furthermore, 208 differentially alternative splicing (DAS) genes in heart and 483 DAS in brain in response to cold stress. The number of AS types for alternative exon end, exon skipping and retention of single intron increased significantly under cold stress. GO enrichment and pathway overrepresentation analysis indicated that many DAS genes, e.g., genes in circadian clock pathway, may influence expression of downstream genes under cold stress. Our study revealed that AS exists extensively in tilapia and plays an important role in cold adaption.
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Affiliation(s)
| | | | | | | | | | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-sen University, Guangzhou, China
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Cho TJ, Rhee MS. Health Functionality and Quality Control of Laver ( Porphyra, Pyropia): Current Issues and Future Perspectives as an Edible Seaweed. Mar Drugs 2019; 18:E14. [PMID: 31877971 PMCID: PMC7024182 DOI: 10.3390/md18010014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022] Open
Abstract
The growing interest in laver as a food product and as a source of substances beneficial to health has led to global consumer demand for laver produced in a limited area of northeastern Asia. Here we review research into the benefits of laver consumption and discuss future perspectives on the improvement of laver product quality. Variation in nutritional/functional values among product types (raw and processed (dried, roasted, or seasoned) laver) makes product-specific nutritional analysis a prerequisite for accurate prediction of health benefits. The effects of drying, roasting, and seasoning on the contents of both beneficial and harmful substances highlight the importance of managing laver processing conditions. Most research into health benefits has focused on substances present at high concentrations in laver (porphyran, Vitamin B12, taurine), with assessment of the expected effects of laver consumption. Mitigation of chemical/microbiological risks and the adoption of novel technologies to exploit under-reported biochemical characteristics of lavers are suggested as key strategies for the further improvement of laver product quality. Comprehensive analysis of the literature regarding laver as a food product and as a source of biomedical compounds highlights the possibilities and challenges for application of laver products.
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Affiliation(s)
| | - Min Suk Rhee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Korea;
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Shi J, Wang W, Lin Y, Xu K, Xu Y, Ji D, Chen C, Xie C. Insight into transketolase of Pyropia haitanensis under desiccation stress based on integrative analysis of omics and transformation. BMC PLANT BIOLOGY 2019; 19:475. [PMID: 31694541 PMCID: PMC6836531 DOI: 10.1186/s12870-019-2076-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pyropia haitanensis, distributes in the intertidal zone, can tolerate water losses exceeding 90%. However, the mechanisms enabling P. haitanensis to survive harsh conditions remain uncharacterized. To elucidate the mechanism underlying P. haitanensis desiccation tolerance, we completed an integrated analysis of its transcriptome and proteome as well as transgenic Chlamydomonas reinhardtii carrying a P. haitanensis gene. RESULTS P. haitanensis rapidly adjusted its physiological activities to compensate for water losses up to 60%, after which, photosynthesis, antioxidant systems, chaperones, and cytoskeleton were activated to response to severe desiccation stress. The integrative analysis suggested that transketolase (TKL) was affected by all desiccation treatments. Transgenic C. reinhardtii cells overexpressed PhTKL grew better than the wild-type cells in response to osmotic stress. CONCLUSION P. haitanensis quickly establishes acclimatory homeostasis regarding its transcriptome and proteome to ensure its thalli can recover after being rehydrated. Additionally, PhTKL is vital for P. haitanensis desiccation tolerance. The present data may provide new insights for the breeding of algae and plants exhibiting enhanced desiccation tolerance.
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Affiliation(s)
- Jianzhi Shi
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Wenlei Wang
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Yinghui Lin
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Kai Xu
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Yan Xu
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Dehua Ji
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Changsheng Chen
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
| | - Chaotian Xie
- Fisheries College, Jimei University, Xiamen, 361021 China
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture, Xiamen, 361021 China
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8
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Expression analysis of potential transcript and protein markers that are related to agar yield and gel strength in Gracilaria changii (Rhodophyta). ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Im SH, Klochkova TA, Lee DJ, Gachon CMM, Kim GH. Genetic toolkits of the red alga Pyropia tenera against the three most common diseases in Pyropia farms. JOURNAL OF PHYCOLOGY 2019; 55:801-815. [PMID: 30897208 DOI: 10.1111/jpy.12857] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Disease outbreaks devastate Pyropia aquaculture farms every year. The three most common and serious diseases are Olpidiopsis-blight and red-rot disease caused by oomycete pathogens and green-spot disease caused by the PyroV1 virus. We hypothesized that a basic genetic profile of molecular defenses will be revealed by comparing and analyzing the genetic response of Pyropia tenera against the above three pathogens. RNAs isolated from infected thalli were hybridized onto an oligochip containing 15,115 primers designed from P. tenera expressed sequence tags (EST)s. Microarray profiles of the three diseases were compared and interpreted together with histochemical observation. Massive amounts of reactive oxygen species accumulated in P. tenera cells exposed to oomycete pathogens. Heat shock genes and serine proteases were the most highly up-regulated genes in all infection experiments. Genes involved in RNA metabolism, ribosomal proteins and antioxidant metabolism were also highly up-regulated. Genetic profiles of P. tenera in response to pathogens were most similar between the two biotrophic pathogens, Olpidiopsis pyropiae and PyroV1 virus. A group of plant resistance genes were specifically regulated against each pathogen. Our results suggested that disease response in P. tenera consists of a general constitutive defense and a genetic toolkit against specific pathogens.
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Affiliation(s)
- Soo Hyun Im
- Department of Biology, Kongju National University, Kongju, 32588, Republic of Korea
| | - Tatyana A Klochkova
- Department of Biology, Kongju National University, Kongju, 32588, Republic of Korea
| | - Da Jeoung Lee
- Department of Biology, Kongju National University, Kongju, 32588, Republic of Korea
| | - Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Gwang Hoon Kim
- Department of Biology, Kongju National University, Kongju, 32588, Republic of Korea
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Jin C, Zhao JY, Liu XJ, Li JL. Expressions of Shell Matrix Protein Genes in the Pearl Sac and Its Correlation with Pearl Weight in the First 6 Months of Pearl Formation in Hyriopsis cumingii. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:240-249. [PMID: 30659442 DOI: 10.1007/s10126-019-09876-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Matrix proteins regulate crystal nucleation, morphology, and polymorphism during pearl biomineralization and have significant correlations with pearl quality traits in nucleated pearls. However, there is little information about the connection between pearl quality traits and matrix proteins in non-nucleated pearls. In this study, we analyzed CaCO3 deposition during the first month of non-nucleated pearl formation and examined the expression patterns of ten shell matrix protein genes (Hcperlucin, hic31, silkmapin, hic22, hic74, hic52, HcTyr, HcCA3, hic24 and Hc-upsalin) in the pearl sac of Hyriopsis cumingii. During pearl formation, CaCO3 crystals were initially deposited in a disorderly manner during days 12 and 15 of pearl formation. On days 18 and 21, CaCO3 crystals gradually nucleated on an organic membrane, and the pattern of crystal deposition changed markedly. Between days 24 and 30, crystals similar to nacre tablets were deposited; they then grew and formed connections in a more orderly fashion, eventually forming the nacreous layer. We observed high expression levels of shell matrix proteins during the phases of disordered or ordered CaCO3 deposition, suggesting they were involved in non-nucleated pearl formation. Furthermore, the expressions of nine matrix proteins were significantly correlated with pearl weight during the first 6 months after grafting. The prismatic-layer matrix protein hic31 and nacreous-layer matrix protein hic22 showed negative correlations with pearl weight, but the other seven nacreous-layer matrix proteins had significantly positive correlations with pearl weight. These results show the involvement of matrix proteins in pearl formation and in determination of quality traits.
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Affiliation(s)
- Can Jin
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China
| | - Jing-Ying Zhao
- Class 1, 2016 Biological Science, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Xiao-Jun Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai, 201306, China.
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China.
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China.
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Wang Z, Cui J, Song J, Gou M, Wang H, Gao K, Qiu X, Wang X, Chang Y. Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:1-13. [DOI: 10.1016/j.cbd.2018.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 10/13/2018] [Indexed: 11/30/2022]
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Na Y, Lee HN, Wi J, Jeong WJ, Choi DW. PtDRG1, a Desiccation Response Gene from Pyropia tenera (Rhodophyta), Exhibits Chaperone Function and Enhances Abiotic Stress Tolerance. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:584-593. [PMID: 29728789 DOI: 10.1007/s10126-018-9828-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
Pyropia are commercially valuable marine red algae that grow in the intertidal zone. They are extremely tolerant to desiccation stress. We have previously identified and reported desiccation response genes (DRGs) based on transcriptome analysis of P. tenera. Among them, PtDRG1 encodes a polypeptide of 22.6 kDa that is located in the chloroplast. PtDRG1 does not share sequence homology with any known gene deposited in public database. Transcription of PtDRG1 gene was upregulated by osmotic stress induced by mannitol or H2O2 as well as desiccation stress, but not by heat. When PtDRG1 was overexpressed in Escherichia coli or Chlamydomonas, transformed cells grew much better than control cells under high temperature as well as osmotic stress induced by mannitol and NaCl. In addition, PtDRG1 significantly reduced thermal aggregation of substrate protein under heat stress condition. These results demonstrate that PtDRG1 has a chaperone function and plays a role in tolerance mechanism for abiotic stress. This study shows that red algae have unknown stress proteins such as PtDRG1 that contributes to stress tolerance.
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Affiliation(s)
- Yeonju Na
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Ha-Nul Lee
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Jiwoong Wi
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea
| | - Won-Joong Jeong
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, South Korea
| | - Dong-Woog Choi
- Department of Biology Education, Chonnam National University and Khumho Research Institute, Gwangju, 61186, South Korea.
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Valledor L, Carbó M, Lamelas L, Escandón M, Colina FJ, Cañal MJ, Meijón M. When the Tree Let Us See the Forest: Systems Biology and Natural Variation Studies in Forest Species. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/124_2018_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Wang Z, Cui J, Song J, Wang H, Gao K, Qiu X, Gou M, Li X, Hu Z, Wang X, Chang Y. Comparative Transcriptome Analysis Reveals Growth-Related Genes in Juvenile Chinese Sea Cucumber, Russian Sea Cucumber, and Their Hybrids. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2018; 20:193-205. [PMID: 29492749 DOI: 10.1007/s10126-018-9796-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 01/24/2018] [Indexed: 06/08/2023]
Abstract
Heterosis is important for sea cucumber breeding, but its molecular mechanism remains largely unexplored. In this study, parental lines of Apostichopus japonicus from Russia (R) and China (C) were used to construct hybrids (CR and RC) by reciprocal crossing. We examined the transcriptional profiles of the hybrids (CR and RC) and the purebreds (CC and RR) at different developmental times. A total of 60.27 Gb of clean data was obtained, and 176,649 unigenes were identified, of which 50,312 unigenes were annotated. A total of 414,536 SNPs were identified. A total of 7011 differentially expressed genes (DEGs) were obtained between the purebreds and hybrids at 45 days after fertilization (DAF), and a total of 8218 DEGs were obtained between the purebreds and hybrids at 75 DAF. In addition, a total of 7652 DEGs were obtained between 45 DAF and 75 DAF. The significant DEGs were mainly involved in the MAPK and FOXO signaling pathways, especially in the Ras-Raf-MEK1/2-ERK module, which may be a key regulator of development and growth in juvenile A. japonicus. In addition, we also identified key growth-related genes, such as fgfs, igfs, megfs and hgfs, which were upregulated in the hybrids (RC and CR); these genes may play important roles in heterosis in A. japonicus. Our study provides fundamental information on the molecular mechanisms underlying heterosis in sea cucumber and might suggest strategies for the selection of rapidly growing strains of sea cucumber in aquaculture.
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Affiliation(s)
- Zhicheng Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jun Cui
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China
| | - Haoze Wang
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Kailun Gao
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xuemei Qiu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Meng Gou
- School of Life Science, Liaoning Normal University, Dalian, 116081, China
| | - Xin Li
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Ziwen Hu
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China
| | - Xiuli Wang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in the North China Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, China.
- College of Fisheries and Life Science, Dalian Ocean University, 52 Heishijiao Street, Shahekou District, Dalian, 116023, China.
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